Contacts of the helix formed by residues 682 - 705 (chain A) in PDB entry 3K23
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 SER 682 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A ASN 4.3 2.9 + - - -
587A LEU* 3.4 26.7 - - - +
588A HIS* 3.3 23.4 + - - +
591A ASP* 2.5 18.6 + - - -
680A LEU* 4.3 0.7 - - - -
681A LYS* 1.3 69.2 - - - +
683A GLN* 1.3 58.8 + - - +
684A GLU 3.6 0.9 - - - -
685A LEU* 3.4 13.6 + - - +
686A PHE* 2.8 24.8 + - - +
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Residues in contact with GLN 683 (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 VAL* 4.4 12.6 - - - +
679A GLY* 3.8 7.6 - - - -
680A LEU* 2.7 54.1 + - - +
681A LYS 3.0 6.1 + - - +
682A SER* 1.3 71.5 - - - +
684A GLU* 1.3 71.7 + - - +
686A PHE* 2.7 31.4 + - - +
687A ASP* 2.7 42.2 + - - +
770A LYS* 6.2 0.4 - - - +
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Residues in contact with GLU 684 (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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682A SER 3.6 0.2 - - - -
683A GLN* 1.3 78.1 - - - +
685A LEU* 1.3 61.0 + - - +
687A ASP* 3.7 7.0 + - - +
688A GLU* 3.4 18.7 + - - +
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Residues in contact with LEU 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A GLY* 5.3 4.3 - - - +
586A ASN* 3.5 51.1 - - + +
587A LEU* 3.6 11.9 - - + -
682A SER* 3.4 17.1 + - - +
683A GLN 2.8 4.2 + - - -
684A GLU* 1.3 73.3 - - - +
686A PHE* 1.3 65.5 + - - +
688A GLU* 3.0 38.7 + - - +
689A ILE* 3.0 17.9 + - + +
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Residues in contact with PHE 686 (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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587A LEU* 3.6 15.4 - - + +
595A LEU* 3.9 24.0 - - + -
672A LEU* 3.5 46.6 - - + +
675A VAL* 3.7 20.9 - - + -
680A LEU* 3.4 24.5 - - + -
682A SER 2.8 14.5 + - - +
683A GLN* 2.7 29.3 + - - +
685A LEU* 1.3 70.4 - - - +
687A ASP* 1.3 69.0 + - - +
689A ILE* 3.1 7.3 + - - +
690A ARG* 2.9 38.4 + - - +
772A LEU* 3.8 14.6 - - + -
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Residues in contact with ASP 687 (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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683A GLN* 2.7 42.5 + - - +
684A GLU* 4.3 6.1 + - - +
686A PHE* 1.3 92.0 - - - +
688A GLU* 1.3 62.5 + - - +
690A ARG* 4.4 9.0 + - - -
691A MET* 3.1 35.3 + - + +
772A LEU* 5.1 5.7 - - - +
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Residues in contact with GLU 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A GLU 3.4 11.2 + - - +
685A LEU* 3.0 31.7 + - - +
687A ASP* 1.3 81.0 - - - +
689A ILE* 1.3 55.4 + - - +
691A MET* 3.4 4.9 + - - +
692A THR* 2.6 33.4 + - - +
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Residues in contact with ILE 689 (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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583A GLY* 4.8 21.5 - - - +
587A LEU* 6.1 2.9 - - + -
672A LEU* 4.7 4.9 - - + -
685A LEU* 3.0 17.4 + - + +
686A PHE* 3.7 8.7 - - + +
688A GLU* 1.3 74.9 - - - +
690A ARG* 1.3 65.9 + - - +
692A THR* 3.1 11.8 + - - -
693A TYR* 3.0 37.4 + - + -
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Residues in contact with ARG 690 (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 LEU* 3.9 13.9 + - + +
672A LEU* 3.2 52.3 + - + +
673A SER* 5.1 1.8 - - - +
686A PHE* 2.9 32.2 + - + +
687A ASP* 4.1 8.5 + - - +
689A ILE* 1.3 76.6 - - - +
691A MET* 1.3 79.5 - - + +
693A TYR* 3.3 3.0 + - - +
694A ILE* 3.2 27.1 + - + +
772A LEU* 3.7 35.3 + - - +
773A LEU 4.9 4.2 + - - -
774A PHE* 3.9 33.9 - - - -
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Residues in contact with MET 691 (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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687A ASP* 3.1 30.7 + - + +
688A GLU* 3.7 5.2 - - - +
690A ARG* 1.3 99.4 - - + +
692A THR* 1.3 62.3 + - - +
694A ILE* 3.4 23.6 + - + +
695A LYS* 3.4 18.9 + - - +
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Residues in contact with THR 692 (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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532A LEU* 4.4 18.3 - - + +
688A GLU* 2.6 27.0 + - - +
689A ILE* 3.2 11.4 + - - -
691A MET* 1.3 77.4 - - - +
693A TYR* 1.3 63.6 + - + +
695A LYS* 3.2 18.6 + - + +
696A GLU* 3.3 12.7 + - - +
699A LYS* 5.8 1.3 + - - +
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Residues in contact with TYR 693 (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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532A LEU* 3.4 27.6 - - + +
536A LEU* 4.0 27.8 - - + -
581A ILE* 3.4 12.2 - - + +
582A PRO* 2.9 56.3 + - - +
665A CYS* 4.3 5.5 - - - +
668A THR* 4.1 19.7 - - + -
669A LEU* 3.8 30.3 - - + +
672A LEU* 4.6 8.3 - - + -
689A ILE* 3.0 34.1 + - + +
690A ARG* 3.3 1.8 + - - +
692A THR* 1.3 75.0 - - - +
694A ILE* 1.3 62.6 + - - +
696A GLU* 3.5 10.1 - - + +
697A LEU* 3.3 15.4 + - - +
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Residues in contact with ILE 694 (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 LEU* 4.1 14.4 - - + -
690A ARG* 3.2 22.4 + - + +
691A MET* 3.6 38.1 - - + +
692A THR 3.2 0.4 - - - -
693A TYR* 1.3 73.2 - - - +
695A LYS* 1.3 67.1 + - - +
696A GLU 3.0 1.9 + - - -
697A LEU* 3.0 7.0 + - + +
698A GLY* 2.8 18.5 + - - -
715A PHE* 3.7 31.9 - - + -
774A PHE* 3.7 30.3 - - + -
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Residues in contact with LYS 695 (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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691A MET 3.4 7.8 + - - +
692A THR* 3.2 13.1 + - + +
694A ILE* 1.3 80.4 - - - +
696A GLU* 1.3 50.7 + - - +
698A GLY* 3.0 4.5 + - - +
699A LYS* 2.7 49.6 + - - +
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Residues in contact with GLU 696 (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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531A THR* 5.0 3.5 - - - -
532A LEU* 3.1 40.2 + - + +
533A VAL* 3.7 24.8 + - + +
536A LEU* 5.2 1.3 - - + -
665A CYS* 3.4 20.8 - - + -
692A THR* 3.3 9.2 + - - +
693A TYR* 3.5 20.4 - - + +
694A ILE 3.0 0.6 - - - -
695A LYS* 1.3 76.2 - - - +
697A LEU* 1.3 54.8 + - - +
698A GLY 3.0 0.9 - - - -
699A LYS* 3.0 33.4 + - - +
700A ALA* 2.8 34.5 + - - +
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Residues in contact with LEU 697 (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 GLU* 3.7 25.1 - - + +
665A CYS* 3.6 15.3 - - + -
666A MET* 3.6 37.7 - - + -
669A LEU* 4.0 16.4 - - + -
693A TYR 3.3 7.3 + - - +
694A ILE* 3.0 10.2 + - + +
696A GLU* 1.3 78.0 - - - +
698A GLY* 1.3 61.1 + - - +
700A ALA* 3.7 1.7 - - - +
701A ILE* 3.2 25.5 + - + +
715A PHE* 5.0 7.6 - - + -
718A LEU* 4.3 21.1 - - + -
719A THR* 4.4 21.8 - - + -
722A LEU* 4.8 1.3 - - + -
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Residues in contact with GLY 698 (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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694A ILE 2.8 13.1 + - - -
695A LYS* 3.1 7.2 - - - -
697A LEU* 1.3 77.3 - - - +
699A LYS* 1.3 61.3 + - - +
701A ILE* 3.0 11.4 + - - +
702A VAL* 3.0 25.7 + - - +
715A PHE* 4.9 12.7 - - - -
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Residues in contact with LYS 699 (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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692A THR* 5.8 1.2 + - - +
695A LYS* 2.7 31.1 + - - +
696A GLU* 3.0 34.8 + - - +
698A GLY* 1.3 72.0 - - - +
700A ALA* 1.3 54.0 + - - +
702A VAL* 3.0 11.3 + - + +
703A LYS* 2.6 39.3 + - + +
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Residues in contact with ALA 700 (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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533A VAL* 5.6 0.9 - - + -
659A SER* 5.1 1.0 + - - -
661A GLU* 4.0 22.2 - - + +
662A GLU* 3.7 39.5 - - + +
665A CYS* 4.4 2.5 - - - -
696A GLU 2.8 18.8 + - - +
697A LEU* 3.7 9.0 - - - +
698A GLY 3.2 0.2 - - - -
699A LYS* 1.3 72.0 - - - +
701A ILE* 1.3 63.4 + - - +
703A LYS* 3.5 2.3 + - - +
704A ARG* 3.0 23.4 + - - +
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Residues in contact with ILE 701 (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 GLU* 3.6 19.3 - - + +
697A LEU* 3.2 16.1 + - + +
698A GLY* 3.0 8.4 + - - +
700A ALA* 1.3 78.3 - - - +
702A VAL* 1.3 60.9 + - + +
704A ARG* 3.1 16.8 - - + +
705A GLU* 3.3 5.9 + - - +
706A GLY 4.0 3.5 + - - -
711A ASN* 3.5 28.0 - - + +
714A ARG* 3.6 29.8 - - + -
715A PHE* 3.5 41.3 - - + +
718A LEU* 3.7 13.5 - - + -
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Residues in contact with VAL 702 (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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698A GLY 3.0 18.8 + - - +
699A LYS* 3.5 11.9 - - + +
701A ILE* 1.3 73.0 - - + +
703A LYS* 1.3 61.6 + - - +
704A ARG 3.1 4.5 - - - -
705A GLU 3.2 21.5 + - - +
706A GLY* 4.4 10.3 - - - +
711A ASN* 4.8 14.4 - - + +
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Residues in contact with LYS 703 (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* 4.2 16.8 - - - +
699A LYS* 2.6 20.4 + - + +
700A ALA 3.9 4.0 - - - +
702A VAL* 1.3 73.4 - - + +
704A ARG* 1.3 61.6 + - - +
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Residues in contact with ARG 704 (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 LEU 4.0 4.2 + - - -
657A GLN* 3.2 34.6 + - - +
659A SER* 3.9 21.6 - - - +
662A GLU* 3.2 24.5 - - - -
700A ALA 3.0 11.4 + - - +
701A ILE* 3.1 12.3 - - - +
702A VAL 3.1 0.2 - - - -
703A LYS* 1.3 80.4 - - - +
705A GLU* 1.3 67.8 + - + +
714A ARG* 3.3 31.6 - - - +
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Residues in contact with GLU 705 (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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701A ILE 3.3 0.8 + - - +
702A VAL 3.2 11.9 + - - +
704A ARG* 1.3 90.7 + - + +
706A GLY* 1.3 62.2 + - - +
707A ASN* 2.7 49.1 + - - +
710A GLN* 5.0 2.9 - - - +
711A ASN* 5.4 0.4 - - - +
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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