Contacts of the helix formed by residues 1170 - 1176 (chain C) in PDB entry 2OM2
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 THR1170 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1066C CYS* 4.5 3.4 - - - -
1154C TYR* 4.5 0.2 + - - -
1161C ARG* 3.4 18.4 + - - +
1168C ILE 4.1 6.3 - - - +
1169C PRO* 1.3 77.5 - - - +
1171C GLN* 1.3 69.0 + - - +
1172C GLN* 3.4 7.4 + - - +
1173C ASP* 3.0 35.3 + - - +
1174C VAL* 3.2 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055C ILE* 3.2 46.7 - - + +
1060C GLY* 4.9 1.2 - - - -
1061C TYR* 4.0 36.3 + - - +
1066C CYS* 4.9 2.4 - - - -
1170C THR* 1.3 78.5 - - - +
1172C GLN* 1.3 66.2 + - - +
1174C VAL* 3.2 12.3 + - - +
1175C LEU* 3.3 12.5 + - + +
1329C THR* 5.8 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1154C TYR* 3.3 27.8 - - + +
1170C THR* 3.4 5.5 + - - +
1171C GLN* 1.3 82.9 - - - +
1173C ASP* 1.3 65.7 + - - +
1175C LEU* 2.9 35.3 + - - +
1176C ARG* 3.0 20.5 + - + +
1327C THR* 2.8 31.7 + - - +
1329C THR* 4.7 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073C VAL* 4.9 1.1 - - + -
1154C TYR* 2.6 36.7 + - - -
1155C TYR* 2.7 30.1 + - + -
1161C ARG* 2.6 42.1 + - - -
1162C ILE* 5.0 0.4 - - - -
1167C TYR* 3.0 25.4 + - - +
1169C PRO* 4.1 3.8 - - + -
1170C THR* 3.0 26.8 + - - +
1171C GLN 3.3 0.2 - - - -
1172C GLN* 1.3 75.7 - - - +
1174C VAL* 1.3 62.7 + - - +
1176C ARG 3.3 2.9 + - - -
1177C THR* 3.3 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051C LYS* 3.4 5.3 + - + +
1061C TYR* 3.7 36.1 - - + +
1066C CYS* 3.9 22.2 - - - -
1069C TYR* 3.7 36.1 - - + -
1169C PRO* 4.2 12.8 - - + -
1170C THR 3.2 16.4 + - - +
1171C GLN* 3.2 7.1 + - - +
1172C GLN 3.1 0.6 - - - -
1173C ASP* 1.3 73.8 - - - +
1175C LEU* 1.3 65.1 + - - +
1177C THR* 2.6 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C GDP 4.6 4.6 + - - -
1048C THR* 3.9 19.7 + - + +
1051C LYS* 2.6 50.1 + - + +
1052C GLN* 3.3 38.6 - - + +
1055C ILE* 3.5 29.6 - - + +
1061C TYR* 6.2 0.2 - - - -
1171C GLN* 3.3 4.6 + - + +
1172C GLN* 2.9 35.5 + - - +
1174C VAL* 1.3 78.6 - - - +
1176C ARG* 1.3 59.9 + - + +
1177C THR 3.7 0.7 - - - +
1327C THR* 3.8 9.6 - - + +
1329C THR* 3.8 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C GDP 3.1 51.0 + - - -
1150C ASP 3.0 26.8 + - - -
1151C SER* 2.9 29.8 + - - +
1154C TYR* 3.5 44.8 - - + +
1155C TYR* 3.1 24.6 + - + +
1172C GLN* 3.0 22.0 + - + +
1173C ASP 3.6 3.1 - - - +
1174C VAL 3.1 0.2 - - - -
1175C LEU* 1.3 74.5 - - + +
1177C THR* 1.3 63.7 + - - +
1178C ARG* 3.8 1.7 + - - +
1272C ASP* 5.2 0.6 + - - -
1327C THR* 3.6 25.4 + - - +
----------------------------------------------------------
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