Contacts of the helix formed by residues 633 - 658 (chain A) in PDB entry 3VF1
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 633 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LYS* 3.4 30.0 + - - +
119A ALA* 3.0 25.1 + - - +
494A ILE* 5.7 1.3 - - + -
495A TYR* 2.7 35.8 + - + +
631A PHE* 3.7 0.9 - - - +
632A GLY* 1.3 78.2 + - - +
634A ALA* 1.3 64.7 + - - +
635A ALA* 4.3 8.7 - - + +
636A ALA* 3.0 18.8 + - + +
637A HIS* 3.3 11.8 + - - -
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Residues in contact with ALA 634 (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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632A GLY 3.3 4.3 + - - +
633A ASP* 1.3 72.3 - - - +
635A ALA* 1.3 61.3 + - - +
637A HIS* 3.4 17.0 + - + +
638A ALA* 3.1 21.1 + - - +
641B ALA 4.6 2.3 - - - +
644B LYS* 4.3 10.1 - - + +
645B SER* 3.9 14.5 - - - +
648B ALA* 4.0 27.4 - - + -
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Residues in contact with ALA 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A ILE* 3.4 37.1 - - + +
633A ASP* 3.1 5.3 - - + +
634A ALA* 1.3 77.2 - - - +
636A ALA* 1.3 63.7 + - - +
638A ALA* 3.3 4.9 + - - +
639A ALA* 3.2 15.9 + - - +
645B SER* 3.5 18.7 + - - +
649B ASN* 6.1 1.3 - - - +
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Residues in contact with ALA 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ILE* 4.1 9.3 - - + +
494A ILE* 3.8 10.2 - - + +
495A TYR* 3.9 10.3 + - - +
631A PHE* 3.5 41.7 - - + -
633A ASP* 3.0 12.6 + - - +
635A ALA* 1.3 77.3 - - - +
637A HIS* 1.3 59.8 + - - +
639A ALA* 3.1 4.3 + - - +
640A MET* 2.9 32.5 + - - +
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Residues in contact with HIS 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A ASN* 3.0 23.3 + - - -
631A PHE* 2.9 29.0 + - + -
632A GLY* 3.7 18.2 - - - -
633A ASP 3.3 7.7 + - - -
634A ALA* 3.6 14.9 - - + +
635A ALA 3.3 0.2 - - - -
636A ALA* 1.3 78.6 - - - +
638A ALA* 1.3 57.7 + - - +
640A MET* 3.4 12.3 + - + +
641A ALA* 2.9 30.0 + - - +
641B ALA* 4.1 6.5 - - + +
644B LYS* 6.2 0.4 + - - -
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Residues in contact with ALA 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ALA 3.1 13.4 + - - +
635A ALA* 3.5 9.6 - - - +
636A ALA 3.2 0.2 - - - -
637A HIS* 1.3 77.9 - - - +
639A ALA* 1.3 61.8 + - - +
641A ALA* 3.4 1.9 + - - +
642A LYS* 3.0 24.3 + - - +
638B ALA 5.2 1.9 - - - +
641B ALA* 3.8 31.4 - - - +
642B LYS* 4.2 7.2 - - + +
645B SER* 4.0 11.4 - - - +
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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
----------------------------------------------------------
487A PHE* 3.7 7.6 - - + -
490A ASP* 4.0 25.9 - - + +
491A ILE* 3.6 23.6 - - + -
494A ILE* 4.5 4.0 - - + -
635A ALA 3.2 8.9 + - - +
636A ALA 3.1 9.0 + - - +
638A ALA* 1.3 80.0 - - - +
640A MET* 1.3 57.3 + - - +
642A LYS* 3.3 9.1 + - - +
643A PHE* 3.0 26.7 + - - +
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Residues in contact with MET 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A PHE* 3.6 27.6 - - + -
491A ILE* 5.1 0.9 - - + -
626A TYR* 3.9 34.7 - - + +
629A ASN* 3.6 41.3 - - + +
631A PHE* 4.1 16.2 - - - -
636A ALA 2.9 21.6 + - - +
637A HIS* 3.7 10.8 - - + +
639A ALA* 1.3 78.4 - - - +
641A ALA* 1.3 56.9 + - - +
643A PHE* 3.1 5.5 - - - +
644A LYS* 3.0 34.9 + - + +
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Residues in contact with ALA 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A HIS 2.9 17.9 + - - +
638A ALA 3.8 2.0 - - - +
639A ALA 3.3 0.4 - - - -
640A MET* 1.3 73.2 - - - +
642A LYS* 1.3 66.7 + - - +
644A LYS* 3.3 12.0 + - - +
645A SER* 3.0 22.3 + - - -
634B ALA 4.5 2.4 - - - +
637B HIS* 4.1 7.5 - - + +
638B ALA* 4.0 15.4 - - - +
641B ALA* 3.6 24.5 - - + -
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Residues in contact with LYS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A GLN* 3.4 27.6 - - - +
490A ASP* 2.9 30.6 + - - +
638A ALA 3.0 17.0 + - - +
639A ALA* 3.6 5.4 - - - +
641A ALA* 1.3 72.1 - - - +
643A PHE* 1.3 60.7 + - - +
645A SER* 3.2 3.5 + - - -
646A ASN* 2.9 48.8 + - - +
638B ALA* 4.1 15.4 - - + +
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Residues in contact with PHE 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A VAL* 3.4 36.8 - - + -
484A ILE* 3.8 22.2 - - + -
487A PHE* 3.4 39.9 - + + +
549A VAL* 5.6 1.8 - - + -
623A LEU* 4.4 10.3 - - + -
624A GLY* 4.0 19.1 - - - -
626A TYR* 3.8 28.3 - + - -
639A ALA 3.0 14.4 + - - +
640A MET 3.1 10.1 - - - +
642A LYS* 1.3 77.3 - - - +
644A LYS* 1.3 63.2 + - - +
646A ASN* 3.1 9.9 + - - +
647A LEU* 3.0 44.3 + - + +
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Residues in contact with LYS 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A GLY* 3.5 35.9 + - - +
625A ASP* 4.9 11.3 + - - +
626A TYR 5.6 0.4 - - - +
640A MET* 3.0 21.2 + - + +
641A ALA* 3.3 12.5 + - - +
643A PHE* 1.3 75.2 - - + +
645A SER* 1.3 57.0 + - - +
647A LEU* 3.4 10.4 + - - +
648A ALA* 3.0 27.7 + - - +
634B ALA* 4.2 7.8 - - + +
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Residues in contact with SER 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A ALA 3.0 13.6 + - - -
642A LYS* 3.5 9.0 - - - -
643A PHE 3.1 0.2 - - - -
644A LYS* 1.3 74.4 - - - +
646A ASN* 1.3 68.6 + - - +
648A ALA* 3.4 3.3 + - - +
649A ASN* 3.2 31.6 + - - +
634B ALA* 3.6 22.6 - - - +
635B ALA* 3.4 24.3 + - - +
638B ALA* 4.0 10.3 - - - +
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Residues in contact with ASN 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A VAL* 3.7 30.2 + - + +
486A GLN* 4.8 10.9 - - - +
642A LYS* 2.9 43.6 + - - +
643A PHE* 3.5 9.3 - - - +
645A SER* 1.3 76.1 + - - +
647A LEU* 1.3 64.5 + - - +
649A ASN* 3.3 15.0 + - - +
650A ILE* 3.2 26.0 + - - +
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Residues in contact with LEU 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 4.0 15.9 - - + -
483A VAL* 3.7 23.1 - - + -
484A ILE* 5.7 0.2 - - + -
623A LEU* 3.4 57.2 - - + +
624A GLY* 3.9 9.6 - - - -
643A PHE* 3.0 29.4 + - + +
644A LYS* 3.6 9.9 - - - +
645A SER 3.3 0.2 - - - -
646A ASN* 1.3 74.7 - - - +
648A ALA* 1.3 60.1 + - - +
649A ASN 3.1 0.2 - - - -
650A ILE* 3.0 7.6 + - + +
651A THR* 2.9 32.8 + - - -
670A PRO* 3.6 13.6 - - + +
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Residues in contact with ALA 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LYS 3.0 17.4 + - - +
645A SER 3.6 6.5 - - - +
647A LEU* 1.3 76.9 - - - +
649A ASN* 1.3 63.7 + - - +
651A THR* 3.5 9.5 - - - -
652A LYS* 3.2 21.0 + - - +
634B ALA* 3.8 20.2 - - + -
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Residues in contact with ASN 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A SER* 3.2 24.4 + - - +
646A ASN* 3.6 16.3 + - - +
647A LEU 3.1 0.8 - - - -
648A ALA* 1.3 79.3 - - - +
650A ILE* 1.3 63.9 + - + +
652A LYS* 3.3 11.4 + - - +
653A GLN* 3.1 31.9 + - - +
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Residues in contact with ILE 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ASP 5.2 0.4 - - - +
479A LEU* 3.6 43.5 - - + +
480A LEU* 4.0 18.6 - - + +
483A VAL* 3.6 33.9 - - + -
646A ASN 3.2 10.6 + - - +
647A LEU* 3.0 10.8 + - + +
649A ASN* 1.3 75.0 - - + +
651A THR* 1.3 65.4 + - - +
653A GLN* 3.1 12.3 + - - +
654A ILE* 2.9 43.5 + - + +
670A PRO* 4.2 10.1 - - + -
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Residues in contact with THR 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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647A LEU 2.9 13.3 + - - -
648A ALA* 3.5 13.4 - - - +
650A ILE* 1.3 77.4 - - - +
652A LYS* 1.3 57.3 + - - +
654A ILE* 3.8 4.6 - - - +
655A THR* 2.9 41.2 + - - +
669A ILE* 4.3 16.4 - - + +
670A PRO* 3.2 29.5 - - - +
671A GLY 4.6 1.7 + - - -
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Residues in contact with LYS 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A ALA 3.2 11.2 + - - +
649A ASN* 3.5 14.6 - - - +
650A ILE 3.1 0.4 - - - -
651A THR* 1.3 79.3 - - - +
653A GLN* 1.3 63.9 + - + +
655A THR* 3.5 5.7 + - - -
656A GLU* 3.1 56.3 + - + +
118B LYS* 6.1 3.8 - - - +
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Residues in contact with GLN 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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479A LEU* 3.6 36.0 - - + +
649A ASN* 3.1 22.9 + - - +
650A ILE* 3.1 14.3 + - - +
652A LYS* 1.3 74.2 - - + +
654A ILE* 1.3 65.7 + - - +
656A GLU* 3.1 13.5 + - - +
657A ARG* 3.0 23.4 + - - +
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Residues in contact with ILE 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ASP* 3.4 31.0 - - + +
479A LEU* 5.3 1.8 - - + -
650A ILE* 2.9 35.6 + - + +
651A THR 3.8 3.8 - - - +
653A GLN* 1.3 76.9 - - + +
655A THR* 1.3 57.0 + - - +
657A ARG* 3.4 19.3 + - - +
658A ASN* 2.9 44.8 + - - +
665A TYR 4.0 2.9 - - - +
668A LEU 3.6 28.3 - - - +
669A ILE* 3.6 27.1 - - + -
670A PRO* 4.4 1.6 - - + -
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Residues in contact with THR 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A THR* 2.9 28.7 + - - +
652A LYS* 3.7 7.6 - - - -
654A ILE* 1.3 78.0 - - - +
656A GLU* 1.3 64.5 + - + +
658A ASN* 3.3 8.2 + - - +
659A GLN* 3.2 31.3 + - - +
669A ILE* 5.2 7.6 - - - +
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Residues in contact with GLU 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A LYS* 3.1 53.0 + - + +
653A GLN* 3.1 11.7 + - - +
655A THR* 1.3 79.0 - - + +
657A ARG* 1.3 63.9 + - - +
659A GLN* 3.2 21.7 - - - +
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Residues in contact with ARG 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A TYR* 3.6 43.1 + - + +
475A ASP* 4.4 10.1 - - - +
476A ASP* 2.9 42.2 + - - -
653A GLN 3.0 15.0 + - - +
654A ILE* 3.7 13.4 - - - +
656A GLU* 1.3 72.5 - - - +
658A ASN* 1.3 81.4 + - - +
659A GLN 3.0 13.4 + - - +
661A MET* 3.4 21.4 - - + +
665A TYR* 3.1 21.8 + - - +
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Residues in contact with ASN 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A ILE* 2.9 26.8 + - - +
655A THR* 3.3 8.2 + - - +
657A ARG* 1.3 103.2 + - - +
659A GLN* 1.3 63.5 + - - +
660A GLY 3.2 3.1 + - - -
661A MET* 3.2 25.2 + - - +
664A PRO* 3.5 27.3 - - + +
665A TYR 2.9 27.8 + - - +
666A THR* 3.7 8.7 - - - +
669A ILE* 4.7 2.8 - - - +
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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