Contacts of the helix formed by residues 1151 - 1163 (chain B) in PDB entry 1G24
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 ASN1151 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142B THR* 3.9 17.9 + - - +
1143B LEU* 4.6 1.5 - - - +
1144B LEU 3.7 7.6 - - - +
1145B ASN* 3.5 26.8 + - - +
1150B ILE* 1.3 71.1 - - - +
1152B LYS* 1.3 56.0 + - - +
1153B THR* 3.0 21.7 + - - +
1154B ALA* 2.8 44.0 + - + +
1155B PHE* 2.7 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1145B ASN* 5.2 0.2 - - - +
1150B ILE* 3.1 10.7 + - + +
1151B ASN* 1.3 73.3 + - - +
1153B THR* 1.3 57.2 + - - +
1155B PHE* 3.7 18.2 - - + -
1156B GLU* 2.8 53.6 + - + +
1230B LEU* 5.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A THR* 3.8 23.0 + - + +
1151B ASN* 3.0 20.6 + - - +
1152B LYS* 1.3 78.8 - - - +
1154B ALA* 1.3 57.7 + - - +
1156B GLU* 3.7 7.5 + - - +
1157B LYS* 3.1 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139B PHE* 3.2 12.9 - - + -
1142B THR* 3.4 34.1 - - + +
1143B LEU* 3.9 16.8 - - + -
1151B ASN* 2.8 23.5 + - + +
1153B THR* 1.3 76.3 - - - +
1155B PHE* 1.3 59.9 + - - +
1157B LYS* 3.0 10.4 + - - -
1158B ALA* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143B LEU* 4.6 1.3 - - - +
1150B ILE* 3.5 20.0 - - + -
1151B ASN 2.7 5.0 + - - +
1152B LYS* 3.5 14.6 - - + +
1154B ALA* 1.3 77.5 - - - +
1156B GLU* 1.3 74.9 + - - +
1158B ALA* 3.2 7.2 + - + +
1159B LYS* 2.9 35.0 + - + +
1228B MET* 3.6 35.0 - - + -
1229B ARG* 3.6 12.8 - - - -
1230B LEU* 3.7 39.0 - - + -
1237B ILE* 3.7 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1152B LYS* 2.8 46.0 + - + +
1153B THR* 3.9 7.6 - - - +
1154B ALA 3.2 0.2 - - - -
1155B PHE* 1.3 89.5 - - - +
1157B LYS* 1.3 61.8 + - + +
1159B LYS* 3.5 26.6 + - - +
1160B ALA* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138B GLU* 5.9 1.8 - - - +
1139B PHE* 3.8 15.9 - - + -
1142B THR* 5.6 7.7 - - + +
1153B THR* 3.1 32.1 - - + +
1154B ALA* 3.0 13.4 + - + +
1156B GLU* 1.3 77.0 - - + +
1158B ALA* 1.3 64.3 + - - +
1160B ALA* 3.6 4.7 + - - +
1161B LYS* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135B LEU* 3.6 33.7 - - + -
1139B PHE* 3.5 16.8 - - + -
1143B LEU* 5.6 0.2 - - + -
1154B ALA 2.9 7.8 + - - +
1155B PHE* 3.5 13.5 - - + +
1157B LYS* 1.3 75.5 - - - +
1159B LYS* 1.3 60.1 + - - +
1161B LYS* 3.2 4.1 + - - -
1162B PHE* 2.9 35.9 + - - +
1228B MET* 4.1 11.0 - - + -
1237B ILE* 5.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1155B PHE* 2.9 24.2 + - + +
1156B GLU* 3.6 29.1 + - - +
1158B ALA* 1.3 75.6 - - - +
1160B ALA* 1.3 60.9 + - - +
1163B LEU* 2.7 66.7 + - + +
1228B MET* 3.8 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156B GLU 3.1 15.1 + - - +
1157B LYS* 4.0 5.8 - - - +
1159B LYS* 1.3 80.5 - - - +
1161B LYS* 1.3 60.1 + - - +
1163B LEU* 4.7 1.7 + - - +
1165B LYS* 3.5 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135B LEU 2.9 20.7 + - - +
1136B GLY* 4.1 5.1 - - - -
1138B GLU* 2.7 31.1 + - - +
1139B PHE* 4.2 8.5 - - + -
1157B LYS 3.1 17.7 + - - +
1158B ALA* 3.5 5.2 - - - +
1159B LYS 3.0 0.8 - - - -
1160B ALA* 1.3 80.0 - - - +
1162B PHE* 1.3 87.4 - - + +
1165B LYS* 3.4 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135B LEU* 3.4 46.7 - - + -
1139B PHE* 5.1 0.2 - + - -
1158B ALA* 2.9 22.0 + - - +
1161B LYS* 1.3 113.0 - - + +
1163B LEU* 1.3 66.9 + - - +
1164B ASN 3.4 0.5 + - - -
1165B LYS* 3.3 20.5 + - - +
1167B ARG* 3.2 47.1 - - + -
1225B ILE* 3.4 33.7 - - + +
1228B MET* 4.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1159B LYS* 2.7 61.3 + - + +
1160B ALA* 5.1 1.3 - - - +
1162B PHE* 1.3 72.9 - - - +
1164B ASN* 1.3 95.7 + - - +
1165B LYS* 3.3 13.3 + - - +
1225B ILE* 4.2 4.9 - - + +
1226B ASP 3.6 29.8 - - - +
1227B ASP* 3.9 11.2 - - - -
1228B MET* 3.9 17.3 - - + +
----------------------------------------------------------
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