Contacts of the helix formed by residues 689 - 697 (chain A) in PDB entry 4ZGA
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 689 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616A THR* 5.9 0.5 - - - +
687A SER* 3.7 3.2 - - - -
688A SER* 1.3 83.5 + - - +
690A PRO* 1.3 63.9 - - - +
691A GLU* 3.3 24.6 + - - +
692A ALA* 2.6 41.8 + - - +
693A LYS* 3.2 8.0 + - - +
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Residues in contact with PRO 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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687A SER* 6.0 0.2 - - - -
689A SER* 1.3 82.5 - - - +
691A GLU* 1.3 73.7 + - + +
693A LYS* 3.5 19.3 + - + +
694A TYR* 4.0 2.6 + - - +
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Residues in contact with GLU 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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689A SER* 2.9 18.9 + - - +
690A PRO* 1.3 95.1 - - + +
692A ALA* 1.3 64.6 + - - +
694A TYR* 3.2 19.6 + - - +
695A ASP* 5.3 0.5 - - - +
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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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616A THR* 4.7 13.2 - - + +
617A ASP* 3.2 26.2 - - - +
688A SER* 3.7 14.1 - - - +
689A SER* 2.6 27.2 + - - +
691A GLU* 1.3 75.7 - - - +
693A LYS* 1.3 60.5 + - - +
695A ASP* 2.8 30.2 + - - +
696A ALA 3.9 0.7 + - - -
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Residues in contact with LYS 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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684A PRO* 4.9 1.6 - - + +
687A SER* 3.4 29.9 + - - +
689A SER 3.2 6.6 + - - +
690A PRO* 3.8 14.8 - - + +
691A GLU 3.2 1.0 + - - -
692A ALA* 1.3 75.3 - - - +
694A TYR* 1.3 54.9 + - - +
696A ALA* 2.7 31.4 + - - +
697A PHE* 3.2 22.1 - - + -
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Residues in contact with TYR 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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654A ARG* 3.5 35.8 + - - +
690A PRO 4.0 2.7 + - - +
691A GLU 3.2 15.7 + - - +
692A ALA 2.9 0.6 + - - -
693A LYS* 1.3 77.2 - - - +
695A ASP* 1.3 64.3 + - - +
697A PHE* 3.5 16.2 + - - +
698A LEU* 3.5 14.1 + - - +
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Residues in contact with ASP 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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615A HIS* 3.7 28.6 - - + +
616A THR* 4.4 8.0 + - - -
617A ASP* 5.1 2.4 - - - +
618A PHE* 3.9 24.8 - - + -
654A ARG* 4.8 3.1 + - - -
691A GLU 5.3 0.3 - - - +
692A ALA* 2.8 18.8 + - - +
693A LYS 2.8 0.6 + - - -
694A TYR* 1.3 79.7 - - - +
696A ALA* 1.3 65.7 + - - +
697A PHE 2.9 2.2 - - - -
698A LEU* 2.9 37.3 + - + +
701A ASN* 4.5 0.9 - - - +
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Residues in contact with ALA 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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617A ASP* 5.7 0.2 + - - -
618A PHE* 4.0 7.1 - - - -
680A PHE* 3.4 15.6 - - - -
682A PHE* 4.2 7.8 - - + +
683A PRO 4.3 1.3 - - - +
684A PRO* 3.5 41.5 - - + -
687A SER* 4.2 5.4 - - - +
692A ALA 3.9 0.8 + - - -
693A LYS 2.7 20.4 + - - +
695A ASP* 1.3 74.7 - - - +
697A PHE* 1.3 56.4 + - + +
701A ASN* 2.9 28.2 + - - +
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Residues in contact with PHE 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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652A CYS* 3.1 47.3 - - + +
653A VAL* 3.4 8.5 - - - +
654A ARG* 3.3 19.5 + - + -
680A PHE* 3.8 23.2 - + - -
684A PRO* 3.6 34.5 - - + -
693A LYS* 3.2 36.1 - - + -
694A TYR* 3.9 10.3 - - - +
695A ASP 2.9 1.6 - - - -
696A ALA* 1.3 76.3 - - - +
698A LEU* 1.3 65.4 + - - +
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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