Contacts of the helix formed by residues 1184 - 1197 (chain B) in PDB entry 2IUK
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 LEU1184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1071B ILE* 3.7 18.8 - - + -
1072B SER 3.1 28.9 - - - +
1073B ALA* 3.8 22.7 - - + -
1121B GLY* 3.9 22.7 - - - +
1122B ALA* 4.8 0.4 - - + -
1170B PHE* 4.1 22.7 - - + -
1171B VAL* 5.2 1.3 - - + -
1175B TYR* 4.8 10.8 - - + +
1180B THR* 4.1 9.4 - - + -
1181B PRO* 3.0 25.8 + - + +
1183B PRO* 1.3 76.8 - - - +
1185B LEU* 1.3 64.1 + - - +
1186B LYS 3.2 3.1 - - - -
1187B TYR* 2.9 18.9 + - + +
1188B ARG* 3.0 10.4 + - - +
1547B LEU* 5.3 0.2 - - + -
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Residues in contact with LEU1185 (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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1177B PRO* 4.0 20.2 - - + +
1178B SER 5.7 1.6 - - - +
1180B THR* 3.8 25.5 - - + +
1181B PRO 2.9 15.6 + - - +
1182B ALA* 4.1 17.0 - - + +
1183B PRO 3.7 0.6 - - - -
1184B LEU* 1.3 73.8 - - - +
1186B LYS* 1.3 61.4 + - - +
1188B ARG* 3.3 13.5 - - - +
1189B LYS* 3.2 30.2 + - + +
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Residues in contact with LYS1186 (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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1081B ASN* 3.0 45.1 + - + +
1124B TYR* 4.8 1.6 + - - -
1182B ALA 4.8 1.8 + - - -
1183B PRO 4.6 1.1 + - - +
1184B LEU 3.0 1.2 + - - -
1185B LEU* 1.3 76.9 - - - +
1187B TYR* 1.3 83.9 + - + +
1188B ARG 3.2 0.2 + - - -
1189B LYS* 3.3 3.6 + - - +
1190B GLU* 2.9 65.9 + - + +
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Residues in contact with TYR1187 (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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1071B ILE* 3.7 26.5 - - + -
1077B ASP* 5.7 0.5 + - - -
1081B ASN* 4.1 12.7 - - + +
1082B GLY 2.8 32.3 + - - -
1084B VAL* 3.8 8.5 - - - +
1124B TYR* 3.1 21.7 + + - -
1168B ILE* 3.4 30.5 - - + -
1170B PHE* 3.7 15.2 - - + -
1183B PRO 3.1 26.9 - - - -
1184B LEU* 2.9 9.5 + - - +
1186B LYS* 1.3 87.9 + - + +
1188B ARG* 1.3 64.9 - - - +
1190B GLU* 3.4 18.9 - - - +
1191B GLU* 3.1 23.4 + - - +
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Residues in contact with ARG1188 (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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1170B PHE* 3.7 15.2 - - + -
1175B TYR* 2.7 33.1 + - - +
1177B PRO* 3.5 13.8 - - - +
1180B THR* 3.2 31.9 + - - -
1184B LEU 3.0 11.2 + - - +
1185B LEU* 3.3 17.0 - - - +
1187B TYR* 1.3 80.1 - - - +
1189B LYS* 1.3 65.2 + - + +
1191B GLU 3.4 16.8 - - - +
1192B PHE* 3.4 9.3 - - - -
1545B SER* 3.4 29.2 + - - +
1547B LEU* 3.7 21.6 - - + +
1548B HIS* 3.5 15.6 - - - +
1670B GLU* 2.8 40.6 + - - +
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Residues in contact with LYS1189 (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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1185B LEU* 3.2 18.4 + - + +
1186B LYS* 4.0 3.4 - - - +
1188B ARG* 1.3 81.7 - - + +
1190B GLU* 1.3 55.2 + - - +
1192B PHE* 3.2 37.9 - - + +
1193B GLU* 3.6 12.9 + - - +
1196B ARG* 3.6 33.5 + - - +
1543B HIS* 5.0 4.6 + - - +
1669B THR* 5.1 10.2 - - - +
1670B GLU* 4.6 18.5 - - - +
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Residues in contact with GLU1190 (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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1124B TYR* 3.9 11.6 + - - -
1165B LYS* 3.6 27.3 + - - +
1186B LYS* 2.9 44.3 + - + +
1187B TYR* 3.4 24.1 - - - +
1188B ARG 3.3 0.2 - - - -
1189B LYS* 1.3 76.2 - - - +
1191B GLU* 1.3 79.2 + - - +
1192B PHE 3.3 3.6 + - - -
1193B GLU* 3.6 11.2 - - - +
1194B VAL* 3.2 23.6 + - - +
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Residues in contact with GLU1191 (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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1124B TYR* 4.7 3.5 - - - -
1165B LYS* 3.7 13.7 - - - +
1166B ASN 3.2 21.6 - - - +
1167B ARG* 6.0 0.9 - - - +
1168B ILE* 3.5 35.6 - - + +
1170B PHE* 5.2 5.0 - - + -
1187B TYR 3.1 13.1 + - - +
1188B ARG 3.4 7.2 - - - +
1190B GLU* 1.3 100.9 - - - +
1192B PHE* 1.3 66.4 - - - +
1194B VAL* 3.7 32.9 - - + +
1195B LEU* 4.0 12.7 - - + +
1208B ARG* 5.4 9.0 - - - +
1545B SER* 5.6 1.6 + - - -
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Residues in contact with PHE1192 (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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1188B ARG 3.4 12.1 - - - +
1189B LYS* 3.2 38.6 - - + +
1191B GLU* 1.3 80.0 - - - +
1193B GLU* 1.3 59.8 - - - +
1194B VAL 3.0 3.9 - - - +
1195B LEU* 3.0 14.9 + - + +
1196B ARG* 2.7 42.8 + - - +
1541B ASN 3.6 14.1 - - - -
1542B ARG 3.8 9.6 - - - -
1543B HIS* 3.2 23.1 - - - -
1544B LEU 3.5 17.5 - - - -
1545B SER* 3.0 33.0 - - - -
1670B GLU* 3.7 22.4 - - - -
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Residues in contact with GLU1193 (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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1164B LYS* 4.2 11.2 + - - +
1165B LYS* 3.3 22.5 + - - -
1189B LYS 3.7 11.1 - - - +
1190B GLU* 3.6 13.8 - - - +
1192B PHE* 1.3 79.0 - - - +
1194B VAL* 1.3 59.2 + - - +
1196B ARG* 4.0 20.3 + - - +
1197B GLY* 3.2 21.7 + - - +
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Residues in contact with VAL1194 (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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1164B LYS* 4.0 16.2 + - + +
1165B LYS* 3.8 27.8 - - + +
1190B GLU 3.2 16.8 - - - +
1191B GLU* 3.7 35.7 - - + +
1193B GLU* 1.3 78.8 - - - +
1195B LEU* 1.3 63.7 + - + +
1196B ARG 3.4 0.2 + - - -
1197B GLY* 3.5 7.4 + - - -
1208B ARG* 4.0 25.5 - - + +
1209B ILE* 4.0 15.4 - - - +
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Residues in contact with LEU1195 (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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1191B GLU* 4.0 20.9 - - + +
1192B PHE* 3.0 15.8 + - + +
1194B VAL* 1.3 83.2 - - + +
1196B ARG* 1.3 57.6 + - - +
1208B ARG* 3.3 49.8 - - + +
1209B ILE* 3.5 1.6 - - - -
1210B TYR* 2.8 49.2 + - + +
1541B ASN* 3.3 32.5 - - + +
1542B ARG* 4.8 0.4 - - - -
1544B LEU 5.8 0.2 - - - +
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Residues in contact with ARG1196 (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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1189B LYS* 3.6 30.9 + - - +
1192B PHE* 2.7 22.7 + - - +
1193B GLU* 4.0 27.5 + - - +
1194B VAL 3.2 0.6 - - - -
1195B LEU* 1.3 75.9 - - - +
1197B GLY* 1.3 66.6 + - - +
1209B ILE* 3.8 4.5 - - - +
1210B TYR 3.1 7.6 - - - +
1211B ASP* 3.4 9.7 - - - +
1542B ARG* 3.0 82.9 + - + +
1543B HIS* 3.1 26.7 + - - +
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Residues in contact with GLY1197 (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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1164B LYS* 6.0 1.6 - - - -
1193B GLU 3.2 13.9 + - - +
1194B VAL 3.5 6.5 + - - -
1196B ARG* 1.3 85.9 - - - +
1198B ASP* 1.3 63.2 + - - -
1199B GLY 3.8 0.4 - - - -
1203B ARG* 6.0 0.2 - - - -
1209B ILE* 3.8 20.6 - - - -
1211B ASP* 5.0 0.2 - - - +
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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
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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