Contacts of the helix formed by residues 2172 - 2178 (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 LEU2172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2087B CYS* 4.1 16.5 - - + +
2088B THR 4.4 7.7 - - - +
2089B GLN* 3.5 28.5 - - + +
2140B HIS* 4.0 4.3 - - + +
2144B LEU 3.5 18.6 - - - +
2145B MET 3.7 8.5 - - - +
2146B VAL* 3.5 27.8 - - - +
2147B GLY 3.7 6.3 - - - +
2170B TYR* 3.4 46.7 - - + +
2171B ARG* 1.3 72.9 - - - +
2173B GLY* 1.3 69.8 + - - +
2174B ILE 3.5 0.2 + - - -
2175B TRP* 3.2 18.6 + - - +
2176B GLY* 3.0 8.9 + - - -
2177B PHE* 4.4 0.7 - - - -
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Residues in contact with GLY2173 (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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2088B THR 5.8 0.2 - - - -
2144B LEU 2.8 15.1 + - - -
2145B MET* 3.7 33.8 - - - +
2172B LEU* 1.3 72.9 - - - +
2174B ILE* 1.3 59.2 + - - -
2175B TRP* 4.9 2.2 - - - -
2176B GLY 3.1 0.7 + - - -
2177B PHE* 2.8 33.8 + - - +
2178B PHE 4.1 0.2 + - - -
2319B LEU* 4.0 8.1 - - - -
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Residues in contact with ILE2174 (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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2065B PHE* 3.3 23.9 - - + -
2145B MET* 4.9 0.6 - - - +
2172B LEU 3.5 0.4 + - - -
2173B GLY* 1.3 70.9 - - - -
2175B TRP* 1.3 72.4 + - + +
2178B PHE* 3.0 41.6 + - + +
2268B ILE* 4.1 22.0 - - + -
2286B LEU* 5.6 0.9 - - + -
2294B LEU* 3.9 28.5 - - + +
2297B THR* 4.3 13.0 - - + -
2298B THR* 3.6 25.7 + - - +
2303B PHE* 4.6 8.7 - - + -
2319B LEU* 3.6 24.1 - - + +
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Residues in contact with TRP2175 (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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2059B PRO 5.9 2.2 - - - -
2064B ARG* 4.0 20.0 - - + +
2065B PHE* 4.2 11.5 + - - -
2087B CYS* 6.5 0.4 - - + -
2088B THR* 3.3 53.8 - - + -
2089B GLN* 4.8 2.9 - - - -
2114B GLU* 2.8 37.0 + - + -
2171B ARG* 3.7 31.2 + - + -
2172B LEU 3.2 15.5 + - - +
2173B GLY* 3.2 2.2 - - - -
2174B ILE* 1.3 84.9 - - + +
2176B GLY* 1.3 57.2 + - - +
2189B TRP* 3.5 15.9 - - - +
2291B GLU* 3.8 10.1 - - + -
2294B LEU* 3.4 30.0 - - + +
2295B LEU* 3.8 20.0 - - + -
2298B THR* 4.0 15.5 - - + -
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Residues in contact with GLY2176 (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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2171B ARG* 3.4 31.4 - - - +
2172B LEU 3.0 10.9 + - - -
2173B GLY 3.7 1.3 - - - -
2175B TRP* 1.3 77.7 - - - +
2177B PHE* 1.3 67.8 + - - +
2189B TRP* 2.8 15.4 + - - -
2190B GLY 2.8 23.3 + - - -
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Residues in contact with PHE2177 (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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2144B LEU* 3.8 46.2 - - + -
2170B TYR* 4.6 4.0 - + - -
2171B ARG 3.4 18.8 - - - -
2172B LEU* 4.4 0.2 - - - -
2173B GLY 2.8 21.8 + - - +
2176B GLY* 1.3 83.1 - - - +
2178B PHE* 1.3 65.8 + - - +
2179B SER* 3.2 9.2 + - - -
2187B GLY* 4.7 1.0 - - - -
2188B ASN* 3.9 16.2 - - - +
2189B TRP* 4.4 0.4 - - - -
2190B GLY* 3.7 22.0 - - - -
2191B HIS* 3.6 31.4 - + - -
2319B LEU* 3.9 25.8 - - + +
2320B GLY* 3.6 31.3 + - - +
2322B VAL* 5.3 1.0 - - - +
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Residues in contact with PHE2178 (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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2065B PHE* 3.6 22.7 - + + -
2174B ILE* 3.0 27.8 + - + +
2176B GLY 4.0 0.4 - - - -
2177B PHE* 1.3 74.9 - - - +
2179B SER* 1.3 59.6 + - - +
2180B THR* 3.7 23.3 - - + -
2185B SER* 3.1 25.4 + - - -
2187B GLY* 3.6 3.5 - - - -
2189B TRP* 3.2 13.7 + - - -
2265B ALA* 3.8 41.7 - - + -
2268B ILE* 4.1 25.4 - - + -
2282B MET* 4.9 5.6 - - + -
2283B VAL* 3.9 12.3 - - + -
2286B LEU* 3.2 33.0 - - + -
2319B LEU* 4.8 4.3 - - - -
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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