Contacts of the helix formed by residues 1156 - 1166 (chain A) 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 TYR1156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1116A MET 3.7 6.6 - - - +
1117A LYS 3.6 17.0 + - - +
1118A ASP 3.6 13.5 - - - +
1119A GLN* 3.4 49.7 + - + +
1122A ASN* 3.8 5.1 - - - +
1154A TYR* 2.8 4.9 + - - +
1155A THR* 1.3 101.8 - - + +
1157A GLY* 1.3 65.7 + - - +
1158A LYS 3.1 2.2 - - - -
1159A HIS* 3.0 19.7 + - - +
1160A ILE* 3.5 4.3 + - - +
13C U 3.1 50.1 + + - -
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Residues in contact with GLY1157 (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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1116A MET 3.6 15.2 + - - -
1117A LYS* 4.4 0.2 - - - +
1151A LEU* 3.5 33.5 - - - +
1154A TYR* 2.9 14.2 + - - +
1156A TYR* 1.3 77.1 - - - +
1158A LYS* 1.3 54.7 + - - +
1160A ILE* 2.7 31.6 + - - +
1161A LEU 3.2 3.8 + - - -
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Residues in contact with LYS1158 (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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1151A LEU 3.2 4.1 + - - -
1152A ARG* 2.9 37.0 - - + +
1153A LYS* 4.8 3.1 - - - +
1154A TYR 3.0 21.4 + - - +
1155A THR* 4.0 13.4 - - - +
1157A GLY* 1.3 75.8 - - - +
1159A HIS* 1.3 57.0 - - + +
1161A LEU* 2.8 38.8 + - + +
1162A ALA* 3.2 5.7 + - - +
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Residues in contact with HIS1159 (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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1122A ASN* 4.4 0.4 - - - +
1126A GLN* 4.3 8.6 + - - +
1155A THR* 3.3 28.5 + - - +
1156A TYR* 3.0 12.5 + + - +
1158A LYS* 1.3 80.4 - - + +
1160A ILE* 1.3 61.8 + - - +
1162A ALA* 3.4 13.2 + - - +
1163A LYS* 3.3 18.4 + - - +
13C U 3.1 92.8 + + + +
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Residues in contact with ILE1160 (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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1116A MET* 3.8 46.0 - - + +
1122A ASN* 3.6 33.7 - - + +
1125A VAL* 4.2 14.4 - - + -
1126A GLN* 3.7 14.4 - - + +
1129A ILE* 5.4 3.6 - - + -
1144A ILE* 4.7 4.3 - - + -
1151A LEU* 4.3 9.0 - - + -
1156A TYR 3.5 3.1 + - - +
1157A GLY* 2.7 21.4 + - - +
1159A HIS* 1.3 70.0 - - - +
1161A LEU* 1.3 64.8 + - - +
1163A LYS* 3.0 8.4 + - + +
1164A LEU* 2.9 35.5 + - + +
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Residues in contact with LEU1161 (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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1148A ILE* 3.5 32.1 - - + +
1151A LEU* 4.0 12.1 - - + -
1152A ARG* 3.8 38.4 - - + +
1157A GLY 3.2 10.8 + - - +
1158A LYS* 2.8 16.5 + - + +
1160A ILE* 1.3 76.2 - - - +
1162A ALA* 1.3 63.8 + - - +
1164A LEU* 2.8 34.1 + - + +
1165A GLU* 3.1 14.6 + - - +
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Residues in contact with ALA1162 (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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1158A LYS 3.2 5.0 + - - +
1159A HIS* 3.4 18.2 - - - +
1161A LEU* 1.3 78.8 - - - +
1163A LYS* 1.3 62.5 + - - +
1165A GLU* 3.1 39.8 + - - +
1166A LYS* 3.9 2.4 + - - +
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Residues in contact with LYS1163 (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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1126A GLN* 3.7 48.7 + - + +
1129A ILE* 4.4 14.6 - - + -
1130A ASP* 2.8 44.3 + - - -
1159A HIS 3.3 3.9 + - - +
1160A ILE* 3.0 9.9 + - - +
1162A ALA* 1.3 79.7 - - - +
1164A LEU* 1.3 63.6 + - - +
1165A GLU 3.2 0.3 + - - -
1166A LYS* 3.0 40.5 + - - +
1167A TYR* 3.3 31.6 - - + -
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Residues in contact with LEU1164 (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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1129A ILE* 4.5 6.7 - - + -
1141A MET* 3.8 31.4 - - + -
1144A ILE* 4.0 34.8 - - + -
1148A ILE* 4.0 25.1 - - + -
1151A LEU* 4.7 0.4 - - + -
1160A ILE* 2.9 19.8 + - + +
1161A LEU* 2.8 29.7 + - + +
1163A LYS* 1.3 74.3 - - - +
1165A GLU* 1.3 65.0 + - - +
1167A TYR* 3.0 17.2 + - + +
1168A TYR* 3.2 16.1 + - + +
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Residues in contact with GLU1165 (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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1161A LEU 3.1 9.1 + - - +
1162A ALA* 3.1 28.5 + - - +
1164A LEU* 1.3 76.9 - - - +
1166A LYS* 1.3 55.3 + - - +
1167A TYR 2.8 10.7 + - - -
1168A TYR* 2.8 49.0 + - + +
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Residues in contact with LYS1166 (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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1130A ASP* 4.4 2.0 + - - -
1162A ALA 3.9 2.8 + - - +
1163A LYS* 3.0 43.8 + - - +
1165A GLU* 1.3 77.7 - - - +
1167A TYR* 1.3 88.9 + - + +
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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