Contacts of the helix formed by residues 1169 - 1190 (chain A) in PDB entry 5B2G
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 LEU1169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1168A GLY* 1.3 79.0 - - - +
1170A GLN* 1.3 63.3 + - - +
1171A VAL 3.2 3.3 + - - -
1172A MET* 3.4 11.5 + - + +
1173A GLY* 3.3 15.2 + - - -
1343A LEU* 3.5 45.1 - - + +
1346A CYS* 4.5 25.8 - - + +
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Residues in contact with GLN1170 (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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1168A GLY 4.5 5.1 - - - +
1169A LEU* 1.3 76.2 - - - +
1171A VAL* 1.3 69.1 + - + +
1173A GLY* 3.6 2.6 - - - +
1174A ILE* 3.0 38.1 + - + +
1278A ALA* 5.0 8.7 - - - +
1281A MET* 3.5 37.7 - - + +
1343A LEU 5.0 4.5 - - - +
1344A LEU* 4.2 17.7 - - + -
1347A SER* 6.0 3.0 - - - -
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Residues in contact with VAL1171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1168A GLY* 3.4 28.0 - - - +
1170A GLN* 1.3 86.6 - - + +
1172A MET* 1.3 66.1 + - + +
1174A ILE* 3.4 10.7 - - + +
1175A ALA* 3.1 30.3 + - - +
68C ASP* 3.3 27.1 - - - +
69C SER* 3.9 24.0 - - - +
70C LEU* 5.1 4.7 - - + -
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Residues in contact with MET1172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1168A GLY 5.4 0.7 - - - +
1169A LEU* 3.4 19.4 + - + +
1170A GLN 3.3 0.2 - - - -
1171A VAL* 1.3 84.0 - - + +
1173A GLY* 1.3 65.6 + - - +
1175A ALA* 4.0 7.3 - - - +
1176A LEU* 3.1 47.5 + - + +
1343A LEU* 5.0 6.7 - - + -
68C ASP* 5.0 10.1 - - - +
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Residues in contact with GLY1173 (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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1169A LEU 3.3 9.0 + - - -
1170A GLN 3.3 4.2 + - - -
1171A VAL 3.2 0.8 - - - -
1172A MET* 1.3 79.8 - - - +
1174A ILE* 1.3 56.6 + - - +
1177A ALA* 3.0 30.1 + - - +
1340A GLY* 3.3 22.7 - - - -
1343A LEU* 3.8 18.1 - - - +
1344A LEU* 4.2 6.1 - - - -
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Residues in contact with ILE1174 (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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1170A GLN* 3.0 21.9 + - + +
1171A VAL* 3.4 11.0 - - + +
1173A GLY* 1.3 72.7 - - - +
1175A ALA* 1.3 64.0 + - + +
1177A ALA* 4.3 5.6 - - - -
1178A VAL* 3.0 38.6 + - + +
1261A SER* 3.6 39.0 - - - +
1281A MET* 4.8 8.7 - - + -
1288A PHE* 5.3 1.1 - - + -
1344A LEU* 3.6 20.2 - - + -
70C LEU* 3.5 37.9 - - + -
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Residues in contact with ALA1175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171A VAL 3.1 21.5 + - - +
1172A MET* 4.0 10.3 - - - +
1174A ILE* 1.3 80.0 - - + +
1176A LEU* 1.3 62.5 + - + +
1178A VAL* 3.9 2.6 - - - +
1179A LEU* 3.1 31.2 + - + +
66C VAL* 4.4 26.9 - - + +
68C ASP* 3.9 14.1 - - - +
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Residues in contact with LEU1176 (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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1172A MET* 3.1 39.8 + - + +
1173A GLY 4.0 2.7 - - - +
1175A ALA* 1.3 79.1 - - + +
1177A ALA* 1.3 58.5 + - - +
1179A LEU* 3.5 11.3 + - + +
1180A GLY 3.0 22.0 + - - -
1336A LEU* 3.3 53.1 - - + +
1339A LEU* 3.6 34.3 - - + -
1340A GLY* 4.0 4.3 - - - +
1343A LEU* 5.2 3.4 - - + -
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Residues in contact with ALA1177 (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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1173A GLY 3.0 18.6 + - - +
1174A ILE* 4.1 2.9 - - - +
1175A ALA 3.3 0.2 - - - -
1176A LEU* 1.3 74.0 - - - +
1178A VAL* 1.3 60.6 + - - +
1180A GLY 3.3 0.5 + - - -
1181A TRP* 2.9 24.8 + - - +
1288A PHE* 3.4 45.8 - - + -
1336A LEU 3.8 8.0 + - - -
1337A LEU* 3.2 14.1 - - + +
1340A GLY* 4.1 8.1 - - - -
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Residues in contact with VAL1178 (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* 3.0 30.4 + - + +
1175A ALA* 3.9 4.7 - - - +
1177A ALA* 1.3 71.9 - - - +
1179A LEU* 1.3 69.3 + - + +
1181A TRP* 3.1 12.0 + - + +
1182A LEU* 3.0 28.2 + - + +
1258A VAL* 4.2 28.3 - - + -
1261A SER* 5.7 3.8 - - - -
1288A PHE* 5.3 2.5 - - + -
51C TRP* 4.3 37.0 - - + -
66C VAL* 5.7 6.1 - - + -
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Residues in contact with LEU1179 (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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1175A ALA* 3.1 23.2 + - + +
1176A LEU* 3.5 17.5 - - + +
1178A VAL* 1.3 79.6 - - + +
1180A GLY* 1.3 56.8 - - - +
1182A LEU* 3.2 9.7 + - + +
1183A ALA* 2.9 27.8 + - - +
1336A LEU* 4.3 19.1 - - + -
52C MET* 3.4 33.2 - - + -
66C VAL* 4.1 18.4 - - + -
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Residues in contact with GLY1180 (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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1176A LEU 3.0 15.5 + - - -
1177A ALA 3.6 4.0 - - - -
1178A VAL 3.2 0.2 - - - -
1179A LEU* 1.3 75.9 - - - +
1181A TRP* 1.3 57.0 + - - +
1183A ALA* 3.9 7.4 - - - -
1184A VAL* 3.0 26.7 + - - +
1333A ALA* 3.3 26.3 - - - +
1336A LEU* 4.4 4.9 - - - +
1337A LEU* 4.1 11.2 - - - +
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Residues in contact with TRP1181 (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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1177A ALA 2.9 14.0 + - - +
1178A VAL* 3.1 13.7 + - + +
1180A GLY* 1.3 73.6 - - - +
1182A LEU* 1.3 87.7 + - + +
1184A VAL* 3.0 25.8 - - + +
1185A MET* 3.2 27.7 + - + +
1251A ILE* 3.0 40.3 + - + +
1254A ALA* 3.7 19.7 - - + -
1255A ALA* 3.7 21.6 - - + +
1258A VAL* 4.1 20.4 - - + -
1337A LEU* 3.9 4.4 - - + +
25C CYS* 3.9 13.2 - - - -
51C TRP* 3.6 26.7 - + - -
85C ILE* 3.6 25.8 - - + -
88C ILE* 4.1 8.1 - - + -
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Residues in contact with LEU1182 (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 VAL* 3.0 16.6 + - + +
1179A LEU* 3.6 10.1 - - + +
1181A TRP* 1.3 101.9 - - + +
1183A ALA* 1.3 58.2 + - - +
1185A MET* 3.6 20.8 - - + +
1186A LEU* 3.0 28.6 + - - +
26C ALA* 4.0 33.0 - - + +
51C TRP* 3.8 39.0 - - + +
52C MET* 4.4 17.0 - - + -
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Residues in contact with ALA1183 (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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1179A LEU 2.9 16.9 + - - +
1180A GLY* 3.4 7.9 - - - +
1181A TRP 3.1 0.2 - - - -
1182A LEU* 1.3 77.0 - - - +
1184A VAL* 1.3 59.2 + - - +
1186A LEU* 3.5 6.7 + - + -
1187A CYS* 2.8 22.9 + - - +
1329A VAL* 3.2 20.3 - - + +
1332A ALA* 4.7 3.4 - - + -
1333A ALA* 3.5 24.7 - - + +
1336A LEU* 6.1 2.5 - - + -
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Residues in contact with VAL1184 (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 GLY 3.0 12.0 + - - +
1181A TRP* 3.0 33.4 - - + +
1183A ALA* 1.3 73.0 - - - +
1185A MET* 1.3 60.8 + - - +
1187A CYS* 3.2 6.8 + - + +
1188A CYS* 2.9 27.0 + - - +
1247A VAL* 4.4 17.2 - - + +
1250A SER* 3.7 11.9 - - - +
1251A ILE* 4.2 15.0 - - + -
1254A ALA* 5.6 0.2 - - + -
1295A VAL* 3.6 35.2 - - + -
1333A ALA* 3.3 15.2 - - + +
1337A LEU* 5.1 5.2 - - + -
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Residues in contact with MET1185 (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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1181A TRP* 3.2 42.7 + - + +
1182A LEU* 3.6 35.9 - - + +
1184A VAL* 1.3 82.4 - - - +
1186A LEU* 1.3 57.3 + - - +
1188A CYS 3.3 1.2 + - - -
1189A ALA* 2.9 29.9 + - - +
1251A ILE* 3.7 23.8 - - + -
22C MET* 3.5 63.4 - - + +
25C CYS* 4.4 2.2 - - + -
26C ALA* 4.7 1.3 - - + -
88C ILE* 3.9 9.9 - - + -
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Residues in contact with LEU1186 (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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1182A LEU 3.0 19.9 + - - +
1183A ALA* 3.5 7.4 - - - +
1185A MET* 1.3 74.7 - - - +
1187A CYS* 1.3 59.1 + - - +
1189A ALA* 4.4 6.7 - - + +
1190A LEU* 2.9 59.2 + - + +
1329A VAL* 4.2 16.8 - - + -
23C LEU* 4.9 17.3 - - + -
26C ALA* 5.6 7.9 - - + -
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Residues in contact with CYS1187 (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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1183A ALA 2.8 18.8 + - - +
1184A VAL* 3.4 11.0 - - - +
1186A LEU* 1.3 76.7 - - - +
1188A CYS* 1.3 59.7 + - - +
1190A LEU 3.6 6.8 - - - +
1193A TRP* 3.2 37.4 + - - -
1247A VAL* 5.9 2.2 - - - -
1295A VAL* 5.3 2.2 - - - -
1299A VAL* 4.3 7.9 - - - -
1326A SER* 3.5 27.8 - - - -
1329A VAL* 3.8 6.7 - - + +
1330A GLY* 3.5 27.1 - - - +
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Residues in contact with CYS1188 (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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1184A VAL 2.9 16.2 + - - +
1185A MET 3.5 5.6 - - - +
1186A LEU 3.2 0.2 - - - -
1187A CYS* 1.3 78.8 - - - +
1189A ALA* 1.3 58.8 + - - +
1190A LEU 3.7 4.0 + - - +
1193A TRP* 4.7 4.3 - - - +
1213A LEU* 4.4 9.5 + - - +
1214A TRP* 3.2 51.1 + - - -
1247A VAL* 3.6 27.4 - - + -
1248A ILE* 5.5 0.2 - - - -
1251A ILE* 4.1 6.1 - - + -
18C TRP* 3.6 27.1 - - - -
19C LEU* 4.4 0.2 - - - -
22C MET* 4.4 1.3 - - + -
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Residues in contact with ALA1189 (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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1185A MET 2.9 16.7 + - - +
1186A LEU* 3.2 8.9 + - + +
1188A CYS* 1.3 77.8 - - - +
1190A LEU* 1.3 63.8 + - + +
1191A PRO* 3.5 6.8 - - - +
1214A TRP* 5.7 0.4 - - - -
1215A MET* 5.6 1.4 - - - +
19C LEU* 3.6 49.0 - - + +
22C MET* 4.1 5.8 - - + -
23C LEU* 5.7 5.4 - - + +
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Residues in contact with LEU1190 (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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1186A LEU* 2.9 48.9 + - + +
1187A CYS 3.6 11.6 - - - +
1188A CYS 3.5 3.5 - - - +
1189A ALA* 1.3 79.9 - - + +
1191A PRO* 1.3 67.5 - - + +
1192A MET* 3.1 37.1 + - + -
1193A TRP* 3.9 8.5 - - - -
1213A LEU 5.1 0.9 + - - -
1325A ALA* 5.6 0.2 - - + -
1326A SER* 4.0 10.2 + - - -
1329A VAL* 4.6 16.2 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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