Contacts of the helix formed by residues 697 - 701 (chain A) in PDB entry 1S0Q
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 ALA 697 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696A SER* 1.3 80.2 + - - +
698A ALA* 1.3 64.6 + - - +
699A HIS* 3.5 24.0 - - + +
700A CYS* 3.0 22.3 + - - +
743A ASP* 3.5 22.0 - - - +
745A MET* 3.5 11.4 - - - +
837A GLY* 3.5 20.3 - - - +
849A ILE* 4.0 3.4 - - + -
850A VAL 4.0 4.7 - - - +
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Residues in contact with ALA 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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697A ALA* 1.3 70.6 - - - +
699A HIS* 1.3 57.8 + - - +
700A CYS 3.0 0.2 - - - -
701A TYR* 3.0 27.2 + - - +
731A VAL* 3.8 9.6 - - + +
735A TYR* 3.5 41.1 - - + -
743A ASP* 2.8 9.7 + - - +
744A ILE 3.4 26.2 - - - +
745A MET* 3.8 10.8 - - - -
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Residues in contact with HIS 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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684A CYS* 5.2 1.1 - - - -
697A ALA* 3.2 13.4 - - + +
698A ALA* 1.3 76.3 - - - +
700A CYS* 1.3 59.0 + - - +
701A TYR 3.3 3.2 + - - +
735A TYR* 3.3 21.2 + - - +
740A LEU* 4.3 10.8 - - + +
743A ASP* 2.8 31.8 + - - +
836A SER* 2.6 38.3 + - - -
850A VAL 3.8 4.0 - - - -
851A SER 3.0 26.0 + - - -
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Residues in contact with CYS 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A LEU* 4.5 0.9 - - + -
683A PHE* 3.3 21.1 - - + -
684A CYS* 2.0 54.1 - - + -
696A SER* 3.8 13.5 - - - +
697A ALA* 3.0 15.8 + - - +
699A HIS* 1.3 77.3 - - - +
701A TYR* 1.3 65.0 + - - +
702A LYS* 3.3 2.6 + - - -
705A ILE* 4.5 0.9 - - - +
745A MET* 4.0 9.1 - - + +
836A SER* 3.6 22.7 - - - -
837A GLY 4.0 2.0 - - - -
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Residues in contact with TYR 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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698A ALA 3.0 17.4 + - - +
699A HIS 3.3 4.3 - - - +
700A CYS* 1.3 79.3 - - - +
702A LYS* 1.3 87.1 + - - +
703A SER* 4.3 12.7 + - - -
729A SER* 4.5 14.6 - - - -
731A VAL* 3.8 17.3 - - + -
745A MET* 3.6 27.6 - - - +
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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