Contacts of the helix formed by residues 1181 - 1199 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125B ILE* 3.8 17.6 - - - +
1153B LEU* 4.3 2.7 - - - -
1159B PHE* 4.8 1.1 - - - -
1179B TYR* 3.6 19.1 - - - +
1180B ARG* 1.3 80.5 - - - +
1182B PRO* 1.4 68.0 - - - +
1183B GLU* 3.3 3.6 + - - -
1184B LEU* 3.1 9.8 + - - +
1185B GLU* 3.0 19.4 + - - +
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Residues in contact with PRO1182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120B ARG* 3.5 43.3 - - - +
1125B ILE* 3.8 7.1 - - + -
1153B LEU* 4.3 10.5 - - + -
1180B ARG* 3.6 44.4 - - + +
1181B GLY* 1.4 87.8 - - - +
1183B GLU* 1.3 57.5 + - + +
1185B GLU* 3.3 2.4 + - - +
1186B MET* 2.9 37.1 + - + +
1241B THR* 6.1 1.1 - - - +
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Residues in contact with GLU1183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172B GLU* 4.1 6.7 - - - +
1179B TYR* 6.0 0.2 - - - +
1180B ARG* 2.7 49.7 + - - +
1181B GLY 3.2 2.5 + - - -
1182B PRO* 1.3 80.3 - - + +
1184B LEU* 1.3 58.1 + - - +
1186B MET* 3.4 6.4 + - - -
1187B TRP 3.2 16.6 + - - -
1236B PRO* 3.5 32.3 - - + +
1237B GLU* 5.3 2.1 - - - +
1239B ARG* 2.9 34.2 + - + +
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Residues in contact with LEU1184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127B ARG* 5.8 9.0 - - + +
1162B PHE* 4.0 28.5 - - + -
1168B TYR 4.6 2.0 - - - +
1169B CYS* 4.3 2.7 - - - -
1170B ALA* 3.4 41.3 - - + +
1172B GLU* 4.3 1.7 + - - +
1173B VAL* 3.9 17.9 - - + -
1179B TYR* 3.8 43.0 - - + +
1181B GLY 3.1 8.7 + - - +
1183B GLU* 1.3 78.0 + - - +
1185B GLU* 1.3 64.8 + - - +
1187B TRP* 3.4 3.6 + - - +
1188B SER* 3.1 22.3 + - - -
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Residues in contact with GLU1185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116B VAL* 3.2 30.3 - - + +
1119B LEU* 5.6 2.8 - - - +
1120B ARG* 2.4 32.9 + - - +
1124B ILE 4.6 3.0 - - - +
1125B ILE* 3.4 30.8 - - + +
1126B HIS* 4.1 7.8 + - - +
1127B ARG 5.2 1.0 + - - +
1129B ILE* 3.9 23.8 - - + +
1181B GLY 3.0 11.2 + - - +
1182B PRO 3.4 8.1 - - - +
1184B LEU* 1.3 76.9 - - - +
1186B MET* 1.3 57.6 + - - +
1188B SER* 2.6 23.2 + - - -
1189B LEU* 3.0 18.9 + - + +
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Residues in contact with MET1186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120B ARG* 4.1 9.4 - - - +
1182B PRO* 2.9 29.2 + - + +
1183B GLU* 3.6 7.9 - - - +
1184B LEU 3.3 0.2 - - - -
1185B GLU* 1.3 73.5 - - - +
1187B TRP* 1.3 65.8 + - - +
1189B LEU* 3.4 13.2 + - + +
1190B GLY 3.2 15.9 + - - -
1231B LEU* 3.4 42.1 - - + +
1239B ARG* 4.1 7.2 - - + -
1240B THR 3.5 18.4 - - - +
1241B THR* 3.8 7.4 - - - -
1242B LEU* 3.7 39.5 - - + +
1245B LEU* 3.6 20.6 - - + -
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Residues in contact with TRP1187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167B GLU 5.0 1.4 + - - -
1168B TYR* 3.3 21.8 + - - +
1169B CYS 3.3 11.3 + - - -
1170B ALA* 3.5 22.0 - - + -
1171B PRO* 3.6 23.8 - - + -
1183B GLU 3.2 4.0 + - - -
1184B LEU 3.7 7.4 - - - +
1185B GLU 3.4 0.2 - - - -
1186B MET* 1.3 79.3 - - - +
1188B SER* 1.3 55.7 + - - +
1190B GLY* 3.1 4.9 + - - -
1191B VAL* 3.1 36.0 + - + +
1203B PHE* 3.5 28.0 - + - -
1209B THR* 3.4 38.1 + - + -
1212B ALA* 3.9 6.1 - - + -
1231B LEU 3.5 12.6 - - - -
1232B LEU* 3.5 43.3 - - + +
1233B GLN 3.8 7.4 - - - -
1234B PRO 4.1 0.4 - - - -
1239B ARG* 3.7 18.0 - - - +
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Residues in contact with SER1188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129B ILE* 3.9 31.8 + - - +
1168B TYR* 3.7 27.3 - - - -
1184B LEU* 3.1 13.7 + - - -
1185B GLU* 2.6 24.8 + - - -
1187B TRP* 1.3 77.9 - - - +
1189B LEU* 1.3 52.9 + - - +
1191B VAL* 3.5 0.8 + - - +
1192B THR* 2.7 37.2 + - - -
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Residues in contact with LEU1189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109B PHE* 3.5 19.3 - - + -
1112B LEU* 3.6 36.8 - - + -
1113B VAL* 5.4 2.7 - - + +
1116B VAL* 4.2 26.0 - - + -
1129B ILE* 4.3 9.2 - - + -
1185B GLU* 3.0 19.7 + - + +
1186B MET* 3.5 26.7 - - + +
1187B TRP 3.2 0.2 - - - -
1188B SER* 1.3 74.7 + - - +
1190B GLY* 1.3 60.2 + - - +
1192B THR* 3.8 2.2 - - - -
1193B LEU* 2.9 31.2 + - - +
1231B LEU* 4.4 7.0 - - + -
1242B LEU* 4.6 1.8 - - + -
1245B LEU* 3.8 22.7 - - + -
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Residues in contact with GLY1190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186B MET 3.2 7.5 + - - -
1187B TRP 3.1 8.0 + - - -
1189B LEU* 1.3 77.0 - - - +
1191B VAL* 1.3 55.3 + - - +
1193B LEU* 3.7 2.9 - - - +
1194B TYR* 2.8 31.4 + - - +
1228B VAL* 5.1 2.8 - - - +
1231B LEU* 3.8 26.4 - - - +
1232B LEU* 3.9 16.3 - - - +
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Residues in contact with VAL1191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167B GLU 3.8 14.1 - - - +
1168B TYR* 3.7 28.7 - - + -
1187B TRP* 3.1 40.4 + - + +
1188B SER* 3.9 0.9 - - - +
1189B LEU 3.4 0.2 - - - -
1190B GLY* 1.3 72.2 - - - +
1192B THR* 1.3 57.9 + - - +
1194B TYR* 4.0 0.7 - - - +
1195B THR* 2.6 38.3 + - - +
1201B ASN* 3.4 25.6 - - - +
1202B PRO* 3.8 19.7 - - + -
1203B PHE* 5.3 2.2 - - + -
1232B LEU* 4.0 7.9 - - + -
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Residues in contact with THR1192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090B LEU* 5.1 7.1 - - + +
1094B ILE* 5.4 0.7 - - - +
1109B PHE* 5.4 2.5 - - + -
1112B LEU* 3.9 14.1 - - + -
1129B ILE* 3.6 12.1 + - - +
1130B LYS* 3.8 7.8 - - - -
1131B ASP* 4.6 5.3 - - + +
1134B ILE* 3.8 28.7 - - + -
1168B TYR* 3.4 17.8 - - - -
1188B SER 2.7 22.8 + - - -
1189B LEU* 3.8 7.2 - - - -
1191B VAL* 1.3 76.4 - - - +
1193B LEU* 1.3 58.2 + - - +
1195B THR* 3.4 5.5 + - - -
1196B LEU* 3.0 28.6 + - + +
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Residues in contact with LEU1193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109B PHE* 3.6 40.6 - - + -
1189B LEU 2.9 18.8 + - - +
1190B GLY 3.7 2.9 - - - +
1192B THR* 1.3 74.0 - - - +
1194B TYR* 1.3 66.6 + - - +
1196B LEU* 3.2 6.6 + - + +
1197B VAL* 3.1 31.3 + - + +
1224B LEU* 4.2 4.5 - - + -
1227B LEU* 3.6 33.2 - - + -
1228B VAL* 3.7 21.5 - - + -
1231B LEU* 4.1 9.0 - - + -
1250B TRP* 3.7 24.5 - - + -
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Residues in contact with TYR1194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190B GLY 2.8 21.8 + - - +
1191B VAL 4.0 0.7 - - - +
1193B LEU* 1.3 73.9 - - - +
1195B THR* 1.3 57.4 + - - +
1197B VAL* 4.0 6.1 - - - -
1198B PHE* 2.9 63.7 + + + +
1200B GLU* 3.1 33.0 + - + -
1201B ASN 4.7 0.2 + - - -
1202B PRO* 3.6 45.4 + - + +
1214B ILE* 4.1 25.3 - - + +
1215B HIS 3.9 7.4 + - - -
1216B PRO* 3.7 9.4 - - + +
1217B PRO* 3.6 17.8 - - - +
1228B VAL* 4.9 6.9 - - + +
1232B LEU* 4.4 11.9 - - + -
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Residues in contact with THR1195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094B ILE* 3.8 18.4 - - + +
1131B ASP* 3.5 25.8 - - - +
1168B TYR* 4.0 9.3 + - - +
1191B VAL* 2.6 29.3 + - - +
1192B THR 3.7 4.5 - - - -
1194B TYR* 1.3 74.1 - - - +
1196B LEU* 1.3 60.5 + - - +
1199B GLU* 2.9 28.5 + - - -
1200B GLU* 3.6 23.9 + - - +
1201B ASN* 4.1 14.5 + - - +
1202B PRO* 4.4 0.2 - - - +
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Residues in contact with LEU1196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090B LEU* 3.8 31.2 - - + -
1093B PHE* 4.6 5.4 - - + -
1094B ILE* 3.8 18.0 - - + +
1098B PRO* 5.7 0.2 - - - +
1100B LEU* 3.9 36.5 - - + +
1105B ALA* 3.6 31.9 - - + +
1108B ILE* 3.9 22.0 - - + -
1109B PHE* 4.4 13.2 - - + +
1192B THR* 3.0 16.8 + - + +
1193B LEU* 3.2 8.0 + - + +
1195B THR* 1.3 78.0 - - - +
1197B VAL* 1.3 64.5 + - + +
1199B GLU* 4.1 10.6 - - - +
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Residues in contact with VAL1197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100B LEU* 5.7 2.4 - - - +
1102B GLU* 5.9 1.1 - - + -
1105B ALA* 3.8 27.8 - - + -
1193B LEU* 3.2 23.6 - - + +
1194B TYR* 3.5 2.5 - - - +
1196B LEU* 1.3 80.7 - - + +
1198B PHE* 1.3 99.7 + - + +
1199B GLU* 3.6 3.5 + - - +
1218B TYR* 3.3 20.1 - - - -
1220B VAL* 5.6 2.0 - - + -
1224B LEU* 4.0 27.8 - - + -
1228B VAL* 5.2 0.4 - - + -
1250B TRP* 4.3 8.7 - - + -
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Residues in contact with PHE1198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1194B TYR* 2.9 56.9 + + + +
1197B VAL* 1.3 95.6 - - + +
1199B GLU* 1.3 69.2 + - - +
1200B GLU* 3.1 10.9 + - - +
1216B PRO* 3.5 27.6 - - + -
1217B PRO* 3.6 29.7 - - + +
1218B TYR* 3.8 30.7 + + + -
1220B VAL* 3.6 41.5 - - + -
1224B LEU* 4.9 2.0 - - + -
1225B MET* 4.5 2.5 - - - -
1228B VAL* 4.7 13.5 - - + -
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Residues in contact with GLU1199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B MG 2.4 31.1 - - - -
1094B ILE* 4.0 28.3 - - + +
1097B HIS* 3.9 20.8 + - - +
1098B PRO* 2.9 28.4 - - + +
1100B LEU* 5.3 2.1 + - - +
1195B THR* 2.9 17.7 + - - -
1196B LEU 4.1 12.6 - - - +
1197B VAL 4.4 4.1 - - - +
1198B PHE* 1.3 79.8 - - - +
1200B GLU* 1.3 58.9 + - - +
1218B TYR* 4.0 13.2 + - - +
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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
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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