Contacts of the helix formed by residues 1256 - 1279 (chain A) in PDB entry 6J8H
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 ASN1256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1248A TYR* 6.1 2.4 - - - -
1252A THR* 4.1 9.4 + - - +
1253A TYR 3.8 4.3 - - - +
1254A PHE 3.1 0.6 - - - -
1255A THR* 1.3 79.9 + - - +
1257A ALA* 1.3 69.2 + - - +
1258A TRP* 3.2 27.3 + - - +
1259A CYS* 3.7 28.4 - - - +
1260A TRP* 3.5 25.4 + - - -
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Residues in contact with ALA1257 (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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1255A THR 4.0 2.0 + - - -
1256A ASN* 1.3 75.7 + - - +
1258A TRP* 1.3 71.8 + - + +
1260A TRP* 3.4 9.4 + - - +
1261A LEU* 3.4 17.5 + - - +
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Residues in contact with TRP1258 (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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1256A ASN* 3.2 14.7 + - - +
1257A ALA* 1.3 81.2 - - + +
1259A CYS* 1.3 62.0 + - - +
1261A LEU* 3.1 29.9 + - + +
1262A ASP* 2.8 28.3 + - - +
1301A LEU* 4.5 23.8 - - + -
1302A SER* 4.2 32.5 - - - +
1308A ARG* 3.6 38.6 - - + +
1311A VAL* 4.0 27.8 - - + -
1312A ASN* 4.9 6.2 + - - -
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Residues in contact with CYS1259 (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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1244A LYS* 6.2 0.7 - - - -
1248A TYR* 5.3 10.8 - - - -
1253A TYR* 3.2 53.0 + - + +
1256A ASN* 3.6 27.2 + - - +
1257A ALA 3.3 0.4 - - - -
1258A TRP* 1.3 75.5 - - - +
1260A TRP* 1.3 55.0 + - - +
1262A ASP* 3.4 7.7 - - - +
1263A PHE* 2.5 39.9 + - - +
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Residues in contact with TRP1260 (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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1254A PHE* 2.9 66.8 + + + +
1256A ASN 3.5 13.3 + - - +
1257A ALA* 3.4 10.9 + - - +
1258A TRP 3.2 1.0 - - - -
1259A CYS* 1.3 78.9 - - - +
1261A LEU* 1.3 63.7 + - - +
1263A PHE* 4.3 14.6 - + - -
1264A LEU* 2.9 60.2 + - + +
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Residues in contact with LEU1261 (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 ALA 3.4 9.1 + - - +
1258A TRP* 3.1 34.6 + - + +
1260A TRP* 1.3 80.7 - - - +
1262A ASP* 1.3 54.8 + - - +
1264A LEU* 3.7 5.6 - - + +
1265A ILE* 2.8 55.5 + - + +
1295A LEU* 6.2 0.9 - - + -
1298A LEU* 4.1 39.0 - - + +
1299A ARG* 5.5 2.5 - - - -
1301A LEU* 4.9 2.2 - - + -
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Residues in contact with ASP1262 (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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1240A GLU* 4.2 16.1 - - - +
1241A MET* 6.5 0.4 - - - -
1244A LYS* 5.0 5.2 + - - +
1253A TYR* 4.9 6.8 + - - +
1258A TRP 2.8 13.9 + - - +
1259A CYS* 3.5 11.4 - - - +
1261A LEU* 1.3 75.1 - - - +
1263A PHE* 1.3 64.3 + - - +
1265A ILE* 3.5 7.5 + - - +
1266A VAL* 3.4 20.6 + - - +
1299A ARG* 3.1 34.3 + - + +
1303A ARG* 4.3 11.6 + - - -
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Residues in contact with PHE1263 (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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1241A MET* 3.8 24.2 - - + -
1245A TRP* 4.3 18.2 - + - -
1253A TYR* 3.9 18.1 + - + +
1254A PHE* 3.9 28.0 - + + -
1259A CYS 2.5 21.2 + - - +
1260A TRP* 3.9 12.8 - + - +
1262A ASP* 1.3 72.7 - - - +
1264A LEU* 1.3 77.7 + - + +
1266A VAL* 2.9 25.9 - - - +
1267A ASP* 3.2 35.4 + - - +
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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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1260A TRP* 2.9 49.8 + - + +
1261A LEU* 3.7 8.3 - - + +
1263A PHE* 1.3 91.0 - - + +
1265A ILE* 1.3 62.7 + - + +
1267A ASP* 3.2 17.7 + - + +
1268A VAL* 3.2 23.2 + - + +
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Residues in contact with ILE1265 (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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1261A LEU* 2.8 37.9 + - + +
1262A ASP* 4.0 4.7 - - - +
1263A PHE 3.3 0.4 - - - -
1264A LEU* 1.3 74.8 - - + +
1266A VAL* 1.3 63.5 + - - +
1267A ASP 3.3 0.5 + - - -
1268A VAL* 3.4 9.1 + - + +
1269A SER* 3.3 20.0 + - - -
1295A LEU* 3.6 35.2 - - + +
1296A ARG* 4.3 13.0 - - + +
1298A LEU* 4.1 2.2 - - + -
1299A ARG* 3.9 49.8 + - + +
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Residues in contact with VAL1266 (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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1234A THR* 5.0 0.9 - - + +
1237A PHE* 4.4 11.4 - - + +
1238A ILE* 3.4 43.7 - - + +
1241A MET* 3.6 28.5 - - + -
1262A ASP* 3.4 9.0 + - - +
1263A PHE 2.9 24.5 - - - +
1265A ILE* 1.3 78.4 - - - +
1267A ASP* 1.3 58.2 + - - +
1269A SER* 2.7 26.2 + - - +
1270A LEU* 2.7 22.2 + - + +
1299A ARG* 4.6 10.9 - - - +
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Residues in contact with ASP1267 (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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1241A MET* 5.6 2.1 - - - +
1263A PHE* 3.2 44.2 - - - +
1264A LEU* 3.2 14.8 + - + +
1265A ILE 3.1 0.6 - - - -
1266A VAL* 1.3 84.0 - - - +
1268A VAL* 1.3 61.8 + - + +
1270A LEU* 3.2 9.1 + - - +
1271A VAL* 2.8 37.6 + - + +
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Residues in contact with VAL1268 (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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1264A LEU* 3.2 23.1 + - + +
1265A ILE* 3.4 10.7 + - + +
1267A ASP* 1.3 76.0 - - + +
1269A SER* 1.3 63.9 + - - +
1271A VAL* 3.4 3.0 + - - +
1272A THR* 3.2 29.9 + - + +
1289A LEU* 3.6 31.9 - - + +
1292A LEU* 4.1 37.5 - - + +
1293A ARG* 6.2 0.4 - - - -
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Residues in contact with SER1269 (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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1230A ASP* 6.0 1.6 - - - -
1234A THR* 4.0 25.2 + - - +
1265A ILE* 3.3 9.4 + - - -
1266A VAL* 2.7 23.1 + - - +
1268A VAL* 1.3 78.2 - - - +
1270A LEU* 1.3 56.6 + - - +
1272A THR* 2.8 23.7 + - - -
1273A LEU* 3.0 15.6 + - - +
1293A ARG* 6.1 7.0 - - - +
1296A ARG* 5.9 7.9 - - - -
1299A ARG* 5.3 5.5 + - - -
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Residues in contact with LEU1270 (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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1234A THR* 4.4 6.3 - - + -
1238A ILE* 2.4 44.2 - - + -
1266A VAL* 2.7 21.1 + - + +
1267A ASP* 3.2 14.8 + - - +
1269A SER* 1.3 72.8 + - - +
1271A VAL* 1.3 69.5 + - + +
1273A LEU* 3.3 11.7 + - + +
1274A VAL* 3.0 31.3 + - + +
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Residues in contact with VAL1271 (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 ASP* 2.8 28.3 + - + +
1268A VAL* 3.9 4.7 - - - +
1270A LEU* 1.3 72.1 - - + +
1272A THR* 1.3 68.5 + - - +
1274A VAL* 3.4 9.9 + - + +
1275A ALA* 2.9 24.9 + - + +
1286A ILE* 4.8 14.4 - - + -
1289A LEU* 4.5 18.2 - - + -
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Residues in contact with THR1272 (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 VAL* 3.2 15.7 + - + +
1269A SER* 2.8 23.5 + - - -
1271A VAL* 1.3 77.2 - - + +
1273A LEU* 1.3 52.9 + - - +
1275A ALA* 4.4 3.4 - - - -
1276A ASN* 2.6 53.0 + - - +
1286A ILE* 5.0 7.6 - - + +
1289A LEU* 4.4 33.2 - - + +
1290A ARG* 4.6 14.1 - - + +
1293A ARG* 5.6 7.0 - - - -
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Residues in contact with LEU1273 (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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1230A ASP* 6.1 0.4 - - - +
1231A LYS* 3.2 40.4 - - + +
1234A THR* 3.7 30.7 - - + +
1235A TYR 5.8 0.7 - - - +
1238A ILE* 5.7 0.2 - - + -
1269A SER 3.0 12.9 + - - +
1270A LEU* 3.6 12.8 - - + +
1271A VAL 3.2 0.2 - - - -
1272A THR* 1.3 82.9 + - - +
1274A VAL* 1.3 55.7 + - + +
1276A ASN* 3.7 3.7 - - - +
1277A THR* 2.3 44.9 + - + +
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Residues in contact with VAL1274 (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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1270A LEU* 3.0 23.8 + - + +
1271A VAL* 3.5 17.3 - - + +
1273A LEU* 1.3 78.6 - - + +
1275A ALA* 1.3 70.1 + - + +
1277A THR* 3.5 5.9 + - - +
1278A LEU* 3.2 23.6 + - - +
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Residues in contact with ALA1275 (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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1271A VAL* 2.9 20.9 + - + +
1272A THR 3.8 2.0 - - - +
1274A VAL* 1.3 79.7 - - + +
1276A ASN* 1.3 59.4 + - - +
1278A LEU* 3.4 9.5 + - + +
1279A GLY 2.7 35.5 + - - +
1280A TYR 5.3 2.7 - - - +
1281A SER* 4.5 2.3 - - - -
1286A ILE* 3.9 34.1 - - + -
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Residues in contact with ASN1276 (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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1231A LYS* 5.6 4.3 - - - +
1272A THR* 2.6 39.4 + - - +
1273A LEU* 3.7 7.9 - - + +
1275A ALA* 1.3 72.4 - - - +
1277A THR* 1.3 67.1 + - - +
1279A GLY* 3.3 10.9 + - - -
1281A SER* 4.2 14.9 + - - -
1286A ILE* 3.9 24.7 - - - +
1290A ARG* 5.4 9.7 - - - +
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Residues in contact with THR1277 (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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1231A LYS* 5.1 8.0 - - - +
1273A LEU* 2.3 44.5 + - + +
1274A VAL* 3.5 7.2 + - - +
1276A ASN* 1.3 76.4 - - - +
1278A LEU* 1.3 63.2 + - - +
1279A GLY* 3.4 1.0 + - - -
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Residues in contact with LEU1278 (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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1274A VAL 3.2 16.6 + - - +
1275A ALA* 3.6 8.1 - - + +
1276A ASN 3.2 0.2 - - - -
1277A THR* 1.3 80.4 - - - +
1279A GLY* 1.3 73.3 + - - +
1280A TYR* 3.4 23.9 + - + +
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Residues in contact with GLY1279 (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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1275A ALA 2.7 19.9 + - - +
1276A ASN 3.3 8.0 + - - -
1277A THR 3.3 4.4 - - - -
1278A LEU* 1.3 80.6 - - - +
1280A TYR* 1.3 74.8 + - - +
1281A SER* 3.1 7.4 - - - -
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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