Contacts of the helix formed by residues 1141 - 1154 (chain A) in PDB entry 4E5W
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 SER1141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064A VAL* 4.6 4.3 - - - -
1139A ARG 3.9 0.6 + - - -
1140A THR* 1.3 87.9 + - - +
1142A PHE* 1.3 63.8 + - - +
1143A GLN* 3.5 8.4 + - - +
1144A ASN* 3.0 24.8 + - - +
1145A LEU* 3.1 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988A CYS* 3.8 36.5 - - - +
991A MET* 3.6 46.0 - - + -
992A ASP* 3.8 18.7 + - + +
1060A ILE* 4.5 13.9 - - + -
1063A ASP* 3.8 26.0 - - + -
1064A VAL* 3.6 25.3 - - + +
1067A PHE* 3.6 28.3 - + + -
1141A SER* 1.3 72.4 - - - +
1143A GLN* 1.3 57.7 + - - +
1145A LEU* 3.2 10.1 + - + +
1146A ILE* 3.0 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989A LYS* 5.8 0.6 - - - +
992A ASP* 2.7 34.7 + - - +
1141A SER* 3.3 8.1 + - - +
1142A PHE* 1.3 78.4 - - - +
1144A ASN* 1.3 59.5 + - - +
1146A ILE* 3.5 26.0 + - - +
1147A GLU* 3.2 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127A LEU* 4.8 5.9 - - - +
1130A LYS* 4.7 10.6 - - - +
1140A THR* 2.9 26.3 + - - +
1141A SER* 3.0 16.6 + - - +
1143A GLN* 1.3 73.2 - - - +
1145A LEU* 1.3 60.0 + - - +
1147A GLU* 3.5 15.3 + - - +
1148A GLY* 3.0 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988A CYS* 3.9 15.0 - - - -
1064A VAL* 4.2 5.8 - - + -
1067A PHE* 3.7 25.6 - - + -
1071A LEU* 5.8 0.2 - - + -
1127A LEU* 3.8 37.3 - - + +
1131A CYS* 3.9 14.6 - - - -
1140A THR* 3.7 15.3 - - + -
1141A SER 3.1 19.2 + - - +
1142A PHE* 3.2 16.6 + - + +
1144A ASN* 1.3 73.7 - - - +
1146A ILE* 1.4 58.9 + - - +
1148A GLY* 3.2 1.6 + - - -
1149A PHE* 2.9 55.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985A VAL* 4.2 13.4 - - + +
988A CYS* 3.6 21.5 - - + +
989A LYS* 3.8 42.6 - - + +
992A ASP* 4.7 0.2 - - + -
1142A PHE 3.0 22.5 + - - +
1143A GLN* 3.7 33.4 - - - +
1144A ASN 3.4 0.2 - - - -
1145A LEU* 1.4 74.0 - - - +
1147A GLU* 1.3 58.5 + - + +
1149A PHE* 3.9 5.5 - - - +
1150A GLU* 2.9 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143A GLN* 3.2 21.1 + - - +
1144A ASN* 3.7 18.0 + - - +
1145A LEU 3.3 0.2 - - - -
1146A ILE* 1.3 76.9 - - + +
1148A GLY* 1.3 57.2 + - - +
1150A GLU* 3.5 13.4 + - - +
1151A ALA* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127A LEU* 3.8 23.3 - - - +
1144A ASN* 3.0 14.8 + - - +
1145A LEU 3.2 3.1 + - - -
1147A GLU* 1.3 75.9 - - - +
1149A PHE* 1.4 60.4 + - - +
1151A ALA* 3.4 7.9 + - - +
1152A LEU* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981A LEU* 3.9 34.7 - - + +
984A ALA* 4.0 13.5 - - + -
985A VAL* 3.5 27.4 - - + -
988A CYS* 4.1 2.9 - - - -
1067A PHE* 3.8 28.0 - + - -
1071A LEU* 3.7 30.3 - - + -
1124A VAL* 4.7 3.8 - - + -
1127A LEU* 3.9 18.8 - - + -
1145A LEU* 2.9 49.0 + - + +
1146A ILE* 4.4 0.9 - - - -
1148A GLY* 1.4 69.4 - - - +
1150A GLU* 1.3 60.5 + - - +
1152A LEU* 3.0 11.5 + - + +
1153A LEU* 2.9 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985A VAL* 4.7 10.2 - - + +
989A LYS* 4.2 14.2 + - - -
1146A ILE* 2.9 42.9 + - + +
1147A GLU* 3.7 13.8 - - - +
1149A PHE* 1.3 74.3 - - - +
1151A ALA* 1.4 56.7 + - - +
1153A LEU* 3.3 13.1 + - + +
1154A LYS* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147A GLU 3.0 14.3 + - - +
1148A GLY* 3.5 11.2 - - - +
1150A GLU* 1.4 74.4 - - - +
1152A LEU* 1.3 65.2 + - + +
1153A LEU 3.5 0.2 + - - -
1154A LYS 3.6 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978A LYS* 5.3 0.2 + - - -
981A LEU* 4.2 16.1 - - + +
1123A GLU* 3.7 33.7 - - + +
1124A VAL* 3.9 26.7 - - + -
1127A LEU* 3.9 26.0 - - + -
1148A GLY 3.4 9.4 - - - +
1149A PHE* 3.0 10.6 + - + +
1151A ALA* 1.3 79.7 - - + +
1153A LEU* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978A LYS* 2.7 71.8 + - + +
981A LEU* 3.9 19.5 - - + +
982A LYS* 4.1 23.8 - - + -
985A VAL* 4.1 23.3 - - + -
1149A PHE 2.9 20.3 + - - +
1150A GLU* 3.3 10.5 + - + +
1152A LEU* 1.3 79.8 - - - +
1154A LYS* 1.4 67.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978A LYS* 5.1 2.0 - - - +
1150A GLU 3.0 14.1 + - - +
1151A ALA* 3.6 18.6 - - - +
1152A LEU 3.5 1.2 - - - -
1153A LEU* 1.4 86.6 - - - +
----------------------------------------------------------
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