Contacts of the helix formed by residues 656 - 676 (chain H) in PDB entry 2W3S
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 ASN 656 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LYS 3.1 9.7 + - - +
6H PRO* 3.4 1.6 - - - +
7H LEU* 2.7 35.8 + - - +
8H PRO 5.2 0.2 + - - -
494H ALA* 5.2 0.6 - - - +
495H LYS* 4.8 5.3 - - + +
498H GLN* 3.5 20.6 + - - +
654H SER* 3.0 3.9 + - - -
655H LEU* 1.3 83.3 - - - +
657H PRO* 1.3 63.3 - - - +
658H ALA* 3.0 12.5 + - - +
659H LEU* 2.9 36.8 + - + +
660H ASP* 2.8 32.1 + - - +
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Residues in contact with PRO 657 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H GLY 3.3 25.6 - - - +
5H LYS 3.7 4.5 - - - +
6H PRO* 3.8 11.0 - - + -
654H SER* 3.1 15.6 - - - +
656H ASN* 1.3 86.2 - - - +
658H ALA* 1.3 56.2 + - - +
660H ASP* 3.1 1.9 + - + +
661H ILE* 2.6 44.9 + - + +
712H LEU* 3.7 23.1 - - + -
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Residues in contact with ALA 658 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G HIS* 3.6 37.0 - - + +
6H PRO* 3.5 26.1 - - + +
656H ASN* 3.0 9.4 + - - +
657H PRO* 1.3 82.2 - - - +
659H LEU* 1.3 63.6 + - - +
661H ILE* 3.1 13.6 + - - +
662H GLY* 3.1 11.1 + - - -
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Residues in contact with LEU 659 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G HIS* 4.8 10.3 - - + +
102G GLN* 5.6 2.7 + - + -
7H LEU 3.9 4.5 - - - +
9H HIS* 3.9 31.6 - - + +
489H GLY 6.1 0.2 - - - +
490H GLN 4.7 5.8 - - - +
491H GLY* 3.7 31.4 - - - +
494H ALA* 3.8 17.5 - - + -
495H LYS* 4.3 12.8 - - + -
656H ASN* 2.9 44.2 + - + +
658H ALA* 1.3 74.3 - - - +
660H ASP* 1.3 58.5 + - - +
662H GLY* 3.5 2.3 + - - +
663H GLN* 3.1 31.3 + - - +
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Residues in contact with ASP 660 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495H LYS* 2.8 32.3 + - - -
651H ALA* 3.5 11.6 - - - +
654H SER* 2.8 27.6 + - - +
655H LEU 4.3 1.6 + - - -
656H ASN 2.8 19.5 + - - +
657H PRO* 3.5 6.3 - - + +
659H LEU* 1.3 75.0 - - - +
661H ILE* 1.3 64.9 + - - +
662H GLY 3.2 1.3 - - - -
663H GLN* 3.4 6.5 + - - +
664H ILE* 3.1 30.7 + - - +
712H LEU* 4.6 9.9 - - + -
726H LYS 4.9 1.9 - - - +
728H VAL* 3.6 18.6 - - + +
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Residues in contact with ILE 661 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G ARG* 6.0 0.7 - - - +
657H PRO* 2.6 33.2 + - + +
658H ALA* 3.8 6.7 - - - +
660H ASP* 1.3 72.8 - - - +
662H GLY* 1.3 54.3 + - - +
664H ILE* 3.0 6.1 + - - +
665H GLU* 2.8 51.6 + - + +
710H VAL* 3.7 40.6 - - + +
711H ALA* 4.7 0.4 - - - -
712H LEU* 3.5 36.6 - - + +
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Residues in contact with GLY 662 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G HIS* 6.3 2.5 - - - -
102G GLN* 3.1 28.8 + - - +
137G THR 4.2 0.8 - - - +
141G PRO* 6.2 1.1 - - - -
658H ALA 3.1 12.8 + - - -
659H LEU* 3.8 4.9 - - - -
660H ASP 3.2 0.2 - - - -
661H ILE* 1.3 77.9 - - - +
663H GLN* 1.3 61.5 + - - +
665H GLU* 3.8 13.3 - - - +
666H GLY* 3.1 18.4 + - - -
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Residues in contact with GLN 663 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G GLN* 3.1 27.1 + - - -
342H ARG* 3.6 10.0 + - - +
490H GLN* 3.6 26.9 + - - +
495H LYS* 5.4 1.1 - - - +
659H LEU 3.1 19.9 + - - +
660H ASP* 3.5 9.4 - - - +
661H ILE 3.2 0.4 - - - -
662H GLY* 1.3 76.9 - - - +
664H ILE* 1.3 52.7 + - + +
667H ALA* 2.8 39.2 + - - +
728H VAL* 4.0 27.7 - - + +
729H GLY* 4.0 7.6 - - - -
732H PRO* 4.6 0.9 - - - -
1778H MTE 3.0 39.7 + - - +
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Residues in contact with ILE 664 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647H ILE* 3.6 23.3 - - + -
649H HIS* 3.7 23.6 - - + -
660H ASP 3.1 18.2 - - - +
661H ILE* 3.0 8.1 + - - +
663H GLN* 1.3 74.4 - - - +
665H GLU* 1.3 65.2 + - - +
667H ALA* 4.0 0.2 - - - +
668H TYR* 3.0 23.7 + - - +
710H VAL* 3.5 23.1 - - + -
712H LEU* 3.6 29.2 - - + -
728H VAL* 4.3 7.6 - - + -
732H PRO* 3.9 22.5 - - + +
735H LEU* 3.9 11.0 - - + -
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Residues in contact with GLU 665 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G THR 3.9 8.1 - - - +
140G ALA* 3.4 12.5 - - - +
141G PRO* 3.7 12.4 - - - +
144G ARG* 3.1 41.9 + - - -
661H ILE* 2.8 32.4 + - + +
662H GLY* 3.8 15.9 - - - +
664H ILE* 1.3 75.0 - - - +
666H GLY* 1.3 59.1 + - - +
669H VAL* 3.1 28.1 + - - +
708H PHE* 3.2 24.4 - - + -
710H VAL* 3.6 23.9 - - + +
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Residues in contact with GLY 666 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G ARG 4.9 2.4 - - - +
136G CYS 3.3 26.6 - - - +
137G THR 3.8 0.9 - - - -
138G GLY* 3.7 16.6 - - - -
342H ARG* 4.6 3.1 - - - -
662H GLY 3.1 8.0 + - - -
665H GLU* 1.3 76.6 - - - +
667H ALA* 1.3 60.6 + - - +
668H TYR 3.2 0.4 - - - -
669H VAL* 3.5 2.3 + - - +
670H GLN* 3.0 28.8 + - - +
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Residues in contact with ALA 667 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342H ARG* 3.3 29.8 - - - +
663H GLN 2.8 21.4 + - - +
666H GLY* 1.3 76.9 - - - +
668H TYR* 1.3 61.9 + - - +
670H GLN* 3.2 4.7 + - - +
671H GLY 3.0 17.8 + - - -
732H PRO* 3.5 25.4 - - + -
733H PHE* 3.5 19.5 - - - +
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Residues in contact with TYR 668 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627H ALA* 4.5 0.7 - - + -
629H THR* 2.6 33.7 + - - +
642H ILE* 4.3 4.1 - - + +
645H THR* 3.1 32.9 + - + -
647H ILE* 3.9 15.7 - - + -
664H ILE 3.0 18.7 + - - +
665H GLU 3.6 3.4 - - - +
666H GLY 3.2 0.2 - - - -
667H ALA* 1.3 75.2 - - - +
669H VAL* 1.3 66.1 + - + +
671H GLY* 3.1 2.1 + - - -
672H ALA* 2.9 40.6 + - + +
705H PRO* 3.8 11.7 - - + -
708H PHE* 3.8 16.6 - + - -
732H PRO 4.1 10.7 + - - +
735H LEU* 3.6 27.8 - - + -
736H GLY* 3.6 21.0 - - - +
738H SER* 3.9 1.1 - - - -
739H ALA* 3.7 5.7 - - - +
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Residues in contact with VAL 669 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G CYS 6.0 0.9 - - - +
138G GLY* 3.7 22.4 - - - +
139G TYR* 4.7 9.6 - - + -
665H GLU 3.1 19.0 + - - +
666H GLY 3.8 5.2 - - - +
667H ALA 3.4 0.2 - - - -
668H TYR* 1.3 80.8 - - + +
670H GLN* 1.3 62.5 + - - +
672H ALA* 4.1 4.1 - - - +
673H GLY 3.0 17.8 + - - -
699H PRO* 3.4 33.5 - - + +
703H ASP 6.0 0.4 - - - -
704H ARG* 5.0 5.8 - - - +
705H PRO* 4.4 8.7 - - + -
708H PHE* 3.7 22.4 - - + -
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Residues in contact with GLN 670 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G ARG* 3.4 47.4 - - - +
171H GLN* 3.4 16.8 + - - +
228H PHE* 3.2 31.8 - - - -
341H PHE* 3.7 18.0 - - + -
342H ARG* 2.8 32.1 + - - -
666H GLY 3.0 16.7 + - - +
667H ALA 3.5 6.1 - - - +
668H TYR 3.1 0.4 - - - -
669H VAL* 1.3 79.3 - - - +
671H GLY* 1.3 63.6 + - - +
673H GLY* 3.4 1.4 + - - -
674H TRP 3.3 13.5 + - - -
678H GLU* 4.2 0.9 - - - +
733H PHE* 3.8 14.1 - - + -
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Residues in contact with GLY 671 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667H ALA 3.0 10.3 + - - -
668H TYR 3.6 2.7 - - - -
670H GLN* 1.3 72.9 - - - +
672H ALA* 1.3 66.9 + - - +
674H TRP* 2.8 23.1 + - - +
675H LEU* 3.4 7.8 + - - +
733H PHE* 3.6 38.1 - - - -
736H GLY* 4.2 6.3 - - - -
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Residues in contact with ALA 672 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642H ILE* 4.1 16.8 - - + -
668H TYR* 2.9 25.9 + - + +
669H VAL* 4.1 4.3 - - - +
671H GLY* 1.3 70.3 - - - -
673H GLY* 1.3 64.7 + - - +
675H LEU* 2.8 15.4 + - - +
676H THR* 3.1 18.1 + - + +
736H GLY* 3.6 17.1 - - - -
739H ALA* 4.0 23.3 - - + -
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Residues in contact with GLY 673 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669H VAL 3.0 13.2 + - - -
670H GLN 3.7 0.4 - - - -
671H GLY 3.2 0.6 - - - -
672H ALA* 1.3 76.1 - - - +
674H TRP* 1.3 60.5 + - - +
675H LEU 3.4 0.5 + - - -
676H THR* 3.6 8.5 - - - -
677H THR 3.5 4.1 + - - -
678H GLU* 2.9 41.0 + - - +
699H PRO* 3.6 26.4 - - - +
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Residues in contact with TRP 674 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168H ILE* 3.3 27.5 - - + +
169H GLY 2.8 21.0 + - - -
170H GLY 3.3 19.9 + - - -
171H GLN* 3.3 34.9 - - + +
269H ARG* 3.6 19.1 - - - +
347H PRO* 3.6 31.9 - - + -
348H GLN* 3.9 14.4 - - + -
351H LEU* 3.9 11.0 - - + -
670H GLN 3.3 5.1 + - - +
671H GLY* 2.8 18.3 + - - +
673H GLY* 1.3 72.0 - - - +
675H LEU* 1.3 89.5 + - + +
676H THR 3.3 0.9 + - - -
678H GLU* 3.7 18.2 - - + +
733H PHE* 3.6 18.8 - + + -
734H LEU* 6.4 0.4 - - - -
737H ILE* 5.0 5.2 - - + -
760H PRO* 3.7 7.4 - - - +
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Residues in contact with LEU 675 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H ILE* 4.4 0.4 - - + -
351H LEU* 3.7 18.4 - - + -
671H GLY 3.9 2.9 - - - +
672H ALA* 2.8 7.5 + - - +
674H TRP* 1.3 120.9 - - + +
676H THR* 1.3 63.0 + - + +
736H GLY 3.9 7.0 - - - +
737H ILE* 3.8 33.4 - - + +
740H PHE* 3.6 36.1 - - + +
743H LEU* 4.6 0.2 - - - +
759H ALA* 4.1 15.0 - - + -
760H PRO* 3.9 3.4 - - - -
761H ALA* 2.8 31.4 + - - +
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Residues in contact with THR 676 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640H ASN* 5.3 5.8 - - - +
642H ILE* 5.0 16.3 - - + +
672H ALA* 3.2 22.0 + - + +
673H GLY* 3.6 7.6 - - - -
674H TRP 3.3 2.0 - - - -
675H LEU* 1.3 84.7 - - + +
677H THR* 1.3 83.2 + - - +
678H GLU 3.4 0.9 - - - -
699H PRO* 5.7 0.2 - - - +
739H ALA* 5.0 5.6 - - + -
740H PHE 5.5 0.2 - - - +
743H LEU* 3.8 22.0 - - + -
760H PRO* 3.5 3.7 - - - +
761H ALA 3.4 10.2 - - - -
762H THR* 3.0 32.0 + - - +
763H PRO* 5.9 0.2 - - - -
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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