Contacts of the helix formed by residues 1190 - 1208 (chain M) in PDB entry 3F5P
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 THR1190 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132M VAL* 3.2 19.2 - - - +
1160M ILE* 5.2 0.2 - - - -
1164M ASP 3.7 12.8 - - - +
1165M PTR 3.7 18.6 - - + -
1182M GLU* 4.9 4.3 + - + +
1188M VAL* 4.3 12.6 - - + +
1189M PHE* 1.3 80.0 - - - +
1191M THR* 1.3 65.4 + - - +
1192M TYR* 2.9 41.4 + - + +
1193M SER* 2.9 22.7 + - - -
1194M ASP 3.3 2.3 + - - -
1253M PRO* 5.3 0.2 - - - +
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Residues in contact with THR1191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127M ASN* 3.6 43.5 - - + +
1130M LYS* 6.4 0.4 - - + +
1132M VAL* 4.3 1.3 - - - +
1160M ILE* 4.3 18.7 - - + +
1164M ASP* 5.9 0.9 - - + +
1190M THR* 1.3 75.7 - - - +
1192M TYR* 1.3 83.1 + - - +
1194M ASP* 2.9 18.3 + - - +
1195M VAL* 3.0 18.6 + - - +
1259M PHE* 4.5 1.0 - - - -
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Residues in contact with TYR1192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182M GLU* 4.6 0.2 - - - +
1190M THR* 3.1 26.0 - - + +
1191M THR* 1.3 93.5 + - - +
1193M SER* 1.3 59.4 + - - +
1195M VAL* 3.4 11.2 + - + +
1196M TRP 3.3 12.6 + - - -
1253M PRO* 3.4 45.3 - - + +
1254M LYS* 4.5 24.7 - - + +
1256M ARG* 2.9 24.1 + - + +
1257M PRO 6.0 1.8 - - - -
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Residues in contact with SER1193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180M SER* 3.5 12.9 + - - -
1182M GLU* 3.7 11.4 + - - -
1183M SER* 3.5 22.7 - - - -
1188M VAL 4.4 1.3 - - - -
1189M PHE* 3.6 15.6 - - - +
1190M THR* 2.9 34.0 + - - -
1192M TYR* 1.3 75.9 - - - +
1194M ASP* 1.3 68.2 + - - +
1196M TRP* 3.2 5.9 - - - +
1197M SER* 3.1 22.8 + - - -
1256M ARG* 4.0 2.4 - - - +
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Residues in contact with ASP1194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123M MET* 3.2 28.7 - - + +
1127M ASN* 3.9 6.0 + - - +
1132M VAL* 3.6 15.6 - - - +
1133M HIS* 2.8 27.2 + - - +
1134M ARG* 3.0 27.8 + - - -
1136M LEU* 4.2 3.3 - - - +
1190M THR 3.3 0.4 + - - -
1191M THR* 2.9 10.9 + - - +
1193M SER* 1.3 79.5 + - - +
1195M VAL* 1.3 53.8 + - - +
1197M SER* 2.9 10.6 + - - -
1198M PHE* 2.7 33.8 + - - +
1259M PHE* 4.0 6.1 - - + -
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Residues in contact with VAL1195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191M THR* 3.0 20.0 + - - +
1192M TYR* 3.5 11.4 - - + +
1193M SER 3.3 0.2 - - - -
1194M ASP* 1.3 74.0 - - - +
1196M TRP* 1.3 65.2 + - - +
1198M PHE* 2.9 5.2 + - - +
1199M GLY 2.7 20.1 + - - -
1248M CYS* 3.5 32.5 - - + +
1256M ARG* 4.1 9.9 - - + -
1257M PRO* 3.4 29.2 - - + +
1258M SER* 4.6 2.0 - - - -
1259M PHE* 3.7 35.2 - - + +
1262M ILE* 4.6 3.8 - - + -
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Residues in contact with TRP1196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177M ARG 5.3 0.2 + - - -
1178M TRP* 3.6 17.3 + - - +
1179M MET 3.2 11.9 + - - -
1180M SER* 3.7 17.9 - - - -
1181M PRO* 3.5 34.5 - - + -
1192M TYR 3.3 8.9 + - - +
1193M SER 3.2 10.3 - - - +
1194M ASP 3.1 0.2 - - - -
1195M VAL* 1.3 77.3 - - - +
1197M SER* 1.3 60.7 + - - +
1199M GLY* 2.9 18.4 + - - -
1200M VAL* 3.1 20.5 + - + +
1213M TYR* 4.1 14.5 + - - -
1225M VAL* 3.7 22.9 - - + -
1229M GLY 4.7 3.1 - - - -
1230M LEU* 4.2 13.5 - - + -
1248M CYS 3.6 10.5 + - - -
1249M TRP* 3.4 58.8 + + + -
1250M GLN 4.2 0.7 - - - -
1251M TYR* 5.2 0.9 - + - -
1256M ARG* 3.7 15.3 - - - +
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Residues in contact with SER1197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134M ARG 4.7 9.9 + - - -
1136M LEU* 3.4 30.5 - - - +
1178M TRP* 2.9 26.0 + - - +
1179M MET* 5.0 0.3 - - - -
1180M SER 5.3 0.2 + - - -
1193M SER 3.1 10.6 + - - -
1194M ASP* 2.9 12.4 + - - -
1196M TRP* 1.3 78.2 - - - +
1198M PHE* 1.3 62.8 + - - +
1200M VAL* 3.0 16.5 + - - +
1201M VAL* 3.0 18.6 + - - +
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Residues in contact with PHE1198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116M ALA* 3.3 33.2 - - + -
1119M ILE* 3.6 31.0 - - + -
1120M ALA* 3.7 13.5 - - + -
1136M LEU* 3.7 12.5 - - + +
1194M ASP 2.7 15.3 + - - +
1195M VAL 2.9 7.4 + - - +
1197M SER* 1.3 71.2 - - - +
1199M GLY* 1.3 64.7 - - - +
1201M VAL* 3.1 10.9 + - + +
1202M LEU* 3.1 49.1 + - + +
1248M CYS* 4.0 5.8 - - - -
1259M PHE* 3.6 23.6 - + + -
1262M ILE* 3.7 35.0 - - + -
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Residues in contact with GLY1199 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195M VAL 2.7 13.9 + - - -
1196M TRP 2.9 6.5 + - - -
1198M PHE* 1.3 75.7 - - - +
1200M VAL* 1.3 58.9 + - - +
1202M LEU* 3.4 10.5 - - - +
1203M TRP 3.2 14.4 + - - -
1245M MET* 4.0 4.7 - - - +
1248M CYS* 3.7 20.2 - - - -
1249M TRP* 3.3 24.5 - - - -
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Residues in contact with VAL1200 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177M ARG 4.1 13.2 - - - +
1178M TRP* 3.3 35.7 - - + +
1196M TRP* 3.1 27.1 + - + +
1197M SER* 3.0 11.0 + - - +
1199M GLY* 1.3 75.6 - - - +
1201M VAL* 1.3 58.6 + - - +
1203M TRP* 2.9 8.1 + - + +
1204M GLU* 2.9 24.0 + - - +
1212M PRO* 4.0 20.6 - - + -
1213M TYR* 4.7 2.2 - - - +
1231M LEU* 4.3 13.7 - - + -
1249M TRP* 3.9 14.6 - - - +
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Residues in contact with VAL1201 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087M LEU* 5.3 2.2 - - + -
1119M ILE* 4.0 28.3 - - + -
1136M LEU* 3.9 10.1 - - + +
1137M ALA* 3.7 26.7 - - - -
1138M ALA* 4.2 9.1 - - + +
1141M CYS* 5.5 1.1 - - - -
1178M TRP* 4.7 0.4 - - + -
1197M SER 3.0 19.1 - - - +
1198M PHE* 3.1 20.6 + - + +
1200M VAL* 1.3 71.8 - - - +
1202M LEU* 1.3 64.6 + - + +
1204M GLU* 3.1 16.7 + - - +
1205M ILE* 2.9 34.9 + - + +
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Residues in contact with LEU1202 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112M MET* 6.2 0.7 - - + -
1116M ALA* 3.4 34.1 - - + -
1198M PHE* 3.1 39.4 + - + +
1199M GLY* 3.4 11.4 - - - +
1201M VAL* 1.3 77.5 - - + +
1203M TRP* 1.3 58.6 + - - +
1205M ILE* 3.3 14.7 + - + +
1206M ALA* 2.9 29.5 + - - +
1241M LEU* 4.3 18.5 - - + +
1244M LEU* 3.9 30.7 - - + -
1245M MET* 3.8 22.1 - - + +
1248M CYS* 4.8 1.6 - - - -
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Residues in contact with TRP1203 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199M GLY 3.2 9.6 + - - +
1200M VAL* 2.9 17.2 + - - +
1202M LEU* 1.3 80.6 - - - +
1204M GLU* 1.3 63.4 + - + +
1206M ALA* 3.4 1.2 + - - +
1207M THR* 3.0 57.9 + - + +
1210M GLU* 3.7 23.6 - - + -
1211M GLN 3.8 15.7 - - - -
1212M PRO* 3.6 34.1 - - + -
1213M TYR 4.8 0.9 - - - -
1231M LEU* 3.7 34.0 - - + +
1232M ASP 3.3 24.2 + - - -
1233M LYS* 5.5 0.2 - - - -
1234M PRO* 3.8 13.2 - - + +
1245M MET* 3.8 25.7 - - - +
1249M TRP* 3.9 4.9 - + + -
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Residues in contact with GLU1204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088M LYS* 4.3 12.0 + - - +
1091M LEU* 3.8 2.6 - - + +
1138M ALA* 3.3 38.5 + - + +
1139M ARG 5.0 0.2 + - - -
1178M TRP* 2.6 44.4 + - + -
1200M VAL* 2.9 18.9 + - + +
1201M VAL* 3.1 14.2 + - - +
1203M TRP* 1.3 83.9 - - + +
1205M ILE* 1.3 65.1 + - - +
1207M THR* 3.1 7.4 + - - -
1208M LEU* 2.9 4.5 + - - -
1209M ALA* 2.7 35.7 + - - +
1210M GLU 4.7 8.8 - - - +
1212M PRO* 4.8 0.9 - - + -
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Residues in contact with ILE1205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087M LEU* 4.4 8.3 - - + -
1091M LEU* 3.9 28.1 - - + +
1107M PRO* 4.4 1.8 - - + +
1112M MET* 3.3 39.3 - - + +
1115M MET* 3.8 33.0 - - + -
1116M ALA 4.7 4.0 - - - +
1119M ILE* 4.3 17.5 - - + -
1201M VAL 2.9 18.5 + - - +
1202M LEU* 3.5 20.4 - - + +
1204M GLU* 1.3 78.4 - - - +
1206M ALA* 1.3 62.3 + - - +
1207M THR 3.2 0.7 + - - -
1208M LEU* 3.3 19.8 + - - +
1241M LEU* 5.2 1.8 - - + -
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Residues in contact with ALA1206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112M MET* 3.2 21.3 - - + +
1202M LEU 2.9 16.6 + - - +
1203M TRP 3.7 5.2 - - - +
1204M GLU 3.2 0.2 - - - -
1205M ILE* 1.3 76.8 - - - +
1207M THR* 1.3 60.2 + - - +
1208M LEU* 3.5 3.4 + - - +
1234M PRO* 3.8 25.4 - - + +
1235M ASP 5.0 4.2 - - - +
1237M CYS* 4.1 12.3 - - + +
1241M LEU* 4.7 2.5 - - + -
1245M MET* 3.8 12.1 - - + -
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Residues in contact with THR1207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095M ARG* 3.5 13.5 + - - -
1203M TRP* 3.0 50.3 + - + +
1204M GLU* 3.1 3.8 + - - -
1206M ALA* 1.3 76.8 - - - +
1208M LEU* 1.3 68.9 + - - +
1210M GLU* 3.0 43.0 + - - +
1234M PRO* 3.7 22.0 - - + -
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Residues in contact with LEU1208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091M LEU* 3.6 21.5 - - + +
1092M ARG* 4.0 4.5 - - - +
1094M LEU* 3.4 44.9 - - + +
1095M ARG* 3.3 33.4 + - + +
1096M PRO* 5.6 0.7 - - + -
1106M PRO 4.3 7.6 - - - +
1107M PRO* 3.5 32.3 - - + -
1204M GLU 2.9 4.0 + - - -
1205M ILE 3.3 7.8 + - - +
1206M ALA 5.0 2.2 - - - +
1207M THR* 1.3 82.2 - - - +
1209M ALA* 1.3 70.6 + - - +
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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