Contacts of the helix formed by residues 646 - 673 (chain H) in PDB entry 3RCW
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 THR 646 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642H ASN* 4.8 3.1 - - - -
643H ALA* 3.0 28.9 + - - +
644H ARG 2.7 20.0 + - - +
645H ASP* 1.3 77.9 - - - +
647H VAL* 1.3 64.6 + - - +
648H PHE* 3.3 14.4 + - - -
649H TYR 3.6 3.3 + - - -
650H ARG* 3.6 8.7 - - - -
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Residues in contact with VAL 647 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594E LYS 3.8 22.2 - - - +
595E GLU* 4.5 8.3 - - - +
597E PRO* 4.1 17.5 - - + +
645H ASP 4.0 0.4 + - - -
646H THR* 1.3 74.8 - - - +
648H PHE* 1.3 61.1 + - + +
650H ARG* 3.3 18.1 + - - +
651H ALA* 2.6 37.3 + - - +
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Residues in contact with PHE 648 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594E LYS* 5.1 10.1 - - + -
586H ILE* 3.7 42.2 - - + -
638H CYS* 3.6 19.5 - - - -
642H ASN* 3.5 36.8 - - + -
646H THR* 3.1 5.1 - - - -
647H VAL* 1.3 85.1 - - + +
649H TYR* 1.3 58.4 + - - +
651H ALA* 4.0 4.7 - - - -
652H ALA* 2.6 37.6 + - - +
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Residues in contact with TYR 649 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638H CYS* 4.6 2.2 - - - -
639H MET* 3.6 59.7 - - + +
642H ASN* 4.4 9.4 - - - +
643H ALA 3.5 7.9 + - - +
644H ARG* 3.5 42.6 - - + +
646H THR 3.6 1.6 + - - -
647H VAL 3.5 0.6 - - - -
648H PHE* 1.3 78.4 - - - +
650H ARG* 1.3 57.6 + - + +
652H ALA* 3.6 4.7 - - - +
653H VAL* 2.7 51.9 + - + +
656H ARG* 5.8 0.7 + - - -
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Residues in contact with ARG 650 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595E GLU 5.8 1.0 + - - -
597E PRO* 5.4 5.3 - - - +
644H ARG* 3.2 27.7 + - - +
645H ASP* 4.5 11.1 + - - +
646H THR 3.6 2.5 - - - -
647H VAL* 3.3 28.1 + - - +
648H PHE 3.3 0.4 - - - -
649H TYR* 1.3 81.4 - - + +
651H ALA* 1.3 54.7 + - - +
653H VAL* 3.0 12.5 + - + +
654H ARG* 2.8 34.2 + - - +
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Residues in contact with ALA 651 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597E PRO* 4.3 19.0 - - + +
586H ILE* 4.2 20.6 - - + -
587H PHE* 4.6 8.6 - - + -
647H VAL 2.6 22.9 + - - +
648H PHE* 3.6 8.7 - - - +
650H ARG* 1.3 68.0 - - - +
652H ALA* 1.3 55.2 + - - +
654H ARG* 3.0 7.2 + - - +
655H LEU* 2.8 36.5 + - - +
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Residues in contact with ALA 652 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587H PHE* 4.0 13.9 - - + -
635H ILE* 3.6 18.4 - - + +
638H CYS* 3.6 21.8 - - - -
639H MET* 3.8 17.7 - - + -
648H PHE 2.6 21.9 + - - +
649H TYR 3.8 3.4 - - - +
651H ALA* 1.3 74.1 - - - +
653H VAL* 1.3 60.8 + - - +
655H LEU* 4.5 2.5 - - - -
656H ARG* 3.1 24.3 + - - +
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Residues in contact with VAL 653 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639H MET* 4.4 10.8 - - - -
649H TYR* 2.7 43.3 + - + +
650H ARG* 3.0 14.7 + - + +
652H ALA* 1.3 74.5 - - - +
654H ARG* 1.3 63.6 + - + +
656H ARG* 3.3 20.9 + - - +
657H ASP* 3.1 39.0 + - - +
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Residues in contact with ARG 654 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598E ASP* 6.1 4.5 - - + -
601E ASP* 5.8 2.2 - - - +
650H ARG 2.8 17.7 + - - +
651H ALA* 3.0 7.1 + - - +
653H VAL* 1.3 74.4 - - + +
655H LEU* 1.3 60.3 + - - +
657H ASP* 3.3 5.1 + - - +
658H GLN* 3.0 52.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU 655 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578H LEU* 4.1 10.5 - - + +
581H LYS* 3.8 36.1 + - + +
582H ASP* 4.8 2.9 - - + +
587H PHE* 3.6 31.2 - - + -
609H PHE* 3.9 21.1 - - + -
631H PHE* 3.3 15.7 - - + -
634H ILE* 4.6 2.9 - - + -
635H ILE* 3.8 21.8 - - + -
651H ALA 2.8 16.2 + - - +
652H ALA* 4.0 1.1 - - - +
654H ARG* 1.3 77.1 - - - +
656H ARG* 1.3 55.7 + - - +
658H GLN* 4.9 1.6 - - - -
659H GLY* 2.7 32.3 + - - +
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Residues in contact with ARG 656 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631H PHE* 4.4 7.3 - - + -
632H ASP* 6.1 0.9 - - - +
635H ILE* 3.7 32.3 - - + +
636H ASP* 5.7 1.3 - - - -
639H MET* 4.4 21.3 - - - +
649H TYR* 5.8 0.8 + - - -
652H ALA 3.1 18.2 + - - +
653H VAL* 3.4 20.4 + - - +
654H ARG 3.2 0.2 - - - -
655H LEU* 1.3 79.1 - - - +
657H ASP* 1.3 80.8 + - - +
660H GLY* 2.9 26.9 + - - -
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Residues in contact with ASP 657 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653H VAL* 3.1 24.3 + - - +
654H ARG* 3.3 4.5 + - - +
656H ARG* 1.3 108.0 + - - +
658H GLN* 1.3 65.3 + - + +
660H GLY* 3.5 1.4 + - - -
661H VAL* 3.4 24.9 + - - +
664H ARG* 4.9 3.4 + - - +
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Residues in contact with GLN 658 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601E ASP* 4.1 26.3 + - - +
581H LYS* 3.5 46.8 - - + +
654H ARG* 3.0 31.9 + - - +
657H ASP* 1.3 76.0 - - + +
659H GLY* 1.3 66.0 + - - +
661H VAL* 3.2 17.0 + - - +
662H VAL* 3.4 15.2 + - - +
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Residues in contact with GLY 659 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578H LEU* 3.5 24.1 - - - +
581H LYS* 4.4 3.4 - - - +
631H PHE* 3.8 8.3 - - - -
655H LEU* 2.7 26.6 + - - -
656H ARG 3.9 0.2 - - - -
658H GLN* 1.3 76.3 - - - +
660H GLY* 1.3 59.5 + - - -
662H VAL* 3.3 5.5 + - - +
663H LEU* 3.1 26.3 + - - +
----------------------------------------------------------
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Residues in contact with GLY 660 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631H PHE* 4.5 2.2 - - - -
656H ARG 2.9 21.1 + - - -
657H ASP 3.5 2.2 + - - -
658H GLN 3.2 0.4 - - - -
659H GLY* 1.3 76.5 - - - +
661H VAL* 1.3 56.3 + - - +
663H LEU* 3.3 8.8 + - - +
664H ARG* 2.9 49.3 + - - +
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Residues in contact with VAL 661 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657H ASP 3.4 15.0 + - - +
658H GLN* 3.2 10.7 + - - +
659H GLY 3.1 0.6 - - - -
660H GLY* 1.3 74.7 - - - +
662H VAL* 1.3 67.3 + - + +
664H ARG* 3.2 29.7 + - - +
665H GLN* 3.1 24.4 + - + +
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Residues in contact with VAL 662 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574H VAL* 3.9 29.8 - - + +
577H GLN* 3.6 39.9 - - + +
578H LEU* 4.1 11.4 - - + -
581H LYS* 4.2 22.0 - - + +
658H GLN 3.7 12.3 - - - +
659H GLY* 3.3 7.4 + - - +
661H VAL* 1.3 78.6 - - + +
663H LEU* 1.3 57.8 + - - +
665H GLN* 3.3 8.7 + - - +
666H ALA* 3.0 24.4 + - - +
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Residues in contact with LEU 663 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574H VAL* 3.9 25.4 - - + -
578H LEU* 4.8 3.6 - - + -
624H LEU* 4.4 17.2 - - + +
627H PHE* 4.1 17.9 - - + -
628H GLU* 4.1 32.4 - - + +
631H PHE* 3.4 39.0 - - + -
632H ASP* 5.6 0.2 - - - +
659H GLY 3.1 18.5 + - - +
660H GLY* 3.8 7.4 - - - +
662H VAL* 1.3 74.0 - - - +
664H ARG* 1.3 61.2 + - + +
665H GLN 3.1 1.6 - - - -
666H ALA* 3.2 4.6 + - - +
667H ARG* 2.9 27.5 + - - +
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Residues in contact with ARG 664 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657H ASP* 4.9 3.2 + - - +
660H GLY* 2.9 38.5 + - - +
661H VAL* 3.2 31.5 - - - +
663H LEU* 1.3 75.8 - - + +
665H GLN* 1.3 60.5 + - - +
667H ARG* 3.4 9.7 + - - +
668H ARG* 3.1 42.2 + - - +
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Residues in contact with GLN 665 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661H VAL* 3.1 16.2 + - + +
662H VAL* 3.4 12.1 - - - +
663H LEU 3.1 0.2 - - - -
664H ARG* 1.3 75.6 - - - +
666H ALA* 1.3 62.7 + - - +
668H ARG* 3.1 38.4 + - - +
669H GLU* 3.3 46.9 + - + +
----------------------------------------------------------
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Residues in contact with ALA 666 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570H LEU* 4.2 9.2 - - + +
574H VAL* 3.6 30.1 - - + -
624H LEU* 3.4 22.4 - - + -
662H VAL 3.0 11.5 + - - +
663H LEU* 3.2 8.7 + - - +
665H GLN* 1.3 73.3 - - - +
667H ARG* 1.3 66.0 + - - +
669H GLU* 3.1 10.8 + - - +
670H VAL* 2.9 24.9 + - - +
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Residues in contact with ARG 667 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624H LEU* 3.0 40.1 - - + +
625H HIS* 4.0 16.2 + - - +
628H GLU* 4.1 6.2 + - - +
663H LEU 2.9 13.4 + - - +
664H ARG* 3.4 15.0 - - - +
666H ALA* 1.3 77.0 - - - +
668H ARG* 1.3 55.2 + - + +
670H VAL* 3.3 29.3 + - - +
671H ASP* 2.9 54.8 + - - +
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Residues in contact with ARG 668 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664H ARG* 3.1 27.8 + - - +
665H GLN* 3.1 42.3 + - - +
667H ARG* 1.3 79.9 - - + +
669H GLU* 1.3 64.6 + - - +
671H ASP* 3.4 15.7 - - - +
672H SER* 3.3 19.4 + - - -
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Residues in contact with GLU 669 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570H LEU* 4.7 18.8 - - + -
665H GLN* 3.4 34.1 + - + +
666H ALA* 3.1 10.7 + - - +
668H ARG* 1.3 76.3 - - - +
670H VAL* 1.3 64.7 + - - +
672H SER* 2.7 26.3 + - - -
673H ILE* 3.1 9.4 + - - +
----------------------------------------------------------
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Residues in contact with VAL 670 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570H LEU* 4.2 13.2 - - + +
624H LEU* 4.1 27.6 - - + +
666H ALA 2.9 16.1 + - - +
667H ARG* 3.4 24.9 - - - +
669H GLU* 1.3 76.3 - - - +
671H ASP* 1.3 64.8 + - - +
673H ILE* 3.0 27.3 + - + +
----------------------------------------------------------
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Residues in contact with ASP 671 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667H ARG* 2.9 40.2 + - - +
668H ARG* 3.4 22.4 - - - +
670H VAL* 1.3 77.6 - - - +
672H SER* 1.3 60.8 + - - +
673H ILE 4.2 3.6 - - - +
----------------------------------------------------------
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Residues in contact with SER 672 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668H ARG 3.3 5.8 + - - -
669H GLU* 2.7 34.0 + - - -
671H ASP* 1.3 79.4 - - - +
673H ILE* 1.3 64.0 + - - +
----------------------------------------------------------
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Residues in contact with ILE 673 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566H PRO* 6.3 3.4 - - + -
669H GLU 3.1 10.9 + - - +
670H VAL* 3.0 21.6 + - + +
671H ASP 4.2 3.3 - - - +
672H SER* 1.3 81.8 + - - +
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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