Contacts of the helix formed by residues 1155 - 1162 (chain B) in PDB entry 1M7N
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 ARG1155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004B GLN 5.5 2.2 - - - -
1083B ASP* 3.4 15.7 - - + +
1086B SER* 3.2 33.7 + - - -
1136B ARG 5.2 1.6 + - - -
1153B MET 3.1 7.4 + - - +
1154B THR* 1.3 84.2 - - - +
1156B ASP* 1.3 64.2 + - - +
1157B ILE* 3.0 45.4 + - + +
1158B TYR* 3.2 28.0 + - + +
1159B GLU 4.4 1.2 + - - -
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Residues in contact with ASP1156 (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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1004B GLN* 4.2 29.0 + - + +
1154B THR 3.4 3.9 + - - -
1155B ARG* 1.3 71.4 + - - +
1157B ILE* 1.3 88.1 + - - +
1158B TYR 3.1 2.0 + - - -
1159B GLU* 3.1 33.1 + - - +
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Residues in contact with ILE1157 (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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1086B SER* 5.6 0.2 - - - -
1089B ARG* 5.8 0.4 - - - +
1155B ARG* 3.0 51.0 - - - +
1156B ASP* 1.3 95.1 + - - +
1158B TYR* 1.3 92.0 + - + +
1159B GLU* 3.4 7.2 + - - +
1160B THR* 4.1 9.0 - - - +
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Residues in contact with TYR1158 (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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1083B ASP* 3.3 19.1 - - - -
1085B LYS* 3.3 39.4 - - + -
1086B SER* 2.7 38.7 + - - -
1089B ARG* 3.8 21.3 - - - -
1136B ARG* 4.1 27.1 - - + -
1154B THR* 4.8 1.3 - - + -
1155B ARG* 3.2 28.6 + - + +
1156B ASP 3.1 1.6 - - - -
1157B ILE* 1.3 104.6 - - + +
1159B GLU* 1.3 50.9 + - - +
1160B THR* 2.8 13.2 - - + +
1161B ASP* 2.5 36.4 + - - +
1162B TYR* 3.8 6.5 - - - -
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Residues in contact with GLU1159 (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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1155B ARG 4.4 0.6 + - - -
1156B ASP* 3.1 24.2 + - - +
1157B ILE* 4.6 6.0 - - - +
1158B TYR* 1.3 77.2 - - - +
1160B THR* 1.3 68.9 + - - +
1162B TYR* 2.9 37.3 + - - +
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Residues in contact with THR1160 (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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1089B ARG* 5.9 1.3 - - - +
1157B ILE 4.1 6.3 - - - +
1158B TYR* 3.8 18.2 - - + +
1159B GLU* 1.3 85.8 - - - +
1161B ASP* 1.3 73.4 + - - +
1162B TYR 3.1 8.4 + - - +
1174B ARG* 5.5 4.0 + - - -
1208B GLN* 4.7 14.2 + - - +
1215B ASN* 5.2 4.3 - - - +
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Residues in contact with ASP1161 (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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1085B LYS* 3.4 25.4 + - - -
1136B ARG* 3.0 39.7 + - - +
1158B TYR* 2.5 24.8 + - - +
1160B THR* 1.3 78.7 - - - +
1162B TYR* 1.3 58.1 + - + -
1172B PRO* 3.6 18.7 - - - +
1173B VAL* 4.6 2.7 + - - +
1174B ARG* 5.2 5.3 + - - +
1175B TRP* 3.4 23.4 - - + -
1208B GLN* 3.3 22.9 + - - -
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Residues in contact with TYR1162 (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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1132B ASP* 2.7 35.9 + - - -
1136B ARG* 2.8 37.1 + - - -
1137B ASN* 3.7 4.2 + - - -
1154B THR* 4.0 15.9 + - + +
1158B TYR 3.8 14.8 - - - -
1159B GLU* 2.9 20.2 + - - +
1160B THR* 3.7 7.3 - - - +
1161B ASP* 1.3 81.6 - - - +
1163B TYR* 1.3 63.7 + - - +
1170B LEU* 4.4 28.0 - - + -
1171B LEU 3.7 4.3 - - - +
1172B PRO* 3.8 25.4 - - + -
1173B VAL* 5.5 0.7 - - - -
1215B ASN* 4.7 2.8 + - - +
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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