Contacts of the helix formed by residues 6975 - 6983 (chain A) in PDB entry 6W4H
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 ASN6975 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6943A SER* 3.3 9.9 + - - -
6944A LYS 2.8 20.5 + - - +
6945A GLU* 4.4 7.3 - - - +
6948A PHE* 3.4 39.0 - - + +
6949A THR* 4.7 3.2 + - - +
6952A CYS* 3.7 6.0 - - - -
6969A ILE* 5.4 1.0 - - - +
6974A TRP* 1.3 80.2 - - - +
6976A ALA* 1.3 63.7 + - - +
6977A ASP* 2.8 21.2 + - - +
6978A LEU* 2.8 39.3 + - + +
6979A TYR* 3.4 16.9 + - - -
7004A LEU* 6.3 0.2 - - - +
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Residues in contact with ALA6976 (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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6943A SER* 2.8 16.4 + - - +
6974A TRP* 3.7 7.4 - - + -
6975A ASN* 1.3 69.6 + - - +
6977A ASP* 1.3 64.5 + - - +
6979A TYR 3.3 2.3 + - - -
6980A LYS* 3.0 25.6 + - - +
7019A GLY* 3.3 27.6 + - - +
7020A TYR* 3.7 30.5 - - + +
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Residues in contact with ASP6977 (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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6952A CYS* 3.9 15.0 - - + -
6975A ASN* 2.8 16.4 + - - +
6976A ALA* 1.3 76.4 - - - +
6978A LEU* 1.3 58.5 + - - +
6980A LYS* 3.3 21.0 + - + +
6981A LEU* 2.9 33.3 + - + +
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Residues in contact with LEU6978 (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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6948A PHE* 3.9 20.9 - - + -
6951A ILE* 4.4 7.0 - - + -
6952A CYS* 3.5 13.9 - - - -
6955A ILE* 4.0 26.7 - - + -
6967A ILE* 3.6 35.4 - - + -
6969A ILE* 4.4 2.5 - - + -
6975A ASN* 2.8 23.9 + - + +
6976A ALA 3.2 0.2 - - - -
6977A ASP* 1.3 73.6 - - - +
6979A TYR* 1.3 65.9 + - - +
6981A LEU* 3.2 8.0 + - + +
6982A MET* 3.2 32.2 + - + +
7004A LEU* 4.0 20.2 - - + -
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Residues in contact with TYR6979 (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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6969A ILE* 3.2 20.9 - - + +
6974A TRP* 4.1 8.7 - + + -
6975A ASN 3.4 18.0 + - - -
6976A ALA 3.3 7.4 + - - +
6978A LEU* 1.3 77.6 - - - +
6980A LYS* 1.3 64.4 + - - +
6982A MET* 3.0 23.9 + - + +
6988A TRP* 4.4 12.3 - + - -
6990A ALA* 5.6 0.2 - - + -
7004A LEU* 3.7 28.0 - - + +
7017A ILE* 3.6 12.2 - - + +
7019A GLY* 3.6 22.9 - - - -
7022A MET* 3.5 34.5 - - + -
7023A HIS* 2.8 44.0 + - + -
7026A TYR* 3.6 15.4 - - + +
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Residues in contact with LYS6980 (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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6976A ALA 3.0 13.1 + - - +
6977A ASP* 3.3 23.4 + - - +
6979A TYR* 1.3 75.5 - - - +
6981A LEU* 1.3 59.5 + - + +
6983A GLY* 3.0 19.1 + - - -
6984A HIS* 3.6 18.9 - - - +
7015A GLU 4.8 1.7 - - - +
7016A GLN* 3.7 25.2 - - - +
7017A ILE* 3.5 32.8 - - - +
7019A GLY* 4.6 1.3 - - - +
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Residues in contact with LEU6981 (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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6952A CYS* 3.6 52.0 - - + +
6955A ILE* 4.8 14.4 - - + -
6956A GLN* 3.5 34.5 - - + +
6977A ASP* 2.9 13.8 + - + +
6978A LEU* 3.2 11.2 + - + +
6980A LYS* 1.3 74.1 - - + +
6982A MET* 1.3 63.4 + - + +
6983A GLY 3.0 2.5 - - - -
6984A HIS* 2.8 48.9 + - + +
6985A PHE* 3.3 14.7 - - + -
7009A TYR* 5.5 1.3 - - + +
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Residues in contact with MET6982 (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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6955A ILE* 5.1 0.7 - - + -
6965A VAL* 4.0 15.5 - - + -
6978A LEU* 3.2 40.2 + - + +
6979A TYR* 3.0 19.3 + - - +
6981A LEU* 1.3 77.6 - - + +
6983A GLY* 1.3 56.4 + - - +
6984A HIS 3.1 4.2 + - - -
6985A PHE* 3.3 39.1 + - + +
6988A TRP* 3.7 42.5 - - + +
7004A LEU* 4.3 19.3 - - + +
7005A ILE 3.7 11.4 - - - +
7006A GLY* 3.7 22.4 - - - -
7017A ILE* 4.3 3.1 - - + -
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Residues in contact with GLY6983 (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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6980A LYS 3.0 9.9 + - - -
6981A LEU 3.0 1.6 - - - -
6982A MET* 1.3 78.5 - - - +
6984A HIS* 1.3 54.8 + - - +
6985A PHE 3.3 4.7 - - - -
7014A ARG* 2.7 36.6 + - - +
7015A GLU* 3.2 36.3 + - - -
7017A ILE* 3.7 7.7 - - - +
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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