Contacts of the helix formed by residues 1181 - 1199 (chain E) in PDB entry 3DLS
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 GLY1181 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125E ILE* 3.7 19.6 - - - +
1153E LEU* 4.4 0.9 - - - -
1159E PHE* 4.7 1.6 - - - -
1179E TYR* 3.5 23.1 - - - +
1180E ARG* 1.3 78.9 - - - +
1182E PRO* 1.4 65.7 - - - +
1183E GLU* 3.5 3.3 + - - -
1184E LEU* 3.4 5.7 + - - +
1185E GLU* 3.0 23.2 + - - +
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Residues in contact with PRO1182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120E ARG* 3.5 37.8 + - - +
1125E ILE* 3.8 5.8 - - + -
1153E LEU* 4.3 11.9 - - + -
1180E ARG* 3.4 44.6 - - + +
1181E GLY* 1.4 88.5 - - - +
1183E GLU* 1.3 64.1 + - - +
1185E GLU* 3.2 4.3 + - - +
1186E MET* 3.1 28.4 + - + +
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Residues in contact with GLU1183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172E GLU* 4.4 2.7 - - - +
1179E TYR* 6.0 0.2 - - - +
1180E ARG* 2.8 55.9 + - - +
1181E GLY 4.5 2.1 + - - -
1182E PRO* 1.3 75.8 - - - +
1184E LEU* 1.3 60.3 + - - +
1186E MET* 3.5 6.7 + - - +
1187E TRP 3.3 13.3 + - - -
1236E PRO* 3.6 32.3 - - + +
1237E GLU* 5.6 0.4 - - - -
1239E ARG* 2.8 35.9 + - + +
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Residues in contact with LEU1184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127E ARG* 6.0 5.8 - - + +
1162E PHE* 4.3 17.0 - - + -
1168E TYR 4.6 2.7 - - - +
1169E CYS* 4.1 11.7 - - - -
1170E ALA* 3.4 35.2 - - + +
1172E GLU* 4.7 1.9 + - - +
1173E VAL* 4.1 13.0 - - + -
1179E TYR* 3.6 51.7 - - + +
1181E GLY 3.4 9.9 + - - +
1182E PRO 3.3 0.4 - - - -
1183E GLU* 1.3 76.7 + - - +
1185E GLU* 1.3 62.8 + - - +
1187E TRP* 3.5 2.4 + - - +
1188E SER* 3.2 21.4 + - - -
1239E ARG* 4.1 4.5 - - - +
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Residues in contact with GLU1185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116E VAL* 3.5 22.1 - - + +
1119E LEU* 5.8 1.7 - - - +
1120E ARG* 2.8 30.3 + - - +
1124E ILE 4.7 2.8 - - - +
1125E ILE* 3.3 20.3 - - + +
1126E HIS* 3.7 21.3 + - - +
1127E ARG 4.7 2.2 + - - +
1129E ILE* 3.6 26.6 - - + +
1181E GLY 3.0 13.6 + - - +
1182E PRO 3.4 8.7 - - - +
1184E LEU* 1.3 77.9 - - - +
1186E MET* 1.3 57.4 + - - +
1188E SER* 2.9 22.8 + - - +
1189E LEU* 3.0 17.4 + - + +
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Residues in contact with MET1186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120E ARG* 3.9 18.4 - - - +
1182E PRO* 3.1 17.9 + - + +
1183E GLU* 3.8 7.9 - - - +
1184E LEU 3.3 0.2 - - - -
1185E GLU* 1.3 74.3 - - - +
1187E TRP* 1.3 65.3 + - - +
1189E LEU* 3.2 14.3 + - + +
1190E GLY 3.1 16.8 + - - -
1231E LEU* 3.2 24.5 - - + +
1239E ARG* 4.3 5.4 - - - -
1240E THR 3.5 21.3 - - - +
1241E THR* 3.4 31.9 - - - +
1242E LEU* 3.5 18.6 - - - +
1245E LEU* 3.6 25.8 - - + -
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Residues in contact with TRP1187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167E GLU 5.2 0.4 + - - -
1168E TYR 3.5 21.2 + - - -
1169E CYS 3.3 12.1 + - - -
1170E ALA* 3.5 16.4 - - + -
1171E PRO* 3.7 18.4 - - + -
1183E GLU 3.3 11.5 + - - +
1184E LEU 3.6 8.1 - - - +
1186E MET* 1.3 79.4 - - - +
1188E SER* 1.3 60.5 + - - +
1190E GLY* 3.2 3.8 + - - -
1191E VAL* 3.1 29.5 + - + +
1203E PHE* 3.7 20.6 - + - -
1209E THR* 2.8 35.2 - - - -
1212E ALA* 4.3 1.6 - - + -
1231E LEU 3.5 17.5 - - - -
1232E LEU* 3.3 37.9 - - + +
1233E GLN 3.6 9.9 - - - -
1234E PRO 4.0 0.9 - - - -
1239E ARG* 3.5 29.7 - - - +
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Residues in contact with SER1188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127E ARG 6.1 0.8 - - - -
1129E ILE* 3.8 31.8 + - - +
1168E TYR* 3.7 27.3 - - - -
1184E LEU* 3.2 13.2 + - - -
1185E GLU* 2.9 18.0 + - - -
1186E MET 3.2 0.4 - - - -
1187E TRP* 1.3 76.0 - - - +
1189E LEU* 1.3 53.1 + - - +
1191E VAL* 3.6 4.4 + - - +
1192E THR* 2.8 37.0 + - - -
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Residues in contact with LEU1189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109E PHE* 3.7 15.2 - - + -
1112E LEU* 3.6 37.0 - - + +
1113E VAL* 5.2 3.6 - - + -
1116E VAL* 4.2 26.7 - - + -
1129E ILE* 3.9 14.8 - - + -
1185E GLU* 3.0 18.8 + - + +
1186E MET* 3.6 23.8 - - - +
1187E TRP 3.2 0.2 - - - -
1188E SER* 1.3 76.5 - - - +
1190E GLY* 1.3 54.1 + - - +
1192E THR* 4.3 1.8 - - - -
1193E LEU* 2.8 34.7 + - - +
1231E LEU* 4.3 4.3 - - + -
1242E LEU* 4.6 2.9 - - + -
1245E LEU* 3.9 25.1 - - + -
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Residues in contact with GLY1190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186E MET 3.1 10.7 + - - -
1187E TRP 3.2 4.6 + - - -
1189E LEU* 1.3 75.9 - - - +
1191E VAL* 1.3 56.3 + - - +
1193E LEU* 3.5 3.7 + - - +
1194E TYR* 2.9 29.8 + - - +
1228E VAL* 5.0 4.1 - - - +
1231E LEU* 3.5 28.6 - - - +
1232E LEU* 3.7 14.4 - - - +
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Residues in contact with VAL1191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167E GLU 3.9 11.9 - - - +
1168E TYR* 3.5 29.4 - - + -
1187E TRP* 3.1 36.8 + - + +
1188E SER 4.0 2.5 - - - +
1189E LEU 3.4 0.2 - - - -
1190E GLY* 1.3 71.3 - - - +
1192E THR* 1.3 60.6 + - - +
1194E TYR* 3.8 5.2 - - - +
1195E THR* 2.9 35.7 + - - +
1201E ASN* 3.5 28.5 - - - +
1202E PRO* 4.0 14.8 - - + -
1203E PHE* 5.3 1.3 - - + -
1232E LEU* 3.7 9.9 - - + -
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Residues in contact with THR1192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090E LEU* 5.0 6.5 - - + -
1109E PHE* 5.3 1.3 - - + -
1112E LEU* 3.7 26.9 - - + -
1129E ILE* 3.2 21.9 + - + +
1130E LYS* 3.7 5.6 - - - -
1131E ASP* 4.5 5.2 - - + +
1134E ILE* 4.0 17.9 - - + -
1168E TYR* 3.5 10.1 - - - -
1188E SER 2.8 22.0 + - - -
1189E LEU* 3.9 7.0 - - - -
1191E VAL* 1.3 74.3 - - - +
1193E LEU* 1.3 62.7 + - - +
1195E THR* 3.6 3.7 + - - -
1196E LEU* 3.2 22.7 + - + +
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Residues in contact with LEU1193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109E PHE* 3.8 33.4 - - + -
1189E LEU 2.8 22.5 + - - +
1190E GLY 3.7 3.6 - - - +
1192E THR* 1.3 71.4 - - - +
1194E TYR* 1.3 64.9 + - - +
1196E LEU* 3.3 7.3 + - + +
1197E VAL* 3.2 33.2 + - + +
1224E LEU* 3.9 3.4 - - + -
1227E LEU* 3.5 36.8 - - + -
1228E VAL* 3.8 20.9 - - + -
1231E LEU* 4.4 6.5 - - + -
1250E TRP* 3.6 30.7 - - + -
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Residues in contact with TYR1194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190E GLY 2.9 19.6 + - - +
1191E VAL 3.8 4.0 - - - +
1193E LEU* 1.3 76.0 - - - +
1195E THR* 1.3 57.5 + - - +
1197E VAL* 4.0 6.1 - - - -
1198E PHE* 2.8 61.3 + + + +
1200E GLU* 3.3 25.0 + - + -
1201E ASN 3.9 2.6 + - - -
1202E PRO* 3.4 49.8 + - + +
1214E ILE* 4.0 14.8 - - + -
1215E HIS 3.6 10.6 + - - -
1216E PRO* 3.5 26.6 - - + +
1217E PRO* 4.0 2.4 - - - +
1228E VAL* 4.7 14.6 - - + +
1232E LEU* 4.2 10.5 - - + -
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Residues in contact with THR1195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094E ILE* 3.5 13.4 - - + +
1131E ASP* 3.3 27.6 - - + +
1168E TYR* 4.2 9.4 + - - +
1191E VAL* 2.9 29.0 + - - +
1192E THR* 4.1 4.0 - - - -
1193E LEU 3.2 0.2 - - - -
1194E TYR* 1.3 73.9 - - - +
1196E LEU* 1.3 61.0 + - - +
1199E GLU* 3.0 26.0 + - - -
1200E GLU 3.6 23.5 + - - +
1201E ASN* 4.1 12.7 + - - +
1202E PRO* 4.4 0.2 - - - +
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Residues in contact with LEU1196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090E LEU* 4.1 22.2 - - + -
1093E PHE* 4.5 9.0 - - + -
1094E ILE* 3.4 31.6 - - + +
1100E LEU* 3.8 26.2 - - + +
1105E ALA* 3.8 30.5 - - + +
1108E ILE* 3.9 22.7 - - + -
1109E PHE* 4.8 10.1 - - + +
1192E THR 3.2 17.9 + - - +
1193E LEU* 3.3 6.7 + - + +
1195E THR* 1.3 78.8 - - - +
1197E VAL* 1.3 63.5 + - + +
1199E GLU* 4.3 6.6 - - - +
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Residues in contact with VAL1197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100E LEU* 5.4 1.6 - - - -
1102E GLU* 6.1 0.9 - - + -
1105E ALA* 4.0 26.2 - - + -
1193E LEU* 3.3 34.8 - - + +
1194E TYR* 3.5 2.9 - - - +
1196E LEU* 1.3 82.4 - - + +
1198E PHE* 1.3 90.4 + - + +
1199E GLU* 3.7 4.6 - - - +
1218E TYR* 2.5 33.2 + - - +
1220E VAL* 5.8 0.2 - - + -
1224E LEU* 4.2 24.2 - - + -
1228E VAL* 5.4 0.4 - - + -
1250E TRP* 4.3 0.7 - - + -
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Residues in contact with PHE1198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1194E TYR* 2.8 59.6 + + + +
1197E VAL* 1.3 95.7 - - + +
1199E GLU* 1.3 67.6 + - - +
1200E GLU* 3.1 14.6 + - + +
1216E PRO* 3.7 12.8 - - + -
1217E PRO* 3.5 30.7 - - + +
1218E TYR* 3.5 47.0 - + - -
1220E VAL* 3.7 30.3 - - + -
1224E LEU* 5.2 0.7 - - + -
1225E MET* 4.1 11.0 - - - -
1228E VAL* 5.0 6.7 - - + -
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Residues in contact with GLU1199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094E ILE* 3.4 30.6 - - + +
1097E HIS* 2.8 33.4 + - + +
1098E PRO* 3.3 31.5 - - - +
1195E THR* 3.0 20.9 + - - -
1196E LEU 4.3 11.2 - - - +
1197E VAL 4.5 4.5 - - - +
1198E PHE* 1.3 78.6 - - - +
1200E GLU* 1.3 58.9 + - - +
1218E TYR* 6.2 0.4 - - + -
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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
------------------------------------------------------------
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