Contacts of the helix formed by residues 684 - 697 (chain A) in PDB entry 2ZNS
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 ILE 684 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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678A PHE* 5.5 3.1 - - + -
682A SER* 3.1 9.2 + - - +
683A LYS* 1.3 78.8 - - - +
685A SER* 1.3 62.3 + - - +
686A THR* 3.8 24.5 - - + -
687A TYR* 3.1 33.1 + - + -
688A GLU* 2.8 27.4 + - - +
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Residues in contact with SER 685 (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 LYS 3.6 3.6 + - - -
684A ILE* 1.3 72.2 - - - +
686A THR* 1.3 55.7 + - - +
688A GLU* 3.0 14.7 + - - +
689A LYS* 2.7 37.2 + - - +
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Residues in contact with THR 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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656A ALA 4.2 0.3 + - - -
657A ASP* 3.8 35.7 + - - +
660A ALA* 3.8 17.5 - - - +
684A ILE* 3.8 16.2 - - + -
685A SER* 1.3 76.5 - - - +
687A TYR* 1.3 70.3 + - + +
689A LYS* 3.3 7.9 + - - +
690A MET* 2.7 40.2 + - - +
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Residues in contact with TYR 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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656A ALA* 4.0 23.4 - - + +
657A ASP* 5.9 0.2 - - - -
678A PHE* 3.7 24.5 - + + -
679A PHE* 3.6 30.3 - + + +
682A SER* 3.2 31.4 - - - +
684A ILE* 3.1 33.4 + - + +
686A THR* 1.3 86.3 - - + +
688A GLU* 1.3 56.3 + - - +
690A MET* 3.3 5.0 + - - -
691A TRP* 2.8 34.1 + - - +
744A ILE* 3.6 34.6 + - + +
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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
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679A PHE 5.0 0.7 - - - -
682A SER* 3.3 24.0 + - - +
683A LYS* 3.7 36.3 + - - +
684A ILE 2.8 14.1 + - - +
685A SER* 3.2 16.4 - - - +
687A TYR* 1.3 71.7 - - - +
689A LYS* 1.3 56.8 + - - +
691A TRP* 3.2 7.5 + - - +
692A ALA* 3.0 27.7 + - - +
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Residues in contact with LYS 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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660A ALA* 3.4 32.9 + - + +
661A LYS* 4.6 10.5 - - - +
667A TYR* 4.1 0.6 + - - +
685A SER 2.7 18.9 + - - +
686A THR* 3.5 8.1 - - - +
688A GLU* 1.3 70.6 - - - +
690A MET* 1.3 65.1 + - - +
692A ALA* 3.4 7.2 + - - +
693A PHE* 3.2 21.3 + - - +
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Residues in contact with MET 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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656A ALA* 3.5 40.8 - - + +
659A LEU* 4.6 6.7 - - + -
660A ALA* 3.6 9.9 - - + -
667A TYR* 3.4 41.1 - - + +
679A PHE* 3.6 33.9 - - + -
686A THR* 2.7 29.6 + - - +
687A TYR* 3.3 7.6 + - - +
689A LYS* 1.3 74.3 - - - +
691A TRP* 1.3 55.9 + - - +
693A PHE* 3.2 3.8 + - - +
694A MET* 2.9 33.0 + - + +
721A LEU* 4.1 14.1 - - + -
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Residues in contact with TRP 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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676A MET* 3.5 40.4 - - + -
679A PHE* 3.4 28.2 - - + +
680A LYS* 3.5 57.6 - - + +
687A TYR 2.8 15.7 + - - +
688A GLU* 3.2 7.5 + - - +
690A MET* 1.3 69.1 - - - +
692A ALA* 1.3 62.6 - - - +
694A MET* 3.8 23.8 - - + -
695A SER* 2.7 58.9 + - - -
702A LEU* 4.4 12.1 - - + -
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Residues in contact with ALA 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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688A GLU 3.0 15.3 + - - +
689A LYS* 3.8 8.3 - - - +
690A MET 3.4 0.2 - - - -
691A TRP* 1.3 78.4 - - - +
693A PHE* 1.3 61.8 + - - +
695A SER* 4.0 5.4 + - - -
696A SER* 3.1 28.1 + - - -
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Residues in contact with PHE 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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662A GLN 4.9 1.3 - - - -
663A THR* 4.1 27.4 - - + -
665A ILE 4.2 3.4 - - - -
666A GLU* 4.0 22.0 - - + -
667A TYR* 3.4 63.9 - + - +
689A LYS 3.2 7.6 + - - +
690A MET 3.2 3.3 + - - +
691A TRP 3.0 0.2 - - - -
692A ALA* 1.3 80.0 - - - +
694A MET* 1.3 67.5 + - - +
696A SER* 3.1 19.7 + - - -
697A ARG* 3.2 65.2 + - + +
701A ALA* 5.2 0.2 - - + -
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Residues in contact with MET 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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667A TYR* 3.9 38.1 - - + +
668A GLY* 3.9 22.9 - - - -
669A ALA* 4.5 5.8 - - + -
676A MET* 5.7 0.4 - - - -
679A PHE* 4.0 33.0 - - + -
690A MET 2.9 21.2 + - - +
691A TRP* 3.8 29.6 - - + -
693A PHE* 1.3 79.5 - - + +
695A SER* 1.3 55.6 + - - +
697A ARG 3.3 1.6 + - - -
698A GLN* 2.8 30.1 + - - +
701A ALA* 3.7 13.2 - - + +
702A LEU* 4.4 12.7 - - + +
721A LEU* 4.3 11.4 - - + -
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Residues in contact with SER 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A TRP* 2.7 60.1 + - - -
692A ALA* 4.0 4.9 + - - -
694A MET* 1.3 73.2 - - - +
696A SER* 1.3 60.7 + - - +
698A GLN* 3.4 33.6 + - - +
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Residues in contact with SER 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A ALA 3.1 17.7 + - - -
693A PHE* 3.1 12.0 + - - -
695A SER* 1.3 78.5 + - - +
697A ARG* 1.3 70.2 + - - +
698A GLN* 3.4 2.7 + - - +
699A GLN* 5.8 1.4 - - - +
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Residues in contact with ARG 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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663A THR* 4.0 25.9 + - - +
666A GLU* 4.1 13.8 + - - +
693A PHE* 3.2 59.3 + - - +
694A MET 3.3 3.3 + - - -
696A SER* 1.3 86.5 + - - +
698A GLN* 1.3 51.7 + - - +
699A GLN* 3.2 6.3 - - - -
700A THR* 2.9 18.9 + - - +
701A ALA* 2.7 39.6 + - + -
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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