Contacts of the strand formed by residues 2164 - 2168 (chain B) in PDB entry 2H7C
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 VAL2164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2121B ILE* 4.0 15.0 - - + -
2122B TYR 3.5 10.3 - - - +
2123B THR* 3.7 22.0 - - - +
2124B PRO* 4.3 0.4 - - - -
2133B LEU* 4.2 10.8 - - + -
2134B PRO 2.9 10.7 + - - +
2135B VAL* 3.5 7.0 - - + +
2136B MET* 2.8 27.2 + - - +
2163B VAL* 1.3 73.1 - - - +
2165B VAL* 1.3 60.7 + - - +
2166B VAL* 4.2 4.7 - - + -
2205B ILE* 3.9 27.1 - - + -
2208B PHE* 4.1 1.6 - - + +
2209B GLY 4.0 6.3 - - - +
2210B GLY* 3.9 25.4 - - - +
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Residues in contact with VAL2165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2121B ILE* 3.5 2.6 - - - +
2122B TYR* 2.7 53.0 + - + +
2136B MET* 3.5 9.0 - - + +
2138B TRP* 5.3 0.2 - - + -
2154B GLY* 4.0 18.6 - - - +
2157B LEU* 4.0 15.0 - - + -
2158B ALA* 3.8 27.4 - - + +
2163B VAL* 3.8 15.9 - - + +
2164B VAL* 1.3 76.4 - - - +
2166B VAL* 1.3 69.4 + - - +
2167B THR* 4.3 5.6 - - + -
2218B PHE* 4.9 5.2 - - + -
2476B PHE* 4.6 15.3 - - + -
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Residues in contact with VAL2166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2119B LEU* 4.2 21.3 - - + -
2120B ASN 3.3 8.7 - - - +
2121B ILE* 4.4 6.5 - - + -
2135B VAL* 4.0 16.2 - - + -
2136B MET 2.9 11.9 + - - +
2137B VAL* 3.3 10.0 - - + +
2138B TRP* 2.8 28.6 + - - +
2164B VAL* 4.2 4.0 - - + -
2165B VAL* 1.3 78.1 - - - +
2167B THR* 1.3 63.6 + - - +
2168B ILE* 3.9 20.6 - - + -
2200B TRP* 6.0 0.2 - - + -
2201B VAL* 4.4 11.0 - - + -
2205B ILE* 4.0 27.1 - - + -
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Residues in contact with THR2167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2119B LEU* 3.1 4.7 - - - +
2120B ASN* 2.8 59.2 + - - +
2122B TYR* 4.2 8.7 - - + -
2138B TRP* 3.8 25.8 - - + -
2149B ALA* 3.7 20.9 + - - +
2152B TYR* 3.8 23.1 + - + +
2154B GLY 5.4 0.4 - - - +
2165B VAL* 4.3 8.7 - - + -
2166B VAL* 1.3 77.0 - - - +
2168B ILE* 1.3 61.1 + - - +
2476B PHE* 5.1 2.5 - - + -
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Residues in contact with ILE2168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2055B PHE* 4.9 0.4 - - + -
2118B TYR 4.0 4.0 - - - +
2119B LEU* 4.0 7.4 - - + -
2137B VAL* 3.8 24.2 - - + -
2138B TRP* 3.3 18.4 + - - +
2139B ILE* 3.8 27.6 - - + -
2140B HIS* 3.6 14.7 + - - -
2149B ALA* 3.5 9.0 - - - +
2166B VAL* 3.9 11.2 - - + -
2167B THR* 1.3 78.6 - - - +
2169B GLN* 1.3 69.3 + - - +
2170B TYR* 4.5 2.0 - - + -
2194B GLN* 4.1 33.7 - - + +
2197B ALA* 3.9 26.9 - - + -
2198B LEU* 5.8 1.1 - - + -
2201B VAL* 5.7 0.4 - - + -
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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