Contacts of the helix formed by residues 1177 - 1198 (chain A) in PDB entry 3L8V
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 THR1177 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175A ASN 4.5 2.2 - - - +
1176A PRO* 1.3 75.5 - - - +
1178A VAL* 1.3 64.1 + - - +
1179A LYS* 3.8 7.0 + - - +
1180A ASP* 3.3 29.2 + - - +
1181A LEU* 3.2 23.0 + - - +
1346A GLY* 3.4 34.9 - - - +
1348A HIS 3.0 17.3 - - - +
1349A TYR* 3.8 26.9 - - + -
1350A VAL* 3.9 3.8 - - - -
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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
----------------------------------------------------------
1177A THR* 1.3 70.4 - - - +
1179A LYS* 1.3 52.3 + - - +
1181A LEU* 3.2 4.3 + - - +
1182A ILE* 2.9 57.6 + - + +
1277A MET* 4.3 6.5 - - + +
1307A TYR* 3.7 22.7 - - + +
1309A PRO* 4.0 7.4 - - + -
1344A PHE* 3.7 32.5 - - + -
1348A HIS* 2.8 34.4 + - + +
1349A TYR 5.5 0.2 - - - -
1350A VAL* 3.7 17.4 - - + +
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Residues in contact with LYS1179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177A THR* 3.8 8.7 + - - +
1178A VAL* 1.3 75.9 - - - +
1180A ASP* 1.3 58.6 + - - +
1182A ILE* 4.6 4.9 - - - +
1183A GLY* 2.8 30.7 + - - -
1341A PHE* 2.8 57.4 + - + -
1342A SER* 4.3 5.3 + - - +
1344A PHE* 2.7 48.8 + - + +
1345A ILE* 4.0 4.5 - - - +
1346A GLY* 4.0 17.0 - - - +
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Residues in contact with ASP1180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175A ASN 4.4 3.1 - - - +
1176A PRO* 3.7 15.4 - - + +
1177A THR* 3.3 33.8 + - - +
1179A LYS* 1.3 79.5 - - - +
1181A LEU* 1.3 57.4 + - - +
1183A GLY* 3.3 2.5 + - - -
1184A PHE* 2.9 46.8 + - + -
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Residues in contact with LEU1181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1169A ILE* 3.7 31.2 - - + -
1176A PRO* 3.8 20.4 - - + -
1177A THR 3.2 6.5 + - - +
1178A VAL 3.2 4.5 + - - +
1180A ASP* 1.3 73.3 - - - +
1182A ILE* 1.3 63.5 + - - +
1184A PHE* 3.3 14.2 + - + +
1185A GLY* 3.1 17.8 + - - -
1273A LEU* 5.7 0.2 - - - +
1276A LEU* 3.5 35.9 - - + +
1277A MET* 3.8 21.3 - - + +
1279A ARG* 4.1 6.3 - - + -
1350A VAL* 3.7 41.5 - - + -
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Residues in contact with ILE1182 (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* 2.9 40.5 + - + +
1179A LYS* 4.2 4.7 - - - +
1181A LEU* 1.3 71.3 - - - +
1183A GLY* 1.3 59.7 + - - +
1185A GLY* 3.2 4.3 + - - +
1186A LEU* 2.9 27.7 + - - +
1273A LEU* 6.0 1.6 - - - -
1277A MET* 4.1 7.0 - - - -
1309A PRO* 3.8 22.4 - - + -
1312A LEU* 4.0 22.0 - - + -
1337A ILE* 3.8 18.8 - - + +
1340A ILE* 3.8 18.4 - - + -
1341A PHE* 3.8 32.1 - - + +
1344A PHE* 3.9 5.4 - - + -
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Residues in contact with GLY1183 (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 LYS 2.8 20.1 + - - -
1180A ASP* 3.4 3.4 - - - -
1181A LEU 3.2 0.2 - - - -
1182A ILE* 1.3 76.1 - - - +
1184A PHE* 1.4 59.4 + - - +
1186A LEU* 3.3 7.4 + - - +
1187A GLN* 3.1 33.3 + - - +
1341A PHE* 3.7 19.9 - - - -
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Residues in contact with PHE1184 (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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1165A LEU* 3.8 18.2 - - + -
1168A PHE* 4.0 31.0 - + - -
1169A ILE* 4.4 0.7 - - + -
1176A PRO* 5.4 2.0 - - + -
1180A ASP* 2.9 36.9 + - + -
1181A LEU* 3.3 26.2 + - + +
1183A GLY* 1.4 73.4 - - - +
1185A GLY* 1.3 61.4 + - - +
1187A GLN* 3.2 12.5 + - - +
1188A VAL* 3.0 26.6 + - - +
1212A LEU* 3.9 18.8 - - + -
1216A PHE* 3.9 19.1 - + + -
1218A VAL* 3.7 26.0 - - + +
1276A LEU* 3.9 15.0 - - + -
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Residues in contact with GLY1185 (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 LEU 3.1 11.6 + - - -
1182A ILE 3.2 4.0 + - - -
1184A PHE* 1.3 73.9 - - - +
1186A LEU* 1.4 55.6 + - - +
1188A VAL* 3.3 5.2 + - - +
1189A ALA 2.9 23.2 + - - -
1269A PHE* 3.3 18.3 - - - -
1273A LEU* 3.8 17.3 - - - -
1276A LEU* 3.4 18.0 - - - +
1337A ILE* 4.7 1.8 - - - -
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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 ILE 2.9 12.8 + - - +
1183A GLY* 3.3 11.0 + - - +
1185A GLY* 1.4 72.6 - - - +
1187A GLN* 1.3 60.4 + - + +
1189A ALA* 3.1 6.6 + - + +
1190A LYS* 2.8 61.2 + - - +
1334A VAL* 3.5 33.9 - - + +
1337A ILE* 3.9 12.2 - - + +
1338A SER* 3.8 28.5 - - - +
1341A PHE* 4.2 26.0 - - + -
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Residues in contact with GLN1187 (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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1138A ASN* 3.2 37.5 + - - +
1183A GLY* 3.1 17.6 + - - +
1184A PHE* 3.5 14.9 - - - +
1186A LEU* 1.3 76.0 - - + +
1188A VAL* 1.4 61.7 + - - +
1190A LYS* 3.3 6.4 + - + +
1191A GLY 3.1 18.0 + - - -
1216A PHE 3.3 18.6 + - - -
1217A THR* 3.3 10.6 + - - +
1218A VAL* 2.9 36.1 + - + +
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Residues in contact with VAL1188 (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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1165A LEU* 4.4 3.8 - - + -
1184A PHE 3.0 19.9 + - - +
1185A GLY 3.5 7.4 - - - +
1187A GLN* 1.4 71.0 - - - +
1189A ALA* 1.3 60.0 + - - +
1191A GLY* 3.3 1.6 + - - -
1192A MET* 2.9 29.9 + - + +
1205A LEU* 3.9 26.0 - - + -
1210A CYS* 3.9 11.9 - - - -
1218A VAL* 3.6 22.7 - - + -
1220A VAL* 4.0 11.2 - - + +
1269A PHE* 3.7 22.9 - - + -
1272A LEU* 4.0 19.5 - - + -
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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 GLY 2.9 14.8 + - - +
1186A LEU* 3.1 12.3 + - - +
1188A VAL* 1.3 76.0 - - - +
1190A LYS* 1.3 51.7 + - - +
1192A MET* 3.3 5.5 + - - +
1193A LYS* 2.8 35.0 + - - +
1269A PHE* 3.7 21.0 - - + -
1330A PHE* 4.3 5.7 - - + +
1333A LEU* 4.6 6.3 - - + -
1334A VAL* 3.5 28.0 - - + +
1337A ILE* 4.7 2.0 - - + -
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Residues in contact with LYS1190 (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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1136A HIS* 3.6 17.3 + - + +
1138A ASN* 3.7 16.6 - - - +
1186A LEU* 2.8 43.6 + - + +
1187A GLN* 3.6 11.8 - - + +
1188A VAL 3.3 0.2 - - - -
1189A ALA* 1.3 75.1 - - - +
1191A GLY* 1.3 59.9 + - - +
1193A LYS* 3.3 7.5 + - + +
1194A PHE* 3.1 18.5 + - - +
1334A VAL* 3.9 26.7 - - + -
1338A SER* 5.8 2.2 - - - -
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Residues in contact with GLY1191 (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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1136A HIS* 4.0 2.7 - - - -
1138A ASN* 3.6 28.8 - - - +
1139A VAL* 3.6 10.7 - - - +
1187A GLN 3.1 11.1 + - - -
1188A VAL 3.3 3.5 + - - -
1190A LYS* 1.3 73.1 - - - +
1192A MET* 1.4 57.1 + - - +
1194A PHE* 3.3 5.7 + - - +
1195A LEU* 3.0 33.4 + - - +
1220A VAL* 4.6 2.0 - - - -
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Residues in contact with MET1192 (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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1188A VAL* 2.9 22.4 + - + +
1189A ALA 3.8 0.2 - - - +
1191A GLY* 1.4 71.3 - - - +
1193A LYS* 1.4 55.8 - - - +
1195A LEU* 3.3 26.2 + - + +
1196A ALA* 2.8 37.2 + - + +
1200A PHE 5.4 1.6 - - - +
1202A HIS* 4.0 10.5 - - + +
1205A LEU* 3.8 37.0 - - + -
1220A VAL* 4.1 7.2 - - + -
1265A ASP* 3.6 31.6 - - + +
1330A PHE* 3.5 42.6 - - + -
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Residues in contact with LYS1193 (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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1189A ALA 2.8 20.4 + - - +
1190A LYS* 3.3 9.8 + - + +
1192A MET* 1.4 70.9 - - - +
1194A PHE* 1.3 62.5 + - - +
1196A ALA* 3.6 3.0 + - - +
1197A SER* 3.2 23.0 + - - -
1330A PHE* 3.7 11.6 - - + +
1331A SER* 3.8 39.9 + - - +
1334A VAL* 4.0 27.0 - - + +
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Residues in contact with PHE1194 (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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1133A ASP 3.7 19.1 - - - -
1134A PHE* 4.2 8.5 - + - -
1135A SER* 3.5 29.8 - - - -
1136A HIS* 3.4 46.9 - + + +
1139A VAL* 3.9 10.5 - - + -
1190A LYS 3.1 6.5 + - - +
1191A GLY 3.4 7.4 - - - +
1193A LYS* 1.3 77.8 - - - +
1195A LEU* 1.3 69.7 + - + +
1197A SER* 2.5 26.2 + - - -
1198A LYS* 3.4 40.2 + - + +
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Residues in contact with LEU1195 (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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1A L8V 3.1 25.4 - - - -
1134A PHE* 3.8 39.5 - - + -
1139A VAL* 4.1 18.2 - - + -
1191A GLY 3.0 18.1 + - - +
1192A MET* 3.3 31.4 + - + +
1194A PHE* 1.3 82.9 - - + +
1196A ALA* 1.3 58.7 + - - +
1198A LYS* 3.2 11.2 + - + -
1200A PHE* 2.9 44.6 + - + +
1202A HIS* 4.6 1.1 - - + -
1220A VAL* 4.1 6.3 - - + -
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Residues in contact with ALA1196 (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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1192A MET* 2.8 21.0 + - + +
1193A LYS* 3.9 5.8 - - - +
1195A LEU* 1.3 72.9 - - - +
1197A SER* 1.3 56.0 + - - +
1199A LYS* 3.0 32.4 + - - +
1200A PHE 4.1 7.8 + - - +
1262A THR* 3.8 32.7 + - + +
1330A PHE* 4.4 10.1 - - + +
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Residues in contact with SER1197 (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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1193A LYS 3.2 13.7 + - - -
1194A PHE* 2.5 26.2 + - - -
1196A ALA* 1.3 76.0 - - - +
1198A LYS* 1.3 73.9 + - - +
1199A LYS* 3.3 15.5 + - - +
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Residues in contact with LYS1198 (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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1133A ASP* 5.4 8.7 - - + +
1134A PHE* 5.9 5.8 - - + -
1194A PHE* 3.6 46.4 - - + +
1195A LEU* 3.2 10.8 + - + +
1197A SER* 1.3 89.4 + - - +
1199A LYS* 1.4 70.1 + - - +
1200A PHE* 3.2 8.1 + - + +
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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
------------------------------------------------------------
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