Contacts of the helix formed by residues 638 - 672 (chain A) in PDB entry 1H41
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 638 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 3.9 25.1 + - + +
637A VAL* 1.3 76.1 - - - +
639A ALA* 1.3 64.7 + - - +
640A ALA* 3.2 9.6 + - - +
641A ARG* 2.8 65.1 + - - +
642A PHE* 3.0 21.5 + - - +
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Residues in contact with ALA 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A VAL 3.7 1.7 + - - -
638A ASP* 1.3 76.2 - - - +
640A ALA* 1.3 62.2 + - - +
642A PHE* 3.9 6.9 - - - +
643A ALA* 3.1 24.6 + - - +
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Residues in contact with ALA 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU 4.3 12.8 - - - +
638A ASP* 3.2 7.7 + - - +
639A ALA* 1.3 83.1 - - - +
641A ARG* 1.3 64.1 + - - +
643A ALA* 3.8 3.4 - - - +
644A GLN* 3.0 24.6 + - - +
185B TYR* 4.6 5.0 + - - +
188B PRO* 4.9 18.6 - - + -
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Residues in contact with ARG 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU* 3.6 47.4 + - - +
6A ASP* 5.3 0.9 - - - -
7A GLY* 4.7 7.8 - - - +
10A MET 5.3 0.6 + - - -
13A ARG* 3.9 9.1 - - - +
457A PRO* 5.4 2.0 - - + -
460A GLN* 5.6 0.8 + - - -
488A THR* 2.9 47.0 + - - +
489A PHE* 3.5 34.7 + - + +
630A TRP* 4.7 0.4 - - - -
637A VAL* 4.3 2.4 - - + +
638A ASP* 2.8 36.7 + - - +
640A ALA* 1.3 75.8 - - - +
642A PHE* 1.3 63.2 + - - +
644A GLN* 4.3 13.0 - - - +
645A VAL* 3.0 32.0 + - + +
1729A CO 3.7 22.9 - - - +
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Residues in contact with PHE 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630A TRP* 3.1 61.1 + + - +
631A ASP* 4.1 20.0 - - - -
633A GLN 4.4 3.8 - - - -
634A GLU* 3.7 58.8 - - + -
637A VAL* 3.8 10.8 - - + +
638A ASP 3.0 21.2 + - - +
639A ALA* 3.9 7.2 - - - +
641A ARG* 1.3 76.4 - - - +
643A ALA* 1.3 61.4 + - + +
646A LYS* 2.9 45.0 + - + +
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Residues in contact with ALA 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A ALA 3.1 18.5 + - - +
640A ALA* 3.8 4.0 - - - +
642A PHE* 1.3 81.7 - - + +
644A GLN* 1.3 66.6 + - - +
646A LYS* 3.6 7.2 - - - +
647A ALA* 3.0 25.3 + - - +
185B TYR* 4.3 8.7 - - + -
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Residues in contact with GLN 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A ASN* 4.0 7.4 + - - +
455A GLY 3.7 22.0 + - - -
457A PRO* 3.6 21.1 - - + +
640A ALA 3.0 16.4 + - - +
641A ARG* 3.8 14.9 - - - +
642A PHE 3.3 0.4 - - - -
643A ALA* 1.3 77.4 - - - +
645A VAL* 1.3 58.8 + - - +
647A ALA* 3.2 3.1 + - - +
648A LEU* 2.9 46.1 + - + +
185B TYR* 3.5 42.4 + - + +
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Residues in contact with VAL 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A LEU* 4.2 8.3 - - + -
456A HIS* 4.9 2.9 - - + -
457A PRO* 3.9 27.8 - - + -
458A PHE* 4.0 26.5 - - + -
489A PHE* 5.2 3.1 - - + -
630A TRP* 3.4 39.7 - - + +
641A ARG 3.0 15.4 + - - +
644A GLN* 1.3 75.1 - - - +
646A LYS* 1.3 64.3 + - - +
648A LEU* 3.3 7.1 + - - +
649A LEU* 3.0 33.8 + - + +
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Residues in contact with LYS 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A GLN* 5.1 0.2 - - - +
630A TRP* 3.5 15.1 - - + +
631A ASP* 2.9 36.2 + - - +
642A PHE* 2.9 36.3 + - + +
643A ALA* 3.6 7.2 - - - +
645A VAL* 1.3 77.9 - - - +
647A ALA* 1.3 61.7 + - - +
649A LEU* 3.4 6.1 + - - +
650A GLN* 3.2 34.5 + - - +
1718A EDO 2.9 32.7 + - - +
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Residues in contact with ALA 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643A ALA 3.0 17.0 + - - +
644A GLN 3.6 4.0 - - - +
646A LYS* 1.3 76.8 - - - +
648A LEU* 1.3 63.5 + - - +
650A GLN* 3.0 24.2 + - - +
651A VAL* 3.1 17.1 + - - +
184B ASN* 3.6 27.5 - - - +
185B TYR* 3.6 22.7 - - + +
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Residues in contact with LEU 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ALA 4.1 14.4 - - - +
399A THR* 3.2 29.3 - - + +
455A GLY 5.0 0.4 - - - +
456A HIS* 3.7 30.1 - - + +
457A PRO* 3.9 22.7 - - + -
644A GLN* 2.9 35.7 + - + +
645A VAL* 3.3 4.7 + - - +
647A ALA* 1.3 75.5 - - + +
649A LEU* 1.3 59.1 + - - +
651A VAL* 3.1 6.1 + - + +
652A GLN 2.8 23.9 + - - -
178B ASP* 5.7 0.4 - - - +
181B SER* 3.9 27.4 - - - -
185B TYR* 5.4 3.1 - - + -
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Residues in contact with LEU 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A LEU* 3.9 25.6 - - + -
456A HIS* 5.8 0.9 - - - +
502A MET* 5.0 0.9 - - - -
623A VAL* 4.3 3.9 - - + +
626A MET* 4.1 28.0 - - + +
627A GLN* 3.8 22.5 - - + +
630A TRP* 3.7 32.5 - - + -
645A VAL* 3.0 28.2 + - + +
646A LYS* 3.7 5.8 - - - +
648A LEU* 1.3 75.6 - - + +
650A GLN* 1.3 58.3 + - - +
652A GLN* 3.4 27.2 + - - +
653A GLU* 2.9 28.9 + - - +
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Residues in contact with GLN 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A GLN* 3.7 12.1 - - - +
646A LYS* 3.2 28.3 + - - +
647A ALA* 3.0 11.3 + - - +
649A LEU* 1.3 74.6 - - - +
651A VAL* 1.3 64.6 + - - +
653A GLU* 3.3 4.3 + - - +
654A ARG* 3.1 22.5 + - - +
1718A EDO 2.9 31.8 + - - +
184B ASN* 3.0 38.3 + - - +
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Residues in contact with VAL 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A THR* 3.8 23.1 - - + +
529A TYR* 4.3 7.6 - - - +
647A ALA 3.1 13.5 + - - +
648A LEU* 3.1 11.1 + - + +
650A GLN* 1.3 74.8 - - - +
652A GLN* 1.3 58.3 + - - +
654A ARG* 3.2 25.0 + - - +
655A GLU* 2.9 30.6 + - + +
180B GLY 3.7 26.0 - - - +
181B SER* 4.3 10.1 - - - -
182B LEU 5.6 0.2 - - - +
184B ASN* 3.7 25.8 - - + +
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Residues in contact with GLN 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A THR 3.8 9.5 + - - +
400A HIS* 3.7 23.7 + - - +
401A LEU* 2.7 52.5 + - - +
456A HIS* 5.1 0.2 + - - -
506A SER 5.5 1.8 + - - -
509A ALA* 5.7 0.2 - - - +
510A GLY 6.0 0.2 - - - +
513A TYR* 2.9 21.8 + - - +
623A VAL* 4.0 23.6 - - + +
626A MET* 4.5 6.2 - - - +
648A LEU 2.8 14.8 + - - +
649A LEU* 3.5 15.8 - - - +
651A VAL* 1.3 78.0 - - - +
653A GLU* 1.3 56.7 + - - +
655A GLU* 3.3 1.6 + - - +
656A ALA* 2.7 28.6 + - - +
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Residues in contact with GLU 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A VAL* 5.1 2.0 - - + -
623A VAL* 3.7 13.7 - - + +
624A ARG* 2.8 47.4 + - + +
627A GLN* 3.3 32.8 - - - +
649A LEU 2.9 14.1 + - - +
650A GLN* 3.8 5.3 - - - +
651A VAL 3.3 0.2 - - - -
652A GLN* 1.3 75.0 - - - +
654A ARG* 1.3 70.3 + - - +
656A ALA* 3.3 3.4 + - - +
657A VAL* 3.0 32.3 + - + +
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Residues in contact with ARG 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A GLN 3.1 13.6 + - - +
651A VAL* 3.5 33.4 + - - +
653A GLU* 1.3 84.0 + - - +
655A GLU* 1.3 69.5 + - - +
657A VAL* 3.4 6.3 + - - +
658A ARG* 3.0 26.2 + - - +
180B GLY 4.9 3.2 + - - -
182B LEU 4.9 1.4 + - - -
183B PRO* 5.0 4.0 - - - +
184B ASN* 3.1 34.4 + - - +
224B LYS* 4.8 13.1 - - - +
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Residues in contact with GLU 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A HIS* 3.5 21.7 + - + +
529A TYR* 3.6 35.6 - - - +
651A VAL* 2.9 22.0 + - + +
652A GLN 3.8 0.7 - - - +
654A ARG* 1.3 88.1 + - - +
656A ALA* 1.3 60.0 + - - +
658A ARG* 2.8 49.1 + - - +
659A TRP* 2.9 41.7 + - + -
696A THR* 3.9 8.4 - - - +
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Residues in contact with ALA 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A TYR* 3.7 46.1 - - + +
620A VAL* 3.3 19.4 - - + +
623A VAL* 4.2 9.2 - - + -
652A GLN 2.7 21.0 + - - +
653A GLU* 3.7 5.8 - - - +
655A GLU* 1.3 69.5 - - - +
657A VAL* 1.3 60.0 + - - +
659A TRP* 3.3 2.3 + - - +
660A ARG* 2.9 25.1 + - - +
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Residues in contact with VAL 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A VAL* 3.8 15.7 - - + -
624A ARG* 3.5 28.5 - - - +
653A GLU* 3.0 30.4 + - - +
654A ARG* 3.6 6.3 - - - +
655A GLU 3.3 0.2 - - - -
656A ALA* 1.3 76.2 - - - +
658A ARG* 1.3 58.1 + - - +
660A ARG* 4.0 11.9 - - - +
661A ASN* 2.9 50.1 + - - +
683A GLU* 6.5 0.4 - - + -
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Residues in contact with ARG 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A TYR* 4.3 5.5 - - - -
530A GLY* 3.8 19.2 - - - -
531A PRO* 3.7 19.2 + - + +
654A ARG 3.0 13.9 + - - +
655A GLU* 2.8 48.2 + - - +
657A VAL* 1.3 78.0 - - - +
659A TRP* 1.3 54.2 + - - +
661A ASN* 4.1 0.3 - - - +
662A SER* 2.7 44.7 + - - +
689A TYR* 4.2 16.9 + - + -
692A LEU* 3.8 42.4 + - + +
693A ALA* 3.8 14.3 - - - +
696A THR* 3.7 22.1 + - - +
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Residues in contact with TRP 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A HIS* 4.9 3.1 + + - -
513A TYR* 3.2 30.5 - + + +
514A ARG* 3.6 51.4 - - + +
522A LEU* 4.2 9.6 - - + -
523A TYR* 3.5 44.4 - + - -
529A TYR 3.5 16.2 + - - -
530A GLY* 3.4 23.9 - - - -
531A PRO* 3.5 37.6 - - + +
655A GLU* 2.9 32.8 + - + -
656A ALA 3.5 7.4 - - - +
658A ARG* 1.3 77.2 - - - +
660A ARG* 1.3 61.5 + - - +
662A SER* 3.7 0.3 - - - -
663A CYS* 3.0 37.5 + - - -
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Residues in contact with ARG 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A TYR* 3.8 1.7 + - + -
616A TYR* 3.8 31.6 - - + +
617A TYR* 3.6 54.6 + - + +
620A VAL* 3.7 35.8 - - + +
621A GLU* 5.3 1.2 + - - -
624A ARG* 4.2 14.3 - - - +
656A ALA 2.9 20.6 + - - +
657A VAL* 3.7 17.5 + - - +
659A TRP* 1.3 71.6 - - - +
661A ASN* 1.3 85.9 + - - +
664A VAL* 2.9 35.3 + - - +
680A GLU* 4.3 22.4 + - - +
682A PRO* 5.0 2.0 - - - +
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Residues in contact with ASN 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657A VAL* 2.9 38.2 + - - +
660A ARG* 1.3 107.2 + - - +
662A SER* 1.3 62.8 + - - +
664A VAL* 4.9 0.9 - - - -
665A LEU* 3.0 32.2 + - - +
682A PRO* 3.6 31.8 - - + +
683A GLU* 4.0 4.9 - - - +
689A TYR* 2.8 41.6 + - + -
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Residues in contact with SER 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A PRO* 3.4 30.1 - - - +
533A PRO* 4.7 0.4 - - - -
534A TRP* 3.9 16.2 - - - -
658A ARG* 2.7 26.5 + - - +
659A TRP 3.7 0.9 - - - -
661A ASN* 1.3 77.9 - - - +
663A CYS* 1.3 58.6 + - - +
665A LEU* 4.0 1.1 - - - -
666A TYR* 3.0 28.8 + - - +
686A LEU* 4.1 1.6 - - - +
689A TYR* 3.4 33.1 + - - +
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Residues in contact with CYS 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A ARG 3.9 7.9 - - - -
522A LEU* 4.5 4.7 - - - -
531A PRO* 4.2 5.6 - - - -
533A PRO* 4.0 23.3 - - - -
616A TYR* 3.4 43.5 - - + +
659A TRP* 3.0 33.6 + - - +
662A SER* 1.3 72.8 - - - +
664A VAL* 1.3 62.5 + - - +
666A TYR* 3.2 0.9 + - - +
667A PHE* 2.8 40.1 + - + -
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Residues in contact with VAL 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A TRP* 3.8 3.6 - - + -
612A LEU* 4.7 3.1 - - + -
613A VAL* 4.3 20.4 - - + -
616A TYR* 3.6 34.5 - - + -
617A TYR* 4.2 20.2 - - + +
660A ARG 2.9 20.6 + - - +
661A ASN* 4.4 2.0 - - - +
663A CYS* 1.3 76.3 - - - +
665A LEU* 1.3 57.3 + - + +
667A PHE* 3.4 3.5 + - - -
668A GLN* 2.8 28.4 + - - +
675A ILE* 3.6 35.9 - - + -
682A PRO* 5.7 0.7 - - + -
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Residues in contact with LEU 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A ASN 3.0 22.0 + - - +
662A SER 4.3 1.3 - - - +
664A VAL* 1.3 72.9 - - - +
666A TYR* 1.3 66.2 + - - +
668A GLN* 3.5 24.4 + - - +
669A SER* 3.0 22.7 + - - -
675A ILE* 4.3 8.5 - - + -
681A GLN* 4.4 8.3 - - - +
682A PRO* 3.7 23.8 - - + -
684A HIS 3.2 26.0 - - - +
685A ASP* 3.9 10.3 - - - -
686A LEU* 4.1 19.3 - - + +
689A TYR* 3.7 20.6 - - + -
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Residues in contact with TYR 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A PRO* 3.5 39.7 - - + -
534A TRP* 3.6 29.3 + + + -
546A VAL* 3.8 10.9 - - - +
549A HIS* 3.3 27.6 + + - -
551A ALA* 5.0 0.7 + - - +
662A SER 3.0 20.3 + - - +
663A CYS 3.2 2.7 + - - +
665A LEU* 1.3 77.3 - - - +
667A PHE* 1.3 86.2 + + - +
669A SER* 2.7 27.8 + - - -
670A VAL* 3.3 29.2 + - + +
686A LEU* 3.8 16.7 - - + +
690A LYS* 5.5 0.9 - - - -
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Residues in contact with PHE 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A LEU* 4.1 15.0 - - + -
522A LEU* 4.0 19.5 - - + -
533A PRO* 4.3 1.8 - - + -
549A HIS* 3.9 22.9 - + + -
551A ALA* 4.0 8.3 - - + -
556A ILE* 3.6 22.9 - - + -
598A TRP* 4.7 4.6 - + + -
609A TRP* 3.8 18.6 - - + -
612A LEU* 4.1 20.4 - - + -
616A TYR* 3.7 21.3 - - - -
663A CYS* 2.8 35.4 + - + +
664A VAL 4.1 0.9 - - - +
666A TYR* 1.3 99.5 - + - +
668A GLN* 1.3 57.6 + - - +
670A VAL* 3.2 4.4 + - - +
671A ALA* 2.8 30.3 + - - +
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Residues in contact with GLN 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A TRP* 3.5 16.0 - - + -
664A VAL 2.8 19.1 + - - +
665A LEU* 3.5 26.4 - - - +
667A PHE* 1.3 78.6 - - - +
669A SER* 1.3 56.2 + - - +
671A ALA* 4.4 0.7 - - - +
672A GLY* 2.7 32.0 + - - +
673A ARG 3.1 25.2 + - - +
674A PRO* 3.8 3.6 - - - +
675A ILE* 3.6 29.1 - - + +
681A GLN* 4.8 6.4 + - - +
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Residues in contact with SER 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A LEU 3.0 13.0 + - - -
666A TYR* 2.7 23.1 + - - -
668A GLN* 1.3 77.8 - - - +
670A VAL* 1.3 65.7 + - - +
672A GLY* 4.4 3.0 + - - -
686A LEU* 3.6 23.6 - - - +
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Residues in contact with VAL 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ALA* 3.6 15.5 - - + +
552A SER* 3.4 37.0 - - - +
553A LYS* 3.5 20.0 + - - +
598A TRP* 5.7 0.2 - - + -
666A TYR* 3.7 40.2 - - + +
667A PHE* 3.2 7.3 + - - +
668A GLN 3.1 0.6 - - - -
669A SER* 1.3 83.2 - - - +
671A ALA* 1.3 63.2 + - - +
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Residues in contact with ALA 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A SER 4.1 1.6 - - - -
553A LYS* 3.2 23.7 + - - +
598A TRP* 3.5 41.3 - - + +
609A TRP* 4.3 12.6 - - + -
667A PHE 2.8 19.9 + - - +
668A GLN 4.4 0.2 - - - +
670A VAL* 1.3 73.2 - - - +
672A GLY* 1.3 64.5 + - - +
673A ARG* 3.9 18.1 + - + +
----------------------------------------------------------
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Residues in contact with GLY 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A LYS* 4.6 12.6 + - - -
668A GLN* 2.7 22.5 + - - -
669A SER 4.4 2.9 - - - -
670A VAL 3.4 2.2 + - - -
671A ALA* 1.3 74.8 - - - +
673A ARG* 1.3 58.1 + - - +
674A PRO* 4.7 0.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il