Contacts of the helix formed by residues 1181 - 1197 (chain u) in PDB entry 6FF7
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 ASP1181 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517 LEU* 6.6 0.4 - - + -
1179u ASP* 3.4 10.1 - - + +
1180u ARG* 1.3 81.7 - - - +
1182u LEU* 1.3 63.5 + - - +
1183u VAL* 3.3 11.1 + - + +
1184u HIS* 3.8 16.8 + - + +
1185u ARG* 3.8 8.5 + - - +
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Residues in contact with LEU1182 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180u ARG 3.7 2.3 + - - +
1181u ASP* 1.3 72.6 - - - +
1183u VAL* 1.3 58.9 + - - +
1184u HIS 3.4 0.2 - - - -
1185u ARG* 3.3 9.3 + - + +
1186u GLN* 2.9 29.1 + - - +
1226u VAL* 4.7 15.0 - - + +
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Residues in contact with VAL1183 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391Z C 4.3 17.7 - - - +
392Z U 4.9 13.5 - - - -
1145u ASN* 5.5 12.0 - - + +
1181u ASP* 3.3 6.6 - - + +
1182u LEU* 1.3 75.8 - - - +
1184u HIS* 1.3 60.0 + - - +
1186u GLN* 3.4 4.2 + - - +
1187u THR* 3.0 31.2 + - - -
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Residues in contact with HIS1184 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144u GLN* 6.4 2.0 - - + -
1145u ASN* 6.1 4.4 - - - +
1148u LEU* 5.1 5.1 - - + +
1176u ALA* 3.6 26.2 - - + +
1179u ASP* 4.1 11.9 - - + -
1181u ASP* 3.8 15.1 + - + +
1182u LEU 3.4 0.2 - - - -
1183u VAL* 1.3 78.5 - - - +
1185u ARG* 1.3 55.2 + - - +
1187u THR* 3.8 4.6 - - - -
1188u ALA* 2.9 30.8 + - - +
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Residues in contact with ARG1185 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176u ALA 4.0 9.8 + - - +
1177u LEU* 4.7 13.7 - - + +
1179u ASP 5.6 1.6 - - - +
1181u ASP 3.8 8.0 + - - +
1182u LEU* 3.3 13.2 + - + +
1183u VAL 3.2 0.4 - - - -
1184u HIS* 1.3 78.4 - - - +
1186u GLN* 1.3 59.6 + - - +
1188u ALA* 3.8 4.8 - - - +
1189u SER* 2.9 28.6 + - - -
1218u ASN* 5.2 15.0 - - + -
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Residues in contact with GLN1186 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182u LEU 2.9 15.6 + - - +
1183u VAL* 3.4 5.6 + - - +
1185u ARG* 1.3 72.9 - - - +
1187u THR* 1.3 60.8 + - - +
1189u SER* 3.3 5.1 + - - -
1190u ALA* 3.0 26.2 + - - +
1225u HIS* 4.7 1.8 - - + +
1226u VAL* 4.0 22.2 - - + +
1229u ALA* 3.8 27.3 - - + +
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Residues in contact with THR1187 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145u ASN* 4.9 6.1 - - - -
1148u LEU* 3.8 34.6 - - - +
1149u LYS* 4.5 8.1 - - - -
1152u SER* 4.5 0.9 - - - -
1183u VAL 3.0 17.9 + - - -
1184u HIS* 4.0 2.2 - - - -
1186u GLN* 1.3 77.1 - - - +
1188u ALA* 1.3 56.8 + - - +
1190u ALA* 3.2 9.7 + - - +
1191u VAL* 2.9 24.9 + - - +
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Residues in contact with ALA1188 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148u LEU* 4.9 3.3 - - + +
1173u LEU* 4.6 13.8 - - + +
1176u ALA* 3.8 22.7 - - + -
1177u LEU* 4.6 8.5 - - + +
1184u HIS 2.9 19.5 + - - +
1185u ARG* 3.9 5.6 - - - +
1187u THR* 1.3 74.0 - - - +
1189u SER* 1.3 61.4 + - - +
1191u VAL* 3.2 9.9 + - - +
1192u VAL* 2.9 28.9 + - - +
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Residues in contact with SER1189 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1185u ARG 2.9 18.7 + - - -
1186u GLN* 3.6 8.1 - - - -
1187u THR 3.3 0.2 - - - -
1188u ALA* 1.3 73.6 - - - +
1190u ALA* 1.3 61.0 + - - +
1192u VAL* 3.4 3.8 + - - +
1193u GLN* 2.9 29.3 + - - +
1215u VAL* 5.8 7.0 - - - -
1229u ALA 3.9 22.7 - - - -
1230u VAL* 4.2 7.9 - - - -
1233u ALA* 3.4 17.9 - - - +
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Residues in contact with ALA1190 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1152u SER* 4.1 16.2 - - - -
1186u GLN 3.0 14.6 + - - +
1187u THR* 3.2 12.3 + - - +
1189u SER* 1.3 73.3 - - - +
1191u VAL* 1.3 58.9 + - - +
1193u GLN* 3.4 6.8 + - - +
1194u HIS* 3.0 31.0 + - - +
1229u ALA* 4.9 6.4 + - + +
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Residues in contact with VAL1191 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148u LEU* 4.7 2.0 - - - +
1151u LEU* 4.7 13.0 - - + +
1152u SER* 4.1 24.4 - - - +
1155u PHE* 4.7 3.2 - - + +
1173u LEU* 6.0 5.2 - - + -
1187u THR 2.9 13.5 + - - +
1188u ALA* 3.2 12.7 + - - +
1190u ALA* 1.3 77.4 - - - +
1192u VAL* 1.3 56.8 + - - +
1194u HIS* 3.4 1.6 + - - +
1195u MET* 2.8 31.7 + - - +
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Residues in contact with VAL1192 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173u LEU* 6.4 1.3 - - + -
1188u ALA 2.9 17.4 + - - +
1189u SER* 4.0 7.0 - - - +
1191u VAL* 1.3 75.9 - - - +
1193u GLN* 1.3 56.5 + - - +
1195u MET* 3.7 5.7 - - - +
1196u SER* 2.9 31.7 + - - -
1211u LEU* 5.0 16.4 - - + -
1215u VAL* 6.2 3.8 - - + -
1233u ALA* 5.2 5.4 - - + -
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Residues in contact with GLN1193 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189u SER 2.9 19.6 + - - +
1190u ALA* 3.5 8.3 - - - +
1192u VAL* 1.3 76.7 - - - +
1194u HIS* 1.3 56.4 + - - +
1196u SER* 3.3 6.7 + - - -
1197u LEU* 2.9 29.2 + - - +
1229u ALA 5.3 0.4 - - - +
1232u GLY* 4.0 9.6 - - - +
1233u ALA* 3.8 25.1 - - - +
1236u GLY* 4.8 5.4 - - - -
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Residues in contact with HIS1194 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1152u SER 3.8 10.5 - - - +
1155u PHE* 4.0 11.9 - - + +
1156u GLU* 3.7 33.0 - - + +
1190u ALA 3.0 17.0 + - - +
1191u VAL 4.0 2.5 - - - +
1193u GLN* 1.3 76.9 - - - +
1195u MET* 1.3 56.4 + - - +
1197u LEU* 3.5 8.3 + - - +
1198u GLY* 2.9 23.2 + - - -
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Residues in contact with MET1195 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155u PHE* 4.1 13.1 - - + +
1166u ILE* 6.2 4.7 - - + -
1191u VAL 2.8 19.8 + - - +
1192u VAL* 3.7 7.6 - - - +
1194u HIS* 1.3 76.0 - - - +
1196u SER* 1.3 58.8 + - - +
1198u GLY* 2.9 2.5 + - - -
1199u VAL* 2.8 34.1 + - - +
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Residues in contact with SER1196 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192u VAL 2.9 19.8 + - - -
1193u GLN* 3.7 4.0 - - - -
1195u MET* 1.3 75.7 - - - +
1197u LEU* 1.3 60.4 + - - +
1198u GLY 3.5 0.3 + - - -
1199u VAL* 4.8 1.3 - - - +
1200u TYR* 3.6 22.3 + - - +
1208u LEU* 5.8 6.7 - - - -
1233u ALA 5.6 0.2 - - - -
1236u GLY 3.6 29.0 - - - +
1237u LEU* 4.2 10.5 - - - -
1240u ALA* 3.9 17.5 - - - +
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Residues in contact with LEU1197 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1159u GLY* 5.2 1.2 - - - -
1193u GLN 2.9 17.6 + - - +
1194u HIS* 3.6 8.7 - - - +
1196u SER* 1.3 75.0 - - - +
1198u GLY* 1.3 58.4 + - - +
1200u TYR* 4.6 8.3 - - - +
1236u GLY* 4.9 4.4 + - - -
74y GLU* 4.5 26.2 - - + +
77y ILE* 6.2 0.3 - - - +
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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
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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