Contacts of the strand formed by residues 853 - 857 (chain A) in PDB entry 3GVJ
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 GLN 853 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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839A ILE* 3.7 18.6 - - + +
840A PHE 3.2 9.0 - - - +
841A CYS* 3.4 25.6 - - - -
845A GLY 3.7 0.8 + - - -
846A THR 2.9 28.1 + - - -
848A SER* 3.5 22.2 - - - +
851A GLY 3.8 4.5 - - - +
852A ALA* 1.3 80.3 - - - +
854A ILE* 1.3 65.7 + - - +
855A THR* 4.2 6.5 + - - +
868A VAL 3.9 1.0 - - - +
870A ASN* 2.8 43.5 + - + +
2C SIA 2.9 22.5 + - - +
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Residues in contact with ILE 854 (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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840A PHE* 3.0 43.7 + - + +
853A GLN* 1.3 78.3 - - - +
855A THR* 1.3 62.8 + - - +
856A LEU* 4.1 14.6 - - + -
867A ILE* 3.9 23.3 - - + -
868A VAL 3.4 4.0 - - - +
869A TYR* 4.0 27.8 - - + -
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Residues in contact with THR 855 (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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837A ARG* 4.2 14.1 - - + +
838A ILE 3.4 14.6 - - - +
839A ILE* 3.8 30.0 - - + +
853A GLN* 4.4 8.5 + - - +
854A ILE* 1.3 73.3 + - - +
856A LEU* 1.3 60.2 + - - +
857A TYR* 3.5 31.3 - - + +
867A ILE* 3.4 7.3 - - - +
868A VAL* 3.0 36.6 + - - +
2C SIA 4.7 2.6 + - - -
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Residues in contact with LEU 856 (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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824A ILE 6.1 0.7 - - - +
837A ARG* 3.2 4.0 - - - -
838A ILE* 3.1 33.3 + - + +
840A PHE* 3.8 31.0 - - + -
854A ILE* 4.1 8.7 - - + -
855A THR* 1.3 72.9 - - - +
857A TYR* 1.3 62.4 + - - +
866A ARG 4.1 1.6 - - - -
867A ILE* 3.9 35.9 - - + -
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Residues in contact with TYR 857 (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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836A GLN 3.8 4.0 - - - -
837A ARG* 3.9 10.4 + - + -
855A THR* 3.5 35.8 - - + +
856A LEU* 1.3 75.3 - - - +
858A GLY* 1.3 64.1 + - - +
861A ASN* 3.4 34.1 - - + -
863A ASP* 3.4 29.2 - - + +
865A ARG* 3.3 15.4 - - - +
866A ARG* 3.0 44.2 + - + +
868A VAL* 4.0 21.8 - - + +
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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