Contacts of the helix formed by residues 1157 - 1165 (chain B) in PDB entry 1M8X
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 GLY1157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1116B MET 3.5 19.9 + - - -
1151B LEU* 3.4 23.4 - - - +
1154B TYR* 3.1 15.5 + - - +
1156B TYR* 1.3 76.5 - - - +
1158B LYS* 1.3 59.9 + - - +
1159B HIS 3.6 0.4 - - - -
1160B ILE* 3.9 11.7 - - - -
1161B LEU* 3.3 22.0 + - - +
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Residues in contact with LYS1158 (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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1154B TYR 3.4 4.9 + - - -
1155B THR* 3.1 44.8 + - - +
1156B TYR 2.7 3.8 + - - -
1157B GLY* 1.3 77.4 - - - +
1159B HIS* 1.3 75.8 + - + +
1161B LEU* 3.1 14.2 + - + +
1162B ALA* 3.1 24.1 + - + +
13D U 5.5 8.5 - - + +
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Residues in contact with HIS1159 (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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1123B TYR* 5.8 0.6 - + - -
1126B GLN* 3.6 19.1 + - - +
1156B TYR 3.7 2.4 + - - +
1158B LYS* 1.3 93.5 - - + +
1160B ILE* 1.3 57.9 + - - +
1161B LEU 3.1 1.6 - - - -
1162B ALA* 3.6 8.7 - - + +
1163B LYS* 2.7 37.4 + - - +
13D U 2.8 46.1 + + - +
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Residues in contact with ILE1160 (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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1116B MET* 3.4 49.8 - - + +
1122B ASN* 3.6 24.7 - - + +
1125B VAL* 4.0 11.7 - - + -
1126B GLN* 4.0 20.0 - - + +
1129B ILE* 5.2 5.1 - - + +
1144B ILE* 4.5 21.1 - - + -
1151B LEU* 4.6 13.4 - - + +
1156B TYR 4.7 0.2 - - - +
1157B GLY* 3.9 10.5 + - - +
1158B LYS 3.2 0.4 - - - -
1159B HIS* 1.3 77.9 - - - +
1161B LEU* 1.3 58.5 + - - +
1163B LYS* 4.2 6.1 - - - -
1164B LEU* 2.9 27.0 + - - +
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Residues in contact with LEU1161 (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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1148B ILE* 3.7 20.2 - - + -
1151B LEU* 3.4 21.5 - - + -
1152B ARG* 4.2 30.3 - - + -
1157B GLY 3.3 15.0 + - - +
1158B LYS* 3.1 18.4 + - + +
1160B ILE* 1.3 79.1 - - - +
1162B ALA* 1.3 57.4 + - - +
1164B LEU* 3.7 5.6 - - + +
1165B GLU* 2.9 40.7 + - + +
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Residues in contact with ALA1162 (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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1158B LYS 3.1 12.3 + - - +
1159B HIS* 3.8 11.2 - - + +
1161B LEU* 1.3 73.5 - - - +
1163B LYS* 1.3 56.3 + - - +
1164B LEU 2.9 4.7 - - - -
1165B GLU* 2.7 43.9 + - - +
1166B LYS* 3.8 3.6 + - - +
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Residues in contact with LYS1163 (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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1126B GLN* 4.3 24.2 - - + +
1129B ILE* 4.3 30.3 - - + +
1130B ASP* 2.7 38.2 + - - -
1137B ARG* 5.6 3.1 + - - +
1141B MET* 4.6 3.6 - - - +
1159B HIS* 2.7 24.1 + - + +
1160B ILE* 4.2 5.8 - - - -
1162B ALA* 1.3 73.1 - - - +
1164B LEU* 1.3 59.7 + - - +
1166B LYS* 3.5 23.4 - - + +
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Residues in contact with LEU1164 (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* 5.6 2.4 - - + +
1141B MET* 3.3 48.5 - - + +
1144B ILE* 4.5 29.4 - - + -
1145B ARG* 5.8 0.7 - - - +
1148B ILE* 6.0 7.9 - - + -
1151B LEU* 6.0 0.9 - - + -
1160B ILE 2.9 21.8 + - - +
1161B LEU* 3.7 8.3 - - + +
1162B ALA 2.8 0.4 + - - -
1163B LYS* 1.3 73.6 - - - +
1165B GLU* 1.3 56.5 + - + +
1166B LYS 2.5 18.6 + - - -
1167B TYR 3.3 8.7 + - - -
1168B TYR* 3.5 36.7 + - + -
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Residues in contact with GLU1165 (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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1161B LEU* 2.9 37.4 - - + +
1162B ALA* 2.7 24.6 + - - +
1164B LEU* 1.3 74.2 - - + +
1166B LYS* 1.3 62.0 + - - +
1167B TYR* 3.1 3.5 + - - -
1168B TYR* 4.1 11.7 + - + +
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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