Contacts of the strand formed by residues 766 - 769 (chain W) in PDB entry 6G0L
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 VAL 766 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704W LEU* 5.2 2.9 - - + -
714W VAL* 3.5 20.4 - - + +
716W ILE* 5.3 8.7 - - + -
731W LEU* 3.6 27.1 - - + -
736W ILE* 3.9 17.7 - - + +
737W ASN 3.2 21.5 - - - +
738W PHE* 3.3 31.4 - - + -
739W GLN 4.2 1.0 + - - -
764W ASP* 4.0 6.5 - - - +
765W PHE* 1.3 80.2 - - + +
767W PHE* 1.3 70.3 + - - +
768W LEU* 5.2 4.5 - - + +
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Residues in contact with PHE 767 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714W VAL 3.4 5.6 + - - +
715W LEU* 3.5 19.1 - - + +
716W ILE* 3.5 17.3 + - - -
738W PHE* 5.5 0.2 - - - -
739W GLN* 3.3 37.7 - - + -
740W ARG 5.0 1.8 - - - -
741W LEU* 3.6 28.9 - - + -
753W SER* 5.4 8.3 - - - -
754W ILE* 5.2 11.4 - - + -
757W PHE* 4.4 30.1 - + + -
764W ASP* 4.6 9.4 - - - -
765W PHE 5.2 0.2 - - - +
766W VAL* 1.3 81.0 - - - +
768W LEU* 1.3 59.6 + - - +
769W LEU* 2.9 37.0 + - + +
780W LEU* 3.9 23.6 - - + -
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Residues in contact with LEU 768 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716W ILE* 3.5 21.3 - - + +
724W LEU* 3.8 53.2 - - + +
727W LEU* 4.8 13.5 - - + -
728W GLY* 5.1 4.9 - - - +
738W PHE* 5.3 11.9 - - + +
739W GLN 3.9 5.6 + - - +
740W ARG* 3.4 35.2 - - + -
741W LEU* 3.0 21.0 + - - +
766W VAL* 5.2 4.2 - - + +
767W PHE* 1.3 71.4 - - - +
769W LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 769 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715W LEU* 5.0 2.0 - - + -
716W ILE 3.1 8.4 + - - +
717W PHE* 2.9 41.3 - - + -
718W SER 3.4 23.9 + - - +
724W LEU* 4.0 8.6 - - - +
741W LEU* 3.6 27.6 - - + -
767W PHE* 2.9 46.2 - - + +
768W LEU* 1.3 73.9 - - - +
770W SER* 1.4 58.4 + - - +
774W GLY* 3.5 22.0 - - - +
778W ILE* 5.3 2.7 - - + -
780W LEU* 4.7 16.4 - - + -
804W ARG* 5.3 1.6 - - + -
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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