Contacts of the helix formed by residues 638 - 661 (chain A) in PDB entry 6UQ2
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 GLY 638 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A VAL 3.0 14.8 + - - +
634A THR* 3.4 19.1 + - - -
635A ARG 5.1 0.7 - - - -
637A LYS* 1.3 79.8 - - - +
639A PRO* 1.3 75.5 - - - +
640A GLN 3.5 2.0 - - - -
641A VAL* 4.1 4.9 - - - -
642A CYS 3.3 12.6 + - - -
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Residues in contact with PRO 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A PRO* 3.5 36.3 - - + +
509A LEU* 4.0 20.2 - - + -
511A ILE* 4.6 0.9 - - - +
634A THR* 4.1 15.2 - - + +
638A GLY* 1.3 81.8 - - - +
640A GLN* 1.3 66.1 + - + +
642A CYS* 3.0 3.8 + - - +
643A ALA* 2.8 29.8 + - - +
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Residues in contact with GLN 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ASP* 4.2 15.4 + - - +
459A ARG* 6.1 0.6 - - - +
508A PRO* 4.0 22.2 - - + +
638A GLY* 3.5 0.4 - - - -
639A PRO* 1.3 87.1 - - + +
641A VAL* 1.3 61.1 + - + +
643A ALA* 4.4 4.3 - - - +
644A LYS* 3.1 32.6 + - - +
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Residues in contact with VAL 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A PRO* 4.3 22.6 - - + +
633A VAL* 4.2 3.4 - - + +
637A LYS* 3.8 40.4 - - + +
638A GLY* 3.8 2.7 + - - +
639A PRO 3.2 0.4 - - - -
640A GLN* 1.3 78.4 - - + +
642A CYS* 1.3 61.6 + - - +
644A LYS* 3.7 8.9 + - + +
645A LEU* 3.0 24.6 + - - +
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Residues in contact with CYS 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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511A ILE* 4.4 5.8 - - + -
630A ILE* 3.6 31.9 - - - -
633A VAL* 3.8 15.8 - - + +
634A THR* 3.0 30.7 - - - +
638A GLY 3.3 18.5 + - - +
639A PRO 3.0 5.6 + - - +
641A VAL* 1.3 76.4 - - - +
643A ALA* 1.3 63.8 + - - +
645A LEU* 3.1 20.4 + - - +
646A PHE* 3.1 22.2 - - - -
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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
----------------------------------------------------------
360A GLU* 4.3 4.4 - - - +
361A LEU* 4.0 22.4 + - + +
362A ASP* 4.8 8.7 - - - +
508A PRO* 3.6 28.3 - - + -
511A ILE* 4.3 2.6 - - + +
639A PRO 2.8 19.1 + - - +
640A GLN* 4.0 8.3 - - - +
642A CYS* 1.3 73.6 - - - +
644A LYS* 1.3 60.9 + - - +
645A LEU 3.3 0.5 + - - -
646A PHE* 3.4 25.7 + - - +
647A GLY 4.1 2.6 + - - -
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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
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360A GLU* 4.3 16.2 - - + +
554A PRO* 5.5 5.6 - - + +
555A ASP* 2.7 41.4 + - - +
640A GLN* 3.1 23.5 + - - +
641A VAL* 3.8 9.6 - - + +
643A ALA* 1.3 75.1 - - - +
645A LEU* 1.3 60.8 + - - +
646A PHE 3.5 0.3 + - - -
647A GLY* 3.7 2.4 + - - -
648A ASN* 2.9 34.4 + - - +
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Residues in contact with LEU 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A ALA* 3.8 21.8 - - + +
582A ILE* 4.8 2.2 - - + -
583A PRO* 4.6 9.6 - - + -
629A LEU* 4.3 15.9 - - + +
630A ILE* 4.9 9.4 - - + -
633A VAL* 3.9 35.9 - - + -
641A VAL 3.0 15.7 + - - +
642A CYS* 3.1 19.4 + - - +
644A LYS* 1.3 76.7 - - - +
646A PHE* 1.3 65.0 + - + +
648A ASN* 3.4 7.2 + - - +
649A ILE* 3.2 51.2 + - + +
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Residues in contact with PHE 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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361A LEU* 3.6 29.2 - - + -
471A ASN* 4.3 1.6 - - - +
473A SER* 3.7 18.6 - - - -
511A ILE* 3.6 25.6 - - + -
521A MET* 3.9 17.0 - - + -
522A GLY* 3.9 23.1 - - - -
523A ILE* 3.6 25.0 - - + +
630A ILE* 3.9 30.7 - - + -
642A CYS* 3.1 23.9 + - - -
643A ALA* 3.6 6.5 - - - +
644A LYS 3.3 0.6 - - - -
645A LEU* 1.3 80.0 - - + +
647A GLY* 1.3 62.4 + - - +
649A ILE* 3.6 2.4 + - - +
650A GLN* 3.0 33.4 + - - +
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Residues in contact with GLY 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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357A PRO 5.8 0.9 - - - -
359A LEU 5.3 3.4 - - - -
360A GLU* 4.3 10.9 + - - -
361A LEU 5.8 0.2 - - - +
471A ASN* 4.8 4.1 - - - +
643A ALA 4.1 3.6 + - - -
644A LYS 3.7 4.7 + - - -
645A LEU 3.3 0.4 - - - -
646A PHE* 1.3 78.7 - - - +
648A ASN* 1.3 55.6 + - - +
650A GLN* 2.9 11.2 + - - -
651A LYS* 2.5 55.9 + - - +
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Residues in contact with ASN 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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360A GLU* 5.1 1.6 - - - +
553A VAL* 4.0 10.2 - - + +
554A PRO* 3.2 33.8 - - - +
555A ASP* 3.2 30.1 + - - -
581A ALA* 3.8 27.7 + - + +
644A LYS* 2.9 25.4 + - - +
645A LEU* 3.4 7.3 + - - +
646A PHE 3.3 0.6 - - - -
647A GLY* 1.3 77.2 - - - +
649A ILE* 1.3 61.3 + - - +
651A LYS* 4.2 2.7 - - - +
652A VAL* 3.3 28.9 + - - +
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Residues in contact with ILE 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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523A ILE* 4.1 24.9 - - + -
527A THR* 4.2 2.5 - - + -
531A ILE* 3.7 29.2 - - + -
578A LEU* 4.1 14.8 - - + -
581A ALA* 3.9 16.8 - - + -
582A ILE* 4.9 7.4 - - + -
622A VAL* 4.8 7.9 - - + -
629A LEU* 5.7 5.4 - - + -
645A LEU* 3.2 39.6 + - + +
646A PHE 4.0 3.6 - - - +
648A ASN* 1.3 75.7 - - - +
650A GLN* 1.3 63.1 + - - +
652A VAL* 3.6 0.6 + - - -
653A VAL* 3.1 37.5 + - + +
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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
----------------------------------------------------------
357A PRO* 4.4 20.6 + - - +
359A LEU 5.5 0.2 - - - -
471A ASN* 2.5 44.2 + - - +
472A LEU* 3.6 23.4 - - - +
473A SER* 4.2 13.6 + - - +
523A ILE* 5.2 2.7 - - + -
527A THR* 3.7 24.7 - - + +
646A PHE* 3.0 26.2 + - - +
647A GLY* 2.9 8.7 + - - +
649A ILE* 1.3 77.8 - - - +
651A LYS* 1.3 57.0 + - - +
654A ASN* 2.6 44.3 + - - +
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Residues in contact with LYS 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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357A PRO 4.6 11.4 + - - +
358A ASN* 4.9 20.1 + - - +
359A LEU 4.9 2.2 + - - -
360A GLU* 2.4 30.7 + - - -
552A TRP* 3.8 55.7 - - + +
554A PRO* 3.9 23.5 - - + +
647A GLY* 2.5 32.1 + - - +
648A ASN* 4.2 3.4 - - - +
650A GLN* 1.3 72.2 - - - +
652A VAL* 1.3 61.5 + - - +
654A ASN* 4.7 2.0 - - - +
655A PHE* 3.3 21.5 + - - +
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Residues in contact with VAL 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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534A LEU* 4.6 11.9 - - + -
549A MET* 3.8 34.1 - - + +
552A TRP* 4.9 2.0 - - + -
553A VAL* 3.7 32.5 - - + +
577A ILE* 4.6 12.3 - - + +
578A LEU* 5.0 11.7 - - + -
581A ALA* 5.2 3.6 - - + -
648A ASN 3.3 20.7 + - - +
649A ILE* 4.2 2.0 - - - +
650A GLN 3.2 0.4 - - - -
651A LYS* 1.3 78.3 - - - +
653A VAL* 1.3 64.4 + - + +
655A PHE* 3.2 5.6 + - - +
656A TRP* 2.9 26.5 + - - +
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Residues in contact with VAL 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ASP 4.1 1.1 - - - +
527A THR* 3.3 34.3 - - + +
530A GLY* 3.6 10.3 - - - +
531A ILE* 3.4 38.8 - - + +
534A LEU* 4.0 16.2 - - + -
578A LEU* 4.4 5.6 - - + -
649A ILE* 3.1 25.9 + - + +
652A VAL* 1.3 73.9 - - + +
654A ASN* 1.3 62.1 + - - +
656A TRP* 3.3 6.8 + - + +
657A LEU* 2.8 28.8 + - - +
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Residues in contact with ASN 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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357A PRO* 3.8 28.6 + - + +
472A LEU* 5.6 3.6 - - - +
526A ASP* 4.2 11.4 - - - +
527A THR* 3.9 23.6 + - - -
650A GLN* 2.6 43.1 + - - +
651A LYS* 4.7 2.6 - - - +
653A VAL* 1.3 76.3 - - - +
655A PHE* 1.3 53.8 + - - +
657A LEU* 3.6 4.6 - - - +
658A LEU* 2.7 37.8 + - - +
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Residues in contact with PHE 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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545A GLN* 4.3 17.0 - - + -
548A ASN* 3.6 36.3 - - + -
549A MET* 4.3 19.7 - - + -
552A TRP* 3.2 34.5 - + + +
651A LYS 3.3 19.9 + - - +
652A VAL* 3.2 5.4 + - - +
654A ASN* 1.3 76.1 - - - +
656A TRP* 1.3 68.1 + - - +
658A LEU* 3.3 16.0 + - + -
659A HIS* 3.1 58.0 - + - -
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Residues in contact with TRP 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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530A GLY 4.2 5.4 - - - -
533A LYS* 3.6 40.2 - - + -
534A LEU* 3.8 26.4 - - + +
539A THR* 3.6 22.3 - - + +
540A PHE 5.7 0.6 + - - -
541A ILE* 3.8 22.6 - - + +
545A GLN* 3.6 25.1 + - - +
549A MET* 3.8 21.5 - - + -
652A VAL 2.9 16.8 + - - +
653A VAL* 3.8 7.0 - - + +
655A PHE* 1.3 81.3 - - - +
657A LEU* 1.3 70.1 + - + +
659A HIS* 3.5 2.8 + - - +
660A ASN* 3.0 68.9 + - + +
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Residues in contact with LEU 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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526A ASP* 3.2 55.0 - - + +
529A CYS* 4.9 3.8 - - + -
530A GLY* 3.9 17.9 - - - +
533A LYS* 4.8 6.5 - - + -
653A VAL* 2.8 17.2 + - + +
654A ASN* 3.8 5.8 - - - +
656A TRP* 1.3 88.7 - - + +
658A LEU* 1.3 60.8 + - - +
660A ASN* 4.2 0.9 - - - -
661A GLY* 2.8 52.6 + - - +
662A PHE* 4.4 9.4 - - + -
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Residues in contact with LEU 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A ASN 2.7 22.6 + - - +
655A PHE* 3.6 14.8 - - + +
656A TRP 3.3 0.2 - - - -
657A LEU* 1.3 74.2 - - - +
659A HIS* 1.3 76.4 + - + +
660A ASN 3.8 0.3 + - - -
661A GLY* 4.6 2.8 + - - -
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Residues in contact with HIS 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A GLN* 4.1 19.9 + - + +
655A PHE* 3.1 63.8 + + - +
656A TRP 3.8 0.7 - - - +
657A LEU 3.2 0.2 - - - -
658A LEU* 1.3 93.1 + - + +
660A ASN* 1.3 59.2 + - - +
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Residues in contact with ASN 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A LYS* 4.2 12.0 + - - +
545A GLN* 5.9 0.7 - - - +
656A TRP* 3.0 61.4 + - + +
657A LEU* 4.1 2.2 - - + +
658A LEU 4.9 0.2 - - - -
659A HIS* 1.3 79.5 - - - +
661A GLY* 1.3 68.8 + - - +
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Residues in contact with GLY 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A LYS* 4.9 3.5 - - - +
657A LEU* 2.8 28.9 + - - +
658A LEU 4.6 3.3 + - - -
660A ASN* 1.3 86.8 - - - +
662A PHE* 1.3 66.0 + - - +
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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