Contacts of the strand formed by residues 2133 - 2139 (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 LEU2133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2124B PRO* 4.0 17.7 - - + -
2125B ALA* 3.7 27.1 - - + +
2131B ASN* 4.4 10.3 - - + +
2132B ARG* 1.3 80.6 - - - +
2134B PRO* 1.3 79.0 - - + +
2162B ASN* 3.2 41.7 - - - +
2164B VAL* 4.2 7.2 - - + +
2209B GLY 2.9 15.8 + - - +
2210B GLY* 3.5 2.3 - - - -
2211B ASN* 2.8 29.6 + - - +
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Residues in contact with PRO2134 (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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2132B ARG 4.4 1.6 - - - +
2133B LEU* 1.3 92.0 - - + +
2135B VAL* 1.3 58.7 + - - +
2162B ASN 4.0 6.1 - - - +
2163B VAL* 3.6 25.8 - - + +
2164B VAL* 2.9 25.3 + - - +
2214B SER* 3.8 24.0 - - - +
2504B ALA* 4.3 19.3 - - + +
2505B ARG* 4.3 26.9 - - + +
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Residues in contact with VAL2135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2133B LEU 3.7 0.9 - - - +
2134B PRO* 1.3 78.2 - - - +
2136B MET* 1.3 59.3 + - - +
2137B VAL* 3.9 21.5 - - + -
2164B VAL* 3.5 11.4 - - + +
2166B VAL* 4.0 15.5 - - + -
2201B VAL* 4.2 6.3 - - + -
2205B ILE* 3.7 26.5 - - + -
2210B GLY* 3.9 3.4 - - - -
2211B ASN 3.7 31.2 - - - +
2214B SER 2.9 10.3 + - - +
2215B VAL* 3.4 7.2 - - + -
2216B THR* 2.7 35.5 + - - +
2504B ALA* 5.2 0.2 - - - +
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Residues in contact with MET2136 (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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2135B VAL* 1.3 75.5 - - - +
2137B VAL* 1.3 63.0 + - - +
2138B TRP 3.8 0.5 + - - -
2157B LEU* 4.3 11.7 - - + -
2163B VAL* 4.0 27.6 - - + -
2164B VAL 2.8 12.3 + - - +
2165B VAL* 3.5 6.6 - - + +
2166B VAL 2.9 26.0 + - - +
2216B THR* 3.5 14.4 - - + -
2218B PHE* 3.6 40.9 - - + -
2244B ILE* 4.5 1.1 - - + -
2500B TRP* 3.9 30.5 - - + +
2501B ALA* 4.4 11.0 - - - -
2504B ALA* 3.8 25.1 - - + -
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Residues in contact with VAL2137 (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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2135B VAL* 3.9 13.0 - - + -
2136B MET* 1.3 73.6 - - - +
2138B TRP* 1.3 61.4 + - - +
2139B ILE* 3.9 3.4 + - + +
2166B VAL* 3.3 13.9 - - + +
2168B ILE* 3.8 36.6 - - + -
2197B ALA* 5.9 0.2 - - + -
2198B LEU* 4.1 23.6 - - + -
2201B VAL* 4.3 10.8 - - + -
2215B VAL* 3.8 24.2 - - + -
2216B THR 2.8 11.9 + - - +
2217B ILE* 3.4 6.3 - - + +
2218B PHE* 3.0 27.5 + - - +
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Residues in contact with TRP2138 (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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2136B MET 5.2 0.2 - - - +
2137B VAL* 1.3 71.9 - - - +
2139B ILE* 1.3 67.1 + - - +
2140B HIS* 3.6 14.5 + - + +
2141B GLY 5.2 0.7 - - - -
2149B ALA* 5.7 0.7 - - - -
2152B TYR* 3.5 45.1 - + - -
2165B VAL* 5.3 1.1 - - + -
2166B VAL 2.8 13.9 + - - +
2167B THR* 4.2 15.7 - - + -
2168B ILE* 3.3 30.2 + - - +
2218B PHE* 3.2 62.0 - + + -
2219B GLY* 3.5 12.1 - - - -
2220B GLU* 3.5 25.4 - - + -
2246B GLU* 3.6 11.7 - - - -
2472B LEU* 3.4 32.8 - - + -
2475B VAL* 5.2 0.4 - - + -
2476B PHE* 3.4 22.4 - + + -
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Residues in contact with ILE2139 (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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2137B VAL* 4.3 6.7 - - + +
2138B TRP* 1.3 78.7 - - - +
2140B HIS* 1.3 64.9 + - - +
2168B ILE* 3.8 21.5 - - + -
2170B TYR* 3.8 13.2 - - + -
2194B GLN* 3.5 29.8 - - + +
2198B LEU* 5.7 1.8 - - + -
2217B ILE* 4.8 8.3 - - + -
2218B PHE 2.9 13.8 + - - +
2219B GLY* 3.1 20.4 - - - -
2220B GLU 3.6 1.4 + - - -
2223B GLY* 3.3 13.3 - - - +
2226B SER* 4.0 13.7 - - - -
2227B VAL* 4.2 16.4 - - + -
2230B LEU* 4.0 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