Contacts of the strand formed by residues 815 - 821 (chain W) in PDB entry 5O9G
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 MET 815 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610W THR* 3.8 28.5 - - + +
612W ARG* 5.3 4.5 - - - -
707W LEU* 6.0 4.7 - - + -
784W ASP* 3.4 5.1 + - - +
785W THR* 3.3 20.5 + - + +
786W VAL 3.1 22.5 + - - -
814W VAL* 1.3 73.6 - - - +
816W VAL* 1.3 65.0 + - - +
817W TYR* 3.5 46.4 - - + +
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Residues in contact with VAL 816 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610W THR 4.0 12.1 + - - +
611W GLU* 3.7 21.3 - - + +
612W ARG 3.0 26.9 + - - -
786W VAL* 3.3 22.4 - - + +
788W ILE* 5.0 7.2 - - + -
802W MET* 3.6 35.4 - - + -
814W VAL* 3.8 20.6 - - + -
815W MET* 1.3 79.6 - - - +
817W TYR* 1.3 75.9 + - - +
818W ARG* 4.9 3.1 - - + +
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Residues in contact with TYR 817 (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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612W ARG* 3.3 49.4 + - + +
614W LEU* 5.9 2.7 - - + -
703W LEU* 3.8 33.0 - - + -
706W ARG* 4.6 14.6 + - - -
707W LEU* 5.2 16.9 - - + +
785W THR* 5.3 4.0 - - + -
786W VAL 3.2 6.9 + - - +
787W VAL* 3.6 25.0 - - + +
788W ILE* 3.1 26.5 + - - +
815W MET* 3.5 40.6 + - + +
816W VAL* 1.3 84.0 - - - +
818W ARG* 1.3 60.9 + - - +
819W LEU* 4.0 7.6 + - + -
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Residues in contact with ARG 818 (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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611W GLU* 2.5 48.0 + - - +
612W ARG 3.2 7.5 + - - -
613W ILE* 3.4 14.1 - - + +
614W LEU* 2.8 32.3 + - - +
788W ILE* 3.9 21.2 - - + +
790W ASP* 5.7 1.8 - - - -
791W SER* 4.3 16.4 + - - +
798W ASP* 3.9 29.3 + - - +
799W LEU* 6.3 0.6 - - - +
802W MET* 5.6 6.9 - - - +
816W VAL* 5.6 2.8 - - + +
817W TYR* 1.3 72.1 - - - +
819W LEU* 1.3 61.1 + - - +
820W VAL* 3.0 25.6 + - + +
830W LEU* 4.5 12.5 - - - +
834W ARG* 3.9 25.6 - - - +
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Residues in contact with LEU 819 (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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614W LEU* 3.5 32.1 - - + -
616W VAL* 4.4 5.8 - - + -
696W LYS* 3.4 43.5 + - + +
699W LEU* 5.5 3.6 - - + -
700W LEU* 5.0 5.6 - - + +
703W LEU* 5.3 5.2 - - + -
787W VAL* 4.4 15.9 - - + -
788W ILE 3.1 12.0 + - - +
789W PHE* 2.8 60.3 - - + +
790W ASP* 4.6 2.5 - - - -
817W TYR* 5.1 7.2 - - + -
818W ARG* 1.3 72.9 - - - +
820W VAL* 1.3 65.0 + - - +
821W SER 3.4 2.6 + - - -
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Residues in contact with VAL 820 (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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613W ILE* 4.1 19.5 - - + -
614W LEU 2.8 14.5 + - - +
615W ARG* 3.2 27.1 - - + +
616W VAL* 2.7 33.2 + - - +
790W ASP* 6.2 0.4 - - - +
818W ARG* 3.0 35.8 + - + +
819W LEU* 1.3 71.2 - - - +
821W SER* 1.3 67.4 + - - +
826W GLU* 6.0 0.9 - - + -
827W GLU* 4.9 11.4 - - + +
830W LEU* 4.4 19.3 - - + -
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Residues in contact with SER 821 (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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616W VAL 3.8 5.8 - - - -
618W LEU* 5.4 2.0 - - - +
659W SER 4.8 3.4 - - - -
660W ASN* 4.3 7.6 - - - +
696W LYS* 3.1 30.1 + - - +
790W ASP* 5.3 0.7 - - - +
819W LEU 3.4 1.0 + - - -
820W VAL* 1.3 78.9 - - - +
822W LYS* 1.3 60.2 + - - +
824W THR* 2.9 38.2 + - - -
826W GLU* 3.7 21.9 + - - +
827W GLU* 3.0 13.7 + - - +
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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