Contacts of the helix formed by residues 1261 - 1272 (chain A) 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 VAL1261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1179A SER* 3.8 18.0 - - - +
1181A GLY* 3.5 35.9 - - - +
1257A LYS* 3.9 31.6 - - + +
1258A LYS 5.4 0.9 - - - +
1259A GLY 3.6 10.5 + - - +
1260A ASP* 1.3 75.3 + - - +
1262A LYS* 1.3 67.2 + - - +
1263A PRO* 3.3 3.4 - - - -
1264A LEU* 3.2 15.6 + - + +
1265A ALA* 3.2 18.9 + - - +
1322A VAL* 4.1 15.0 - - + -
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Residues in contact with LYS1262 (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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1180A THR* 3.9 22.0 + - - +
1181A GLY* 5.4 0.2 - - - -
1260A ASP* 3.1 19.4 + - - +
1261A VAL* 1.3 80.0 - - - +
1263A PRO* 1.3 68.2 - - + +
1265A ALA* 3.1 7.1 + - - +
1266A GLU* 2.9 48.2 + - - +
1276A THR 5.5 1.7 + - - -
1278A THR* 5.4 2.6 - - - +
1279A SER* 3.9 15.9 + - - +
1282A MET* 3.2 34.1 - - + -
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Residues in contact with PRO1263 (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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1260A ASP* 3.3 26.5 - - + +
1261A VAL 3.4 4.3 - - - -
1262A LYS* 1.3 94.1 - - + +
1264A LEU* 1.3 62.3 + - - +
1266A GLU* 3.2 15.1 + - - +
1267A GLN* 3.0 22.2 + - - +
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Residues in contact with LEU1264 (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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1257A LYS* 4.6 10.8 - - + -
1261A VAL* 3.2 16.4 + - + +
1263A PRO* 1.3 77.9 - - - +
1265A ALA* 1.3 64.0 + - - +
1267A GLN* 3.1 11.4 + - - +
1268A ILE* 3.0 41.0 + - + +
1301A MET* 4.3 9.2 - - + -
1316A GLN* 3.0 45.3 - - + +
1319A LEU* 3.6 19.1 - - + -
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Residues in contact with ALA1265 (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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1178A PHE* 3.8 25.6 - - + -
1179A SER 3.1 26.6 + - - +
1180A THR* 4.1 12.1 - - + -
1261A VAL 3.2 4.2 + - - +
1262A LYS* 3.1 11.1 + - - +
1264A LEU* 1.3 80.1 - - - +
1266A GLU* 1.3 56.4 + - - +
1268A ILE* 3.2 6.8 + - - +
1269A ALA* 2.9 28.9 + - - +
1282A MET* 4.1 6.7 - - + +
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Residues in contact with GLU1266 (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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1262A LYS* 2.9 43.6 + - - +
1263A PRO* 3.6 15.3 - - - +
1265A ALA* 1.3 72.3 - - - +
1267A GLN* 1.3 60.7 + - - +
1269A ALA* 3.7 0.4 - - - +
1270A ILE* 2.9 41.6 + - + +
1276A THR* 4.0 26.3 + - + +
1282A MET* 3.8 22.0 - - - -
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Residues in contact with GLN1267 (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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1263A PRO 3.0 13.5 + - - +
1264A LEU* 3.1 16.7 + - - +
1266A GLU* 1.3 75.5 - - - +
1268A ILE* 1.3 55.0 + - - +
1270A ILE* 3.8 7.7 - - - +
1271A THR* 2.7 41.0 + - - +
1301A MET* 3.9 27.1 - - + +
1314A GLU 5.2 5.7 + - - +
1316A GLN* 4.9 9.0 - - - +
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Residues in contact with ILE1268 (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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1174A ILE* 4.0 23.1 - - + -
1178A PHE* 4.1 29.2 - - + -
1264A LEU* 3.0 28.0 + - + +
1265A ALA* 3.5 7.0 - - - +
1267A GLN* 1.3 73.9 - - - +
1269A ALA* 1.3 67.8 + - - +
1271A THR* 3.2 3.2 + - - -
1272A ALA* 3.0 22.0 + - - +
1286A LEU* 4.6 9.6 - - + -
1297A THR* 4.0 6.4 - - + +
1301A MET* 3.9 19.7 - - + -
1303A PHE* 4.6 1.3 - - + -
1319A LEU* 3.5 40.6 - - + -
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Residues in contact with ALA1269 (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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1265A ALA 2.9 16.7 + - - +
1266A GLU 3.7 4.3 - - - +
1268A ILE* 1.3 75.9 - - - +
1270A ILE* 1.3 57.3 + - - +
1272A ALA* 3.2 6.3 + - - +
1273A GLY 3.1 4.3 + - - -
1274A CYS* 2.7 45.6 + - + +
1276A THR* 4.1 5.6 - - + -
1282A MET* 3.8 31.6 - - + -
1286A LEU* 4.5 11.2 - - + +
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Residues in contact with ILE1270 (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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1266A GLU* 2.9 28.4 + - + +
1267A GLN* 3.8 6.7 - - - +
1269A ALA* 1.3 73.9 - - - +
1271A THR* 1.3 66.9 + - - +
1273A GLY* 2.9 14.6 + - - -
1274A CYS 4.0 8.5 - - - +
1276A THR* 3.7 21.8 - - + +
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Residues in contact with THR1271 (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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1267A GLN* 2.7 26.4 + - - +
1268A ILE 3.7 3.8 - - - -
1270A ILE* 1.3 78.6 - - - +
1272A ALA* 1.3 58.6 + - - +
1273A GLY 3.2 0.9 + - - -
1297A THR* 4.2 17.1 + - + +
1300A LYS* 3.7 52.8 + - + +
1301A MET* 3.6 15.5 - - - -
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Residues in contact with ALA1272 (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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1268A ILE 3.0 16.5 + - - +
1269A ALA 3.6 5.2 - - - +
1270A ILE 3.1 0.2 - - - -
1271A THR* 1.3 77.1 - - - +
1273A GLY* 1.3 58.7 + - - +
1274A CYS* 4.5 2.2 - - - -
1286A LEU* 3.8 24.9 - - + -
1289A LYS* 3.2 27.9 + - + +
1294A LEU* 4.9 3.6 - - + -
1297A THR* 3.4 24.0 + - + +
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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