Contacts of the helix formed by residues 661 - 683 (chain A) in PDB entry 3IAY
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 661 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621A ASN* 2.9 19.3 + - - -
623A CYS* 3.8 7.0 - - - -
625A THR* 3.6 13.9 - - - -
626A THR* 3.6 11.2 - - - -
659A ARG 3.5 2.2 + - - -
660A ARG* 1.3 76.8 - - - +
662A ILE* 1.3 63.7 + - - -
664A PRO* 3.6 13.3 - - - +
665A ILE* 3.7 17.0 - - - +
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Residues in contact with ILE 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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202A ILE* 4.8 2.5 - - + -
564A LEU* 4.3 9.6 - - + -
567A LYS* 3.3 34.8 - - + +
568A CYS* 4.0 21.5 - - - +
571A ILE* 3.1 36.8 - - + -
623A CYS* 3.1 9.8 - - - -
625A THR* 3.7 20.6 + - + +
660A ARG 5.1 2.5 - - - +
661A GLY* 1.3 71.7 - - - -
663A LEU* 1.3 69.1 + - - +
664A PRO 3.2 1.6 - - - -
665A ILE* 3.0 12.6 + - + +
666A ILE* 3.0 28.8 + - + +
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Residues in contact with LEU 663 (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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560A VAL* 5.7 3.1 - - + -
564A LEU* 3.8 27.6 - - + -
617A MET* 3.5 30.1 - - + -
622A LEU 3.6 5.8 - - - +
623A CYS* 3.4 14.2 - - - -
624A TYR* 3.9 15.9 - - + -
662A ILE* 1.3 78.1 - - - +
664A PRO* 1.3 70.5 - - + +
666A ILE* 3.2 11.6 + - + +
667A LEU* 2.9 29.4 + - - +
707A VAL* 4.2 16.6 - - + +
710A PHE* 6.4 0.4 - - + -
711A THR* 3.7 23.1 - - + -
723A ILE* 4.0 11.9 - - + -
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Residues in contact with PRO 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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617A MET 3.7 19.3 - - - +
618A MET* 3.9 27.7 - - + +
621A ASN* 4.1 20.9 - - - +
622A LEU 3.5 11.4 - - - +
623A CYS* 4.0 1.6 - - + -
661A GLY* 3.6 15.5 - - - +
662A ILE 3.5 2.9 - - - +
663A LEU* 1.3 95.4 - - + +
665A ILE* 1.3 58.1 + - + +
667A LEU* 3.5 4.4 + - + +
668A ASP* 2.9 28.6 + - - +
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Residues in contact with ILE 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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567A LYS* 3.7 28.9 - - + -
660A ARG* 5.2 11.9 - - + +
661A GLY 3.7 17.0 - - - +
662A ILE* 3.0 14.1 + - + +
664A PRO* 1.3 75.4 - - + +
666A ILE* 1.3 67.0 + - - +
668A ASP* 3.2 7.5 + - + +
669A GLU* 3.0 31.4 + - + +
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Residues in contact with ILE 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A VAL* 5.1 3.8 - - + +
563A GLN* 3.5 55.3 - - + +
564A LEU* 4.0 13.9 - - + +
567A LYS* 3.8 17.9 - - + +
662A ILE* 3.0 30.4 + - + +
663A LEU* 3.6 14.6 - - + +
665A ILE* 1.3 75.8 - - - +
667A LEU* 1.3 63.7 + - - +
669A GLU* 3.3 10.3 + - - +
670A LEU* 3.1 23.5 + - + +
707A VAL* 4.0 23.6 - - + -
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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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614A PRO* 3.9 26.5 - - + +
617A MET* 3.6 46.4 - - + -
618A MET* 4.1 13.7 - - + -
663A LEU 2.9 22.8 + - - +
664A PRO* 3.8 4.3 - - + +
666A ILE* 1.3 74.6 - - - +
668A ASP* 1.3 59.4 + - - +
670A LEU* 3.2 4.0 + - + +
671A ILE* 2.8 36.9 + - - +
704A ALA* 3.5 32.3 - - + +
707A VAL* 3.8 19.7 - - + -
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Residues in contact with ASP 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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618A MET* 4.2 12.8 - - + +
664A PRO 2.9 18.7 + - - +
665A ILE* 3.2 10.1 + - + +
667A LEU* 1.3 75.5 - - - +
669A GLU* 1.3 59.4 + - + +
671A ILE* 3.5 5.0 + - - +
672A SER* 2.8 39.6 + - - -
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Residues in contact with GLU 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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543A VAL* 5.1 10.7 - - + +
563A GLN* 5.6 2.6 - - - +
567A LYS* 3.1 37.9 + - - -
665A ILE* 3.0 22.7 + - + +
666A ILE* 3.7 6.0 - - - +
668A ASP* 1.3 77.0 - - + +
670A LEU* 1.3 65.4 + - + +
672A SER* 3.5 7.4 + - - -
673A ALA* 3.1 22.3 + - - +
676A ARG* 4.7 1.9 + - - -
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Residues in contact with LEU 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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543A VAL* 3.7 23.3 - - + -
544A THR* 4.5 4.5 - - + -
563A GLN* 3.6 28.3 - - - +
666A ILE* 3.1 21.2 + - + +
667A LEU* 3.7 4.7 - - - +
669A GLU* 1.3 76.8 - - + +
671A ILE* 1.3 58.9 + - - +
673A ALA* 3.4 6.7 + - - +
674A ARG* 2.9 27.4 + - - +
700A LEU* 4.5 13.9 - - + +
703A SER* 3.9 23.8 - - - +
704A ALA* 3.8 34.3 - - + +
707A VAL* 4.0 15.0 - - + -
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Residues in contact with ILE 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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611A SER* 4.2 24.5 - - - +
614A PRO* 3.7 17.3 - - + -
618A MET* 3.4 35.0 - - + -
667A LEU* 2.8 20.3 + - + +
668A ASP* 4.0 6.1 - - - +
670A LEU* 1.3 75.9 - - - +
672A SER* 1.3 55.0 + - - +
674A ARG* 3.2 10.9 + - + +
675A LYS* 2.8 66.6 + - + +
704A ALA* 4.7 13.0 - - + -
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Residues in contact with SER 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 ASP* 2.8 31.3 + - - -
669A GLU* 3.5 8.5 - - - -
671A ILE* 1.3 73.4 - - - +
673A ALA* 1.3 65.9 + - - +
675A LYS* 3.1 11.1 + - - +
676A ARG* 3.0 44.0 + - - +
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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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539A GLU* 4.7 7.8 - - - +
543A VAL* 4.4 17.3 - - + -
669A GLU 3.1 11.2 + - - +
670A LEU* 3.6 9.9 - - - +
672A SER* 1.3 77.9 - - - +
674A ARG* 1.3 65.4 + - - +
676A ARG* 3.0 36.5 + - - +
677A ALA* 3.0 12.3 + - - +
700A LEU* 3.8 23.6 - - + +
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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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611A SER* 3.4 18.5 + - - -
670A LEU 2.9 15.3 + - - +
671A ILE* 3.2 14.6 + - - +
673A ALA* 1.3 75.5 - - - +
675A LYS* 1.3 58.2 + - + +
677A ALA* 3.1 4.4 + - - +
678A LYS* 2.8 54.6 + - + +
697A GLN* 2.8 51.6 + - + +
698A LEU* 4.9 0.6 - - - +
700A LEU* 3.8 17.4 - - + +
701A LYS* 3.8 28.7 - - - +
986A DCP 2.7 48.1 + - - -
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Residues in contact with LYS 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 ILE* 2.8 48.1 + - + +
672A SER* 3.1 9.8 + - - +
674A ARG* 1.3 69.5 - - + +
676A ARG* 1.3 66.6 + - + +
678A LYS* 3.8 16.0 - - + +
679A LYS* 3.1 23.6 + - - +
682A ARG* 5.2 0.7 + - - -
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Residues in contact with ARG 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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539A GLU* 5.3 5.4 + - - +
543A VAL* 5.4 4.6 - - - +
669A GLU 4.7 2.0 + - - -
672A SER* 3.0 30.5 + - - +
673A ALA* 3.0 35.2 + - - +
675A LYS* 1.3 76.3 - - + +
677A ALA* 1.3 63.9 + - - +
679A LYS* 3.4 7.0 + - - +
680A ASP* 3.1 27.8 + - - +
696A ARG* 4.6 7.9 - - - +
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Residues in contact with ALA 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 3.0 11.1 + - - +
674A ARG 3.4 8.5 - - - +
676A ARG* 1.3 77.0 - - - +
678A LYS* 1.3 56.5 + - - +
680A ASP* 3.1 5.9 + - - +
681A LEU* 2.9 26.3 + - - +
693A LEU* 4.8 4.6 - - - +
696A ARG* 3.8 44.2 + - + +
697A GLN* 3.9 20.9 - - + +
700A LEU* 4.4 4.5 - - + -
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Residues in contact with LYS 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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610A ASN* 5.8 1.6 + - - -
674A ARG* 2.8 60.6 + - + +
675A LYS* 3.8 16.2 - - + +
676A ARG 3.3 0.2 - - - -
677A ALA* 1.3 72.7 - - - +
679A LYS* 1.3 56.5 + - - +
681A LEU* 3.1 12.5 + - + +
682A ARG* 2.7 61.8 + - - +
697A GLN* 3.7 19.6 + - + +
800A GLU* 5.7 2.8 + - - -
986A DCP 5.2 2.8 + - - -
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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 LYS 3.1 18.0 + - - +
676A ARG* 3.7 7.6 - - - +
678A LYS* 1.3 76.0 - - - +
680A ASP* 1.3 59.8 + - - +
682A ARG* 3.1 17.4 + - + +
683A ASP* 2.9 53.7 + - - +
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Residues in contact with ASP 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 ARG* 3.1 14.1 + - - +
677A ALA 3.1 9.8 + - - +
679A LYS* 1.3 77.8 - - - +
681A LEU* 1.3 61.0 + - - +
683A ASP* 3.3 16.7 + - - +
684A GLU* 3.4 10.4 + - - +
693A LEU* 3.5 19.0 - - + +
696A ARG* 2.7 36.2 + - - +
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Residues in contact with LEU 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 ALA 2.9 12.5 + - - +
678A LYS* 3.1 13.4 + - + +
680A ASP* 1.3 74.7 - - - +
682A ARG* 1.3 64.7 + - - +
683A ASP 3.3 0.3 + - - -
684A GLU* 3.4 8.0 + - - +
690A ARG* 3.2 77.7 + - + +
693A LEU* 3.9 15.1 - - + +
694A ASN* 3.7 33.2 - - + +
697A GLN* 4.5 9.4 - - + -
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Residues in contact with ARG 682 (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 LYS 5.2 0.6 + - - -
678A LYS* 2.7 62.9 + - - +
679A LYS* 3.1 20.8 + - + +
681A LEU* 1.3 74.3 - - - +
683A ASP* 1.3 65.3 + - - +
684A GLU 3.3 2.3 + - - +
690A ARG* 4.1 13.8 + - - +
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Residues in contact with ASP 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A LYS* 2.9 49.6 + - - +
680A ASP* 3.3 8.9 + - - +
681A LEU 3.2 0.4 - - - -
682A ARG* 1.3 84.4 - - - +
684A GLU* 1.3 58.4 + - - +
685A LYS 4.1 0.7 + - - -
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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