Contacts of the helix formed by residues 1161 - 1165 (chain C) in PDB entry 3LW0
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 TYR1161 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086C ASP* 3.6 15.9 - - - -
1088C LYS* 3.7 36.2 - - + +
1089C SER* 2.7 41.1 + - - -
1092C ARG* 4.0 18.9 - - - -
1139C ARG* 3.9 26.0 - - + -
1156C MET* 3.9 24.7 + - + +
1159C ASP* 3.1 1.2 + - - +
1160C ILE* 1.3 105.9 - - + +
1162C GLU* 1.3 57.5 - - - +
1163C THR* 3.1 4.5 - - - +
1164C ASP* 2.9 39.6 + - - +
1165C TYR* 3.8 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156C MET 3.9 4.3 + - - -
1157C THR 3.3 25.7 - - - +
1158C ARG* 4.2 10.0 - - - +
1159C ASP 3.0 22.2 + - - +
1160C ILE* 3.4 4.1 - - - +
1161C TYR* 1.3 76.9 - - - +
1163C THR* 1.3 68.1 + - + +
1164C ASP 3.1 0.4 - - - -
1165C TYR* 3.2 29.0 + - - +
1173C LEU* 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1160C ILE 4.6 8.1 + - - +
1161C TYR* 3.1 1.1 - - - -
1162C GLU* 1.3 83.3 - - + +
1164C ASP* 1.3 65.2 + - - +
1165C TYR 3.1 12.6 + - - +
1177C ARG* 5.1 3.5 + - - -
1211C GLN* 4.9 14.2 + - - -
1218C ASN* 5.0 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088C LYS* 2.8 31.7 + - - +
1139C ARG* 2.9 43.4 + - - +
1161C TYR* 2.9 22.9 + - - +
1163C THR* 1.3 82.0 + - - +
1165C TYR* 1.3 60.4 + - + +
1175C PRO* 3.4 23.4 - - - +
1176C VAL* 4.3 2.8 + - - +
1177C ARG* 5.2 4.4 + - - +
1178C TRP* 3.6 18.0 - - + -
1211C GLN* 5.3 8.3 + - - +
1218C ASN* 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135C ASP* 2.6 36.7 + - - -
1139C ARG* 2.9 31.5 + - - -
1140C ASN* 3.6 3.8 + - - -
1156C MET* 3.9 20.7 + - - +
1157C THR* 3.8 34.3 - - + +
1161C TYR 3.8 7.4 - - - -
1162C GLU 3.2 20.0 + - - +
1163C THR* 3.1 7.3 - - - +
1164C ASP* 1.3 80.3 - - + +
1166C TYR* 1.3 60.8 + - - +
1173C LEU* 4.0 29.8 - - + +
1174C LEU 3.4 6.5 - - - +
1175C PRO* 3.8 25.6 - - + -
1176C VAL* 5.6 0.4 - - - -
1218C ASN* 4.5 6.8 + - - -
----------------------------------------------------------
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