Contacts of the helix formed by residues 657 - 682 (chain A) in PDB entry 2YGG
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 657 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A VAL 3.6 2.8 + - - -
656A ALA* 1.3 71.0 - - - +
658A PRO* 1.3 68.4 - - - +
659A TYR* 2.9 37.6 + - - +
660A GLU* 3.1 22.8 + - + +
661A GLU* 2.9 32.8 + - - +
76B LYS* 3.7 25.6 + - - +
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Residues in contact with PRO 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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656A ALA 3.5 7.8 - - - +
657A ASP* 1.3 90.2 - - - +
659A TYR* 1.3 71.8 + - + +
661A GLU* 3.9 6.0 - - + +
662A ALA* 3.0 29.3 + - - +
20B PHE* 3.3 10.1 - - + -
33B LEU* 4.2 13.0 - - + -
36B VAL* 3.8 26.2 - - + +
37B MET* 4.0 23.6 - - + -
40B LEU* 4.4 7.4 - - + -
52B MET* 4.3 13.0 - - + -
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Residues in contact with TYR 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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657A ASP* 2.9 22.1 + - - +
658A PRO* 1.3 88.8 - - + +
660A GLU* 1.3 66.0 + - - +
662A ALA* 3.9 2.1 - - - +
663A TRP* 3.0 26.5 + - - +
20B PHE* 3.7 32.1 - + - -
28B ILE* 5.3 2.9 - - + +
33B LEU* 4.2 14.8 - - + +
52B MET* 4.3 13.2 + - + +
56B VAL* 3.8 16.8 - - + +
64B ILE* 4.1 14.3 - - + +
69B PHE* 4.4 11.9 - + - -
72B MET* 3.2 34.5 - - + -
73B MET* 4.0 22.6 - - - +
76B LYS* 4.3 10.5 - - + -
1155B MRD 5.4 0.4 - - - -
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Residues in contact with GLU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ASP* 3.1 26.9 + - + +
659A TYR* 1.3 75.9 - - - +
661A GLU* 1.3 64.2 + - - +
663A TRP* 3.4 1.1 + - - +
664A ASN* 2.8 51.5 + - - +
76B LYS* 5.2 9.0 + - - +
1155B MRD 4.0 36.3 - - + +
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Residues in contact with GLU 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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656A ALA* 3.9 19.3 - - - +
657A ASP 2.9 20.8 + - - +
658A PRO* 3.9 7.6 - - + +
660A GLU* 1.3 84.1 - - - +
662A ALA* 1.3 60.5 + - - +
664A ASN* 3.3 9.6 + - + +
665A GLN* 2.8 32.0 + - - +
40B LEU* 4.1 24.9 - - + -
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Residues in contact with ALA 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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658A PRO 3.0 19.4 + - - +
659A TYR 3.9 2.5 - - - +
661A GLU* 1.3 75.6 - - - +
663A TRP* 1.3 60.1 + - - +
665A GLN* 3.3 8.9 + - - +
666A MET* 2.9 29.1 + - - +
16B ALA* 4.3 7.8 - - + +
19B LEU* 4.3 22.8 - - + +
20B PHE* 3.4 25.8 - - + -
36B VAL* 6.0 2.0 - - + -
69B PHE* 6.2 0.2 - - + -
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Residues in contact with TRP 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A TYR 3.0 19.9 + - - +
660A GLU* 3.7 4.3 - - - +
662A ALA* 1.3 76.7 - - - +
664A ASN* 1.3 68.1 + - - +
666A MET* 3.3 27.0 + - + +
667A LEU* 2.8 52.5 + - + +
12B GLU* 4.0 26.7 - - + -
13B PHE* 3.3 52.7 - + - -
16B ALA* 3.9 10.2 - - + +
73B MET* 3.4 23.8 - - + -
77B MET* 4.7 12.8 - - + -
1155B MRD 3.9 29.4 + - + +
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Residues in contact with ASN 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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660A GLU* 2.8 41.9 + - - +
661A GLU* 3.6 9.6 - - - +
663A TRP* 1.3 88.2 - - - +
665A GLN* 1.3 59.7 + - - +
667A LEU* 3.7 11.8 - - - +
668A LEU* 2.8 33.4 + - - +
1155B MRD 5.0 7.5 - - - +
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Residues in contact with GLN 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 GLU 2.8 20.8 + - - +
662A ALA* 3.7 7.8 - - - +
664A ASN* 1.3 72.7 - - - +
666A MET* 1.3 60.2 + - - +
668A LEU* 4.0 9.4 - - + +
669A ARG* 3.3 24.4 + - + +
19B LEU* 3.2 34.2 - - + +
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Residues in contact with MET 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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662A ALA 2.9 16.2 + - - +
663A TRP* 3.3 50.3 - - + +
665A GLN* 1.3 76.3 - - - +
667A LEU* 1.3 81.8 + - + +
669A ARG* 3.5 3.8 - - - +
670A ARG* 3.2 40.4 + - - +
12B GLU* 3.7 23.3 - - + +
15B GLU* 3.4 40.6 - - + +
16B ALA* 4.1 5.8 - - + +
19B LEU* 4.8 3.6 - - + +
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Residues in contact with LEU 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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663A TRP* 2.8 41.4 + - + +
664A ASN* 3.7 12.1 - - - +
666A MET* 1.3 102.9 - - + +
668A LEU* 1.3 61.8 + - - +
670A ARG* 3.2 6.3 + - + +
671A GLN* 3.0 25.4 + - - +
674A ARG* 5.1 1.4 + - - -
12B GLU* 4.3 16.2 - - - +
1155B MRD 5.4 7.2 - - + -
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Residues in contact with LEU 668 (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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664A ASN 2.8 18.0 + - - +
665A GLN* 4.0 8.7 - - + +
667A LEU* 1.3 77.6 - - - +
669A ARG* 1.3 57.9 + - - +
671A GLN* 3.3 12.3 + - - +
672A LYS* 3.0 52.4 + - + +
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Residues in contact with ARG 669 (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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665A GLN* 3.3 14.5 + - + +
666A MET 3.5 6.7 - - - +
668A LEU* 1.3 80.6 - - - +
670A ARG* 1.3 85.6 - - - +
672A LYS* 3.6 9.5 + - - +
673A ALA* 3.2 38.7 + - - +
15B GLU* 2.6 43.4 + - - +
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Residues in contact with ARG 670 (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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666A MET* 3.2 29.8 + - - +
667A LEU* 3.6 7.4 - - + +
668A LEU 3.2 0.2 - - - -
669A ARG* 1.3 103.3 - - - +
671A GLN* 1.3 63.8 + - - +
673A ALA* 3.4 3.3 + - - +
674A ARG* 3.1 36.2 + - - +
8B GLU* 4.3 13.9 + - - +
11B ALA* 3.4 31.5 + - - +
12B GLU* 3.8 29.6 + - - +
15B GLU* 3.1 24.0 + - - +
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Residues in contact with GLN 671 (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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667A LEU 3.0 15.9 + - - +
668A LEU* 3.9 13.3 - - - +
670A ARG* 1.3 73.4 - - - +
672A LYS* 1.3 63.2 + - + +
674A ARG* 3.1 28.5 + - - +
675A GLN* 2.9 54.7 + - + +
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Residues in contact with LYS 672 (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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668A LEU* 3.0 40.3 + - + +
669A ARG* 3.8 8.5 - - - +
671A GLN* 1.3 77.4 - - + +
673A ALA* 1.3 58.6 + - - +
675A GLN* 3.8 16.5 + - - +
676A LEU* 3.4 21.5 + - - +
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Residues in contact with ALA 673 (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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669A ARG* 3.2 31.2 + - - +
670A ARG* 3.8 4.3 - - - +
671A GLN 3.1 1.0 - - - -
672A LYS* 1.3 75.0 - - - +
674A ARG* 1.3 64.7 + - - +
676A LEU* 3.9 6.6 + - - +
677A GLU* 3.5 27.9 + - - +
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Residues in contact with ARG 674 (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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667A LEU 5.1 0.8 + - - -
670A ARG* 3.1 19.0 + - - +
671A GLN* 3.1 39.7 + - - +
673A ALA* 1.3 76.3 - - - +
675A GLN* 1.3 59.2 + - + +
677A GLU* 3.7 5.9 + - - +
678A GLN* 3.2 27.4 + - - +
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Residues in contact with GLN 675 (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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671A GLN* 2.9 43.0 + - + +
672A LYS* 4.0 16.4 - - - +
673A ALA 3.4 0.2 - - - -
674A ARG* 1.3 75.7 - - - +
676A LEU* 1.3 60.0 + - - +
678A GLN* 3.1 6.8 + - - +
679A LYS* 2.9 39.7 + - + +
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Residues in contact with LEU 676 (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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672A LYS 3.4 15.4 + - - +
673A ALA* 4.1 7.6 - - - +
674A ARG 3.4 0.6 - - - -
675A GLN* 1.3 77.7 - - - +
677A GLU* 1.3 75.2 + - - +
678A GLN 3.2 0.9 + - - -
679A LYS* 3.4 26.4 + - - +
680A ILE* 3.3 38.1 + - + +
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Residues in contact with GLU 677 (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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673A ALA 3.5 18.2 + - - +
674A ARG* 4.0 7.2 - - - +
675A GLN 3.3 0.2 - - - -
676A LEU* 1.3 89.5 - - - +
678A GLN* 1.3 58.0 + - - +
680A ILE* 3.9 19.5 - - - +
681A ASN* 3.1 27.2 + - - +
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Residues in contact with GLN 678 (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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674A ARG 3.2 18.1 + - - +
675A GLN* 3.1 9.2 + - - +
676A LEU 3.1 0.4 - - - -
677A GLU* 1.3 77.7 - - - +
679A LYS* 1.3 65.7 + - + +
680A ILE 3.2 0.4 - - - -
681A ASN* 3.4 15.2 + - - +
682A ASN* 3.1 49.4 + - - +
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Residues in contact with LYS 679 (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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675A GLN* 2.9 21.1 + - + +
676A LEU* 3.9 30.0 - - - +
678A GLN* 1.3 76.5 - - + +
680A ILE* 1.3 59.0 + - - +
682A ASN* 3.3 6.8 + - - +
683A TYR* 3.0 27.0 + - - +
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Residues in contact with ILE 680 (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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676A LEU* 3.3 33.4 + - + +
677A GLU* 3.9 22.9 - - - +
678A GLN 3.2 0.4 - - - -
679A LYS* 1.3 79.5 - - + +
681A ASN* 1.3 58.5 + - - +
683A TYR* 2.9 34.0 + - + +
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Residues in contact with ASN 681 (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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677A GLU 3.1 16.9 + - - +
678A GLN* 3.4 21.0 + - - +
680A ILE* 1.3 79.4 - - - +
682A ASN* 1.3 62.2 + - - +
683A TYR 3.4 0.4 - - - -
685A THR* 3.9 9.0 + - - -
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Residues in contact with ASN 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A GLN* 3.1 40.4 + - - +
679A LYS* 3.6 5.8 - - - +
680A ILE 3.1 0.6 - - - -
681A ASN* 1.3 82.1 + - - +
683A TYR* 1.3 66.8 + - - +
684A LEU 3.2 2.8 + - - -
685A THR* 3.5 21.8 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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