Contacts of the helix formed by residues 1160 - 1177 (chain A) in PDB entry 1K3A
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 THR1160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102A VAL* 3.5 15.3 - - - +
1130A ILE* 5.5 0.4 - - - -
1134A ASP 4.2 10.3 - - - +
1135A PTR 4.0 17.5 - - + -
1152A GLU* 4.7 4.6 + - + +
1158A VAL* 4.4 13.2 - - + +
1159A PHE* 1.3 78.8 - - - +
1161A THR* 1.3 64.4 + - - +
1162A TYR* 2.9 42.8 + - + +
1163A SER* 2.8 24.3 + - - -
1164A ASP 3.1 5.2 + - - -
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Residues in contact with THR1161 (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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1097A ASN* 3.2 44.9 - - + +
1102A VAL* 4.4 1.9 - - + +
1130A ILE* 4.0 22.6 - - + +
1134A ASP 5.1 1.3 + - - +
1160A THR* 1.3 74.2 - - - +
1162A TYR* 1.3 75.4 + - - +
1164A ASP* 3.2 9.8 + - - +
1165A VAL* 3.0 31.9 + - - +
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Residues in contact with TYR1162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1152A GLU* 4.6 0.2 - - - +
1160A THR* 2.9 27.8 + - + +
1161A THR* 1.3 91.1 + - - +
1163A SER* 1.3 58.7 + - - +
1165A VAL* 3.2 11.4 + - + +
1166A TRP 3.1 13.9 + - - -
1223A PRO* 3.7 48.7 - - + +
1224A LYS* 5.2 10.0 - - + +
1226A ARG* 3.1 22.0 + - + +
1227A PRO 5.9 2.0 - - - -
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Residues in contact with SER1163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102A VAL* 4.8 0.9 - - - +
1148A TRP 5.0 0.2 - - - +
1150A SER* 3.5 15.0 + - - -
1152A GLU* 3.9 4.7 + - - -
1153A SER* 3.5 21.5 - - - -
1158A VAL 4.6 0.7 - - - -
1159A PHE* 3.4 14.6 - - - +
1160A THR* 2.8 35.2 + - - -
1162A TYR* 1.3 76.5 - - - +
1164A ASP* 1.3 65.5 + - - +
1166A TRP* 3.2 5.0 + - - +
1167A SER* 3.2 24.3 + - - -
1226A ARG* 3.9 7.4 - - - +
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Residues in contact with ASP1164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093A MET* 3.4 21.4 - - + +
1097A ASN* 3.3 18.0 + - - -
1102A VAL* 3.5 13.9 - - - +
1103A HIS* 2.8 24.0 + - - +
1104A ARG* 2.9 27.4 + - - -
1106A LEU* 3.8 6.1 - - - +
1160A THR 3.1 5.6 + - - +
1161A THR* 3.3 11.2 - - - +
1163A SER* 1.3 78.5 + - - +
1165A VAL* 1.3 58.4 + - - +
1167A SER* 3.3 8.2 + - - -
1168A PHE* 3.0 22.9 + - - +
1229A PHE* 3.6 12.7 - - + -
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Residues in contact with VAL1165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1161A THR 3.0 19.5 + - - +
1162A TYR* 3.2 13.0 + - + +
1164A ASP* 1.3 75.3 - - - +
1166A TRP* 1.3 64.3 + - - +
1168A PHE* 3.2 3.7 + - - +
1169A GLY 3.1 16.3 + - - -
1218A CYS* 3.4 32.3 - - + +
1226A ARG* 4.2 8.7 - - + -
1227A PRO* 3.4 28.0 - - + +
1228A SER* 4.5 2.2 - - - -
1229A PHE* 3.7 35.4 - - + +
1232A ILE* 4.1 6.5 - - + -
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Residues in contact with TRP1166 (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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1147A ARG 5.6 0.6 + - - -
1148A TRP 3.5 18.3 + - - -
1149A MET 3.4 9.1 + - - -
1150A SER* 3.6 26.0 - - - -
1151A PRO* 3.5 27.6 - - + -
1162A TYR 3.1 10.5 + - - +
1163A SER 3.4 9.4 - - - +
1164A ASP 3.2 0.2 - - - -
1165A VAL* 1.3 77.4 - - - +
1167A SER* 1.3 58.9 + - - +
1169A GLY* 2.9 18.2 + - - -
1170A VAL* 3.2 20.5 + - + +
1183A TYR* 4.5 12.4 + - - -
1195A VAL* 3.9 16.6 - - + +
1199A GLY 4.9 1.3 - - - -
1200A LEU* 3.9 23.8 - - + -
1218A CYS 3.6 22.9 + - - -
1219A TRP* 3.4 38.9 + + + -
1220A GLN 3.9 6.3 - - - -
1221A TYR* 4.8 2.0 - + - -
1226A ARG* 3.5 18.2 - - - +
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Residues in contact with SER1167 (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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1104A ARG 5.4 4.5 + - - -
1106A LEU* 3.5 34.4 + - - +
1148A TRP* 2.6 27.8 + - - +
1149A MET* 4.7 1.2 - - - -
1163A SER 3.2 10.5 + - - -
1164A ASP* 3.6 9.8 + - - -
1166A TRP* 1.3 75.0 - - - +
1168A PHE* 1.3 66.5 + - - +
1170A VAL* 2.9 17.6 + - - +
1171A VAL* 2.9 15.8 + - - +
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Residues in contact with PHE1168 (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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1086A ALA* 3.4 30.5 - - + -
1089A ILE* 3.8 24.0 - - + -
1090A ALA* 3.8 18.6 - - + -
1106A LEU* 3.6 10.3 - - + +
1164A ASP 3.0 8.2 + - - +
1165A VAL 3.3 8.7 - - - +
1166A TRP 3.2 0.2 - - - -
1167A SER* 1.3 76.2 - - - +
1169A GLY* 1.3 61.8 + - - +
1171A VAL* 3.1 7.2 + - + +
1172A LEU* 2.9 57.6 + - + +
1214A LEU* 4.9 1.8 - - + -
1218A CYS* 3.8 18.4 - - - -
1229A PHE* 3.5 24.5 - + + -
1232A ILE* 3.9 29.2 - - + -
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Residues in contact with GLY1169 (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 VAL 3.1 6.5 + - - -
1166A TRP 2.9 10.8 + - - -
1168A PHE* 1.3 76.9 - - - +
1170A VAL* 1.3 60.1 + - - +
1172A LEU* 3.2 11.7 + - - +
1173A TRP 3.1 16.1 + - - -
1215A MET* 3.8 4.9 - - - +
1218A CYS* 3.8 17.9 - - - -
1219A TRP* 3.3 23.7 - - - -
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Residues in contact with VAL1170 (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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1147A ARG 4.1 14.8 - - - +
1148A TRP* 3.5 31.0 - - + +
1166A TRP* 3.2 27.6 + - + +
1167A SER* 2.9 10.3 + - - +
1169A GLY* 1.3 77.9 - - - +
1171A VAL* 1.3 56.8 + - - +
1173A TRP* 3.0 4.9 + - + +
1174A GLU* 2.8 26.4 + - - +
1182A PRO* 4.1 20.0 - - + -
1183A TYR* 5.1 1.8 - - - +
1201A LEU* 4.2 15.9 - - + -
1219A TRP* 3.9 15.3 - - - +
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Residues in contact with VAL1171 (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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1057A LEU* 4.5 6.1 - - + -
1089A ILE* 3.8 31.2 - - + -
1106A LEU* 3.7 17.9 - - + -
1107A ALA* 3.5 32.8 - - - +
1108A ALA* 4.5 9.4 - - + +
1111A CYS* 4.9 2.5 - - - -
1148A TRP* 4.9 0.4 - - + -
1167A SER 2.9 18.1 + - - +
1168A PHE* 3.1 11.4 + - + +
1170A VAL* 1.3 76.0 - - - +
1172A LEU* 1.3 63.3 + - + +
1174A GLU* 3.1 9.6 + - - +
1175A ILE* 2.9 29.7 + - + +
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Residues in contact with LEU1172 (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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1082A MET 5.6 0.2 - - - +
1086A ALA* 3.5 32.5 - - + -
1168A PHE* 2.9 42.8 + - + +
1169A GLY* 3.4 9.2 - - - +
1171A VAL* 1.3 77.8 - - + +
1173A TRP* 1.3 63.1 - - - +
1175A ILE* 3.1 14.6 + - + +
1176A ALA* 3.0 23.4 + - - +
1211A LEU* 4.2 22.2 - - + +
1214A LEU* 3.6 36.6 - - + -
1215A MET* 4.0 17.8 - - + +
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Residues in contact with TRP1173 (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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1169A GLY 3.1 10.4 + - - +
1170A VAL* 3.0 11.2 + - - +
1172A LEU* 1.3 77.7 - - - +
1174A GLU* 1.3 71.7 + - + +
1176A ALA* 3.3 1.7 + - - +
1177A THR* 3.0 44.5 + - + +
1180A GLU* 3.3 39.3 - - + -
1181A GLN 3.6 16.6 - - - -
1182A PRO* 3.6 22.0 - - + -
1183A TYR 4.7 1.1 - - - -
1184A GLN* 5.7 0.4 - - + -
1201A LEU* 3.7 30.4 - - + +
1202A ASP* 3.0 46.9 + - - -
1204A PRO* 3.5 16.5 - - + +
1215A MET* 3.9 13.4 - - - -
1219A TRP* 4.0 10.8 - + + -
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Residues in contact with GLU1174 (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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1058A LYS* 4.9 11.8 - - - +
1061A LEU* 3.7 2.5 - - + +
1108A ALA* 3.0 44.4 + - + +
1109A ARG 4.9 1.0 + - - -
1148A TRP* 3.0 37.2 + - - +
1170A VAL 2.8 12.5 + - - +
1171A VAL* 3.1 15.0 + - - +
1173A TRP* 1.3 86.7 - - + +
1175A ILE* 1.3 62.2 + - - +
1177A THR* 3.7 6.1 - - - -
1178A LEU* 3.0 4.0 + - - -
1179A ALA* 2.7 34.0 + - - +
1180A GLU 4.5 7.6 - - - +
1182A PRO* 4.5 8.2 - - + +
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Residues in contact with ILE1175 (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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1057A LEU* 4.2 9.6 - - + -
1061A LEU* 3.8 20.9 - - + +
1077A PRO* 5.0 1.6 - - + +
1082A MET* 3.8 27.3 - - + +
1085A MET* 3.6 46.9 - - + -
1086A ALA 4.7 2.5 - - - +
1089A ILE* 4.1 20.0 - - + -
1171A VAL* 2.9 18.8 + - + +
1172A LEU* 3.1 21.5 + - + +
1174A GLU* 1.3 77.2 - - + +
1176A ALA* 1.3 63.0 + - - +
1178A LEU* 3.2 21.1 + - - +
1211A LEU* 5.3 3.1 - - + -
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Residues in contact with ALA1176 (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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1082A MET* 4.2 16.6 - - - +
1172A LEU 3.0 15.2 + - - +
1173A TRP 3.3 0.6 + - - +
1175A ILE* 1.3 76.0 - - - +
1177A THR* 1.3 59.7 + - - +
1178A LEU* 3.5 3.1 - - - +
1204A PRO* 3.8 22.0 - - + +
1205A ASP 4.8 5.9 - - - +
1207A CYS* 3.6 34.4 - - + +
1211A LEU* 5.1 2.0 - - + -
1215A MET* 4.6 0.9 - - + -
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Residues in contact with THR1177 (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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1065A ARG* 3.2 15.9 + - - -
1173A TRP* 3.0 42.3 + - + +
1174A GLU* 3.4 5.4 + - - -
1176A ALA* 1.3 76.3 - - - +
1178A LEU* 1.3 69.9 + - - +
1180A GLU* 3.2 29.9 + - + +
1202A ASP* 5.1 0.7 - - - +
1204A PRO* 3.5 29.6 - - + -
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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
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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