Contacts of the helix formed by residues 1255 - 1267 (chain C) in PDB entry 3O2X
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 PRO1255 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1235C ASP* 6.5 0.2 - - - -
1237C GLY 3.2 29.4 - - - +
1238C ALA* 4.2 3.6 - - - -
1239C LEU* 3.9 5.8 - - + +
1252C PHE* 4.5 0.4 - - + -
1253C MET 3.2 7.2 - - - +
1254C LEU* 1.3 92.6 - - + +
1256C ASP* 1.3 65.6 + - - +
1257C ASP* 3.2 4.0 - - + +
1258C ASP* 3.1 35.4 + - - +
1259C VAL* 3.2 10.4 + - - +
1801C 3O2 3.8 23.3 - - + -
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Residues in contact with ASP1256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254C LEU 5.0 1.7 - - - +
1255C PRO* 1.3 72.8 - - - +
1257C ASP* 1.3 58.2 - - - +
1259C VAL* 3.3 9.1 + - - +
1260C GLN* 2.9 43.5 + - + +
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Residues in contact with ASP1257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233C SER* 2.6 36.6 + - - -
1235C ASP* 3.7 25.2 + - - +
1238C ALA* 3.7 12.4 - - + +
1255C PRO* 3.2 2.3 + - + +
1256C ASP* 1.3 78.7 - - - +
1258C ASP* 1.3 60.1 + - - +
1260C GLN* 3.4 8.5 + - - +
1261C GLY* 2.9 25.1 + - - -
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Residues in contact with ASP1258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145C TRP* 4.1 10.4 - - + -
1230C LEU* 4.3 5.0 - - - +
1238C ALA* 3.4 7.8 - - - +
1239C LEU* 2.7 30.3 + - - -
1240C MET* 3.0 36.0 + - + +
1254C LEU* 3.6 22.2 - - + -
1255C PRO* 3.1 23.0 + - - +
1257C ASP* 1.3 73.0 - - - +
1259C VAL* 1.3 60.9 + - - +
1261C GLY* 3.3 1.5 + - - +
1262C ILE* 2.9 33.0 + - - +
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Residues in contact with VAL1259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148C VAL* 4.7 11.7 - - + -
1254C LEU* 3.8 28.0 - - + +
1255C PRO 3.2 14.3 + - - +
1256C ASP* 3.5 10.8 - - - +
1258C ASP* 1.3 76.7 - - - +
1260C GLN* 1.3 64.2 + - + +
1262C ILE* 3.3 7.2 - - - +
1263C GLN* 2.9 57.9 + - + +
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Residues in contact with GLN1260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256C ASP* 2.9 34.4 + - + +
1257C ASP* 3.6 8.1 - - - +
1259C VAL* 1.3 77.0 - - + +
1261C GLY* 1.3 56.9 + - - +
1263C GLN* 3.9 4.4 - - - +
1264C SER* 3.0 28.8 + - - -
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Residues in contact with GLY1261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230C LEU* 3.5 21.0 - - - +
1257C ASP 2.9 15.4 + - - -
1258C ASP* 3.7 3.1 - - - -
1259C VAL 3.2 0.4 - - - -
1260C GLN* 1.3 76.2 - - - +
1262C ILE* 1.3 59.6 + - - +
1264C SER* 2.5 26.6 + - - -
1265C LEU* 3.5 4.5 + - - +
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Residues in contact with ILE1262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145C TRP* 3.8 20.9 - - + -
1148C VAL* 3.8 26.5 - - + -
1149C THR* 3.5 22.2 - - + -
1225C GLY 5.2 0.2 - - - +
1228C LEU* 4.0 18.8 - - + -
1230C LEU* 3.7 24.5 - - + +
1258C ASP 2.9 19.2 + - - +
1259C VAL* 3.3 12.1 - - - +
1261C GLY* 1.3 72.6 - - - -
1263C GLN* 1.3 65.7 + - + +
1265C LEU* 3.1 7.9 + - + +
1266C TYR* 2.8 48.3 + - + +
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Residues in contact with GLN1263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148C VAL* 3.3 30.3 + - - +
1149C THR* 5.4 0.4 - - + -
1259C VAL* 2.9 40.5 + - + +
1260C GLN* 4.1 4.9 - - - +
1262C ILE* 1.3 75.4 - - + +
1264C SER* 1.3 63.1 - - - +
1265C LEU 3.1 1.8 - - - -
1267C GLY* 2.7 47.4 + - - +
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Residues in contact with SER1264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1260C GLN 3.0 14.9 + - - -
1261C GLY* 2.5 23.1 + - - -
1263C GLN* 1.3 76.4 - - - +
1265C LEU* 1.3 66.1 + - - +
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Residues in contact with LEU1265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110C THR* 3.9 26.5 - - + +
1111C LEU 4.4 9.0 - - - +
1112C LYS* 3.0 30.4 - - + +
1228C LEU 3.7 13.9 - - - +
1229C GLY* 3.6 34.3 - - - +
1230C LEU* 4.1 16.8 - - + +
1261C GLY 3.9 5.6 - - - +
1262C ILE* 3.1 10.4 + - + +
1263C GLN 3.1 0.2 - - - -
1264C SER* 1.3 85.7 + - - +
1266C TYR* 1.3 73.8 + - + +
1267C GLY 3.9 0.2 - - - -
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Residues in contact with TYR1266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112C LYS* 3.6 13.7 - - + -
1113C TRP* 3.0 50.0 + + + -
1116C MET* 4.0 20.0 - - + +
1149C THR* 4.1 7.2 - - + -
1150C PRO* 3.6 28.7 - - + +
1151C LEU* 4.0 26.2 - - + -
1228C LEU* 2.6 35.0 + - + -
1262C ILE* 2.8 34.7 + - + +
1265C LEU* 1.3 89.0 - - + +
1267C GLY* 1.3 65.1 + - - +
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Residues in contact with GLY1267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148C VAL 4.3 5.4 - - - +
1149C THR* 4.5 0.3 - - - -
1150C PRO* 3.9 16.4 - - - +
1263C GLN* 2.7 50.3 + - - +
1265C LEU 3.9 0.4 - - - -
1266C TYR* 1.3 75.6 - - - +
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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