Contacts of the helix formed by residues 1155 - 1163 (chain A) in PDB entry 5JHN
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 GLY1155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1113A HIS* 4.6 0.8 + - - -
1153A ASP* 2.8 22.5 + - - -
1154A TYR* 1.3 80.7 - - - +
1156A ASP* 1.3 68.3 + - - -
1157A ARG 3.3 3.1 - - - -
1158A PHE* 3.2 12.8 + - - +
1159A TRP* 3.3 16.3 + - - -
1177A HIS* 5.3 0.2 - - - -
10F SER* 4.7 8.3 - - - -
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Residues in contact with ASP1156 (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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1153A ASP* 5.6 0.3 - - - +
1155A GLY* 1.3 69.1 - - - -
1157A ARG* 1.3 56.0 + - - +
1158A PHE 3.1 5.1 + - - -
1159A TRP* 4.2 4.7 - - - +
1160A ASP* 2.9 54.1 + - - +
1177A HIS* 3.3 26.7 + - - -
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Residues in contact with ARG1157 (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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1088A ASP* 3.6 22.8 + - - +
1091A ASN* 2.8 47.3 + - - +
1155A GLY 3.3 1.0 - - - -
1156A ASP* 1.3 74.3 - - - +
1158A PHE* 1.3 55.8 + - - +
1160A ASP* 4.8 3.6 - - - -
1161A ILE* 4.1 12.4 - - - +
4F LYS* 3.8 22.1 - - + +
6F THR 4.6 0.7 - - - +
7F ALA* 3.8 5.9 - - - -
8F ARG* 3.4 28.4 + - + +
10F SER* 3.7 23.3 + - - +
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Residues in contact with PHE1158 (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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1083A ASP 4.3 6.1 - - - -
1084A SER 4.5 7.9 - - - -
1086A LEU 5.6 0.4 - - - -
1154A TYR* 3.6 47.6 - + + +
1155A GLY 3.2 9.5 + - - +
1156A ASP 3.1 0.4 - - - -
1157A ARG* 1.3 77.8 - - - +
1159A TRP* 1.3 90.3 + + - +
1160A ASP 3.3 1.3 - - - -
1161A ILE* 3.2 6.6 + - - +
1162A LYS* 2.9 63.3 + - + +
1166A PHE* 4.0 3.6 - + - -
1205A SAM 3.6 22.4 - + - -
7F ALA* 3.9 13.6 - - + +
8F ARG 3.5 12.6 + - - +
9F ALA* 4.3 12.1 - - + -
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Residues in contact with TRP1159 (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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1113A HIS* 3.3 49.1 + + + -
1154A TYR* 4.4 0.2 - - - +
1155A GLY 3.3 22.7 + - - +
1156A ASP* 3.3 4.2 + - - +
1158A PHE* 1.3 94.6 - + - +
1160A ASP* 1.3 62.3 + - - +
1162A LYS* 4.1 1.1 - - + +
1163A SER* 2.7 53.1 + - - -
1166A PHE* 3.7 40.6 - + - -
1167A THR* 4.1 0.7 - - - -
1168A CYS* 3.7 34.8 - - + -
1177A HIS* 3.5 50.3 - + + +
1205A SAM 4.1 10.5 - + - -
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Residues in contact with ASP1160 (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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1156A ASP* 2.9 39.9 + - - +
1157A ARG* 5.0 2.9 - - - -
1159A TRP* 1.3 79.1 - - - +
1161A ILE* 1.3 65.2 + - + +
1163A SER* 4.2 6.2 + - - -
1164A LYS* 4.3 12.3 + - - +
1177A HIS* 5.9 1.0 - - - -
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Residues in contact with ILE1161 (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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1083A ASP* 4.1 7.2 - - - +
1157A ARG 4.1 10.5 + - - +
1158A PHE 3.2 7.4 + - - +
1159A TRP 3.1 0.2 - - - -
1160A ASP* 1.3 86.4 - - + +
1162A LYS* 1.4 65.7 + - + +
1163A SER 3.6 0.3 + - - -
1164A LYS* 3.7 18.4 - - - +
1165A TYR* 3.7 22.8 - - + -
4F LYS* 3.5 27.8 - - + +
5F GLN 4.3 7.6 - - - +
6F THR 3.4 28.0 - - - +
7F ALA* 3.8 21.5 - - + +
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Residues in contact with LYS1162 (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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1083A ASP* 2.9 44.7 + - - +
1084A SER* 2.9 26.2 + - - -
1158A PHE* 2.9 45.0 + - + +
1159A TRP* 3.2 2.2 + - + -
1161A ILE* 1.4 70.5 - - + +
1163A SER* 1.3 60.1 + - - +
1164A LYS 3.1 3.6 - - - -
1165A TYR* 2.8 34.4 + - + +
1166A PHE* 3.1 38.5 + - + +
1205A SAM 4.0 12.5 + - - -
7F ALA* 3.8 11.7 - - + -
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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
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1159A TRP* 2.7 34.8 + - - -
1160A ASP* 4.2 6.1 + - - -
1161A ILE 3.4 0.2 - - - -
1162A LYS* 1.3 77.2 - - - +
1164A LYS* 1.3 61.9 + - - +
1166A PHE 3.1 21.6 + - - +
1167A THR* 4.1 7.8 - - - +
1177A HIS* 5.9 0.7 - - - -
1182A ILE* 3.9 26.7 - - - +
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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