Contacts of the helix formed by residues 1157 - 1166 (chain A) in PDB entry 5JQE
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 LEU1157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101A TYR* 4.9 0.7 - - + -
1104A MET* 4.3 20.0 - - + -
1152A LEU* 4.6 3.1 - - + -
1153A GLY 3.4 17.5 - - - +
1154A GLU 4.8 5.2 - - - +
1155A GLY* 3.8 6.2 + - - -
1156A LYS* 1.3 87.8 - - - +
1158A ASP* 1.3 59.3 + - - +
1159A ILE 3.3 2.7 - - - -
1160A LEU* 3.2 17.7 + - + -
1161A LYS* 2.7 50.7 + - + +
1175A ILE* 4.2 19.5 - - + -
1178A TYR* 4.3 18.4 - - + -
1179A GLU* 4.2 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156A LYS 3.9 0.4 - - - -
1157A LEU* 1.3 79.4 + - - +
1159A ILE* 1.3 65.9 + - + +
1161A LYS* 3.4 17.5 + - - +
1162A ARG* 3.2 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124A LEU* 3.6 30.5 - - + -
1127A GLU* 4.3 11.7 - - - +
1146A MET* 3.9 15.0 - - + -
1151A ILE* 3.5 48.4 + - + +
1157A LEU 3.3 0.4 - - - -
1158A ASP* 1.3 76.6 - - + +
1160A LEU* 1.3 63.5 + - - +
1162A ARG* 3.3 31.4 + - - +
1163A VAL* 3.3 17.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104A MET* 4.2 14.6 - - + -
1105A LEU* 4.0 14.6 - - + -
1108A ILE* 4.4 2.9 - - + -
1120A PHE* 4.5 7.4 - - + -
1143A PHE* 3.7 30.7 - - + -
1146A MET* 4.9 4.9 - - + +
1151A ILE 5.5 0.4 + - - -
1152A LEU* 3.6 31.1 - - + +
1156A LYS 5.5 0.2 + - - -
1157A LEU* 3.2 15.2 + - + +
1159A ILE* 1.3 79.9 - - - +
1161A LYS* 1.3 62.5 + - - +
1162A ARG 3.3 0.7 + - - -
1163A VAL* 3.5 2.7 + - - +
1164A CYS* 3.3 46.7 + - - -
1175A ILE* 3.7 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157A LEU* 2.7 38.0 + - - +
1158A ASP* 3.9 16.7 + - - +
1159A ILE 3.3 0.2 - - - -
1160A LEU* 1.3 74.3 - - - +
1162A ARG* 1.3 64.1 + - + +
1165A ALA* 3.6 8.7 + - - +
1172A LEU* 3.1 35.2 - - + +
1175A ILE* 3.8 33.7 - - + -
1176A ASN* 4.6 9.8 + - - +
1179A GLU* 3.3 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127A GLU* 2.4 42.4 + - - +
1158A ASP* 3.2 35.6 + - - +
1159A ILE* 3.7 22.4 - - - +
1160A LEU 3.2 0.4 - - - -
1161A LYS* 1.3 77.0 - - + +
1163A VAL* 1.3 66.3 + - + +
1165A ALA* 3.1 16.0 + - - +
1166A GLN* 3.3 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120A PHE* 3.4 52.3 - - + +
1123A GLY* 3.4 27.6 - - - +
1124A LEU* 3.9 22.4 - - + -
1127A GLU* 5.2 5.6 - - + +
1159A ILE* 3.3 17.0 + - + +
1160A LEU* 4.4 1.6 - - - +
1162A ARG* 1.3 78.4 - - + +
1164A CYS* 1.3 62.4 + - - +
1166A GLN* 3.4 17.0 + - - +
1167A ILE* 3.2 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108A ILE* 4.5 13.0 - - - -
1120A PHE* 4.5 11.7 - - - -
1160A LEU* 3.3 39.4 + - - +
1161A LYS 4.5 2.5 - - - +
1162A ARG 3.2 0.8 - - - -
1163A VAL* 1.3 73.3 - - - +
1165A ALA* 1.3 54.0 + - - +
1166A GLN 3.0 4.7 - - - -
1167A ILE* 3.0 17.8 + - - -
1168A ASN 2.6 27.1 + - - +
1171A LEU* 3.9 34.5 - - + +
1172A LEU* 4.6 4.9 - - + +
1175A ILE* 4.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1161A LYS 3.6 12.5 + - - +
1162A ARG* 3.1 11.3 + - - +
1164A CYS* 1.3 76.7 - - - +
1166A GLN* 1.3 61.0 + - + +
1167A ILE 3.4 0.2 - - - -
1168A ASN 4.3 4.9 - - - -
1169A LYS* 4.0 33.3 + - + +
1172A LEU* 4.4 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123A GLY* 4.0 25.7 + - - +
1126A GLU* 4.6 8.1 + - - -
1162A ARG* 3.3 28.8 - - - +
1163A VAL* 3.7 12.7 + - - +
1164A CYS 3.0 1.0 - - - -
1165A ALA* 1.3 80.9 - - + +
1167A ILE* 1.3 64.9 + - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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