Contacts of the helix formed by residues 1151 - 1157 (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 SER1151 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C GDP 2.9 29.5 + - - -
1076C ASN* 5.9 0.2 - - - -
1080C SER* 4.8 0.2 - - - -
1149C ASN* 2.9 13.0 + - - -
1150C ASP* 1.3 78.4 - - - +
1152C ALA* 1.3 66.8 + - - +
1153C ALA 3.6 1.3 - - - -
1154C TYR* 3.3 11.0 + - - +
1155C TYR* 3.2 34.5 + - - -
1176C ARG* 2.9 33.2 + - - +
1178C ARG* 4.2 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080C SER* 3.5 30.2 - - - +
1084C ILE* 5.3 0.7 - - + -
1140C PHE* 5.2 1.8 - - + -
1148C LEU* 3.9 24.5 - - + -
1149C ASN* 3.1 20.1 + - - +
1150C ASP 3.5 0.2 - - - -
1151C SER* 1.3 79.6 - - - +
1153C ALA* 1.3 64.2 + - - +
1155C TYR* 3.4 2.1 + - - +
1156C LEU* 3.0 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131C TRP* 4.2 13.5 - - + -
1140C PHE* 3.8 29.4 - - + -
1150C ASP 5.3 1.4 - - - -
1152C ALA* 1.3 78.4 - - - +
1154C TYR* 1.3 65.0 + - - +
1157C ASN* 2.9 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1150C ASP 4.9 1.9 + - - +
1151C SER* 3.3 17.4 + - - +
1152C ALA 3.2 0.2 - - - -
1153C ALA* 1.3 81.1 - - - +
1155C TYR* 1.3 88.4 + + - +
1157C ASN* 4.5 1.1 - - - +
1158C ASP* 3.5 34.9 + - - +
1161C ARG* 4.2 2.1 + - - -
1170C THR* 4.5 0.3 + - - -
1172C GLN* 3.3 24.1 - - + +
1173C ASP* 2.6 41.1 + - - -
1176C ARG* 3.5 46.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073C VAL* 3.8 27.8 - - + -
1076C ASN* 4.1 23.3 - - + -
1077C THR* 3.2 29.4 - - + +
1080C SER* 5.6 0.4 - - - -
1151C SER* 3.2 27.5 + - - +
1152C ALA* 4.1 2.2 - - - +
1154C TYR* 1.3 101.8 - + - +
1156C LEU* 1.3 61.7 + - - +
1157C ASN 3.2 0.2 - - - -
1158C ASP* 2.8 22.9 + - + +
1159C LEU* 3.2 9.5 + - - -
1162C ILE* 3.9 16.7 - - + +
1173C ASP* 2.7 31.6 + - + -
1176C ARG* 3.1 31.3 - - + -
1177C THR* 3.1 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077C THR* 3.6 25.4 - - + +
1080C SER* 4.4 4.0 - - - -
1081C ILE* 4.3 21.8 - - + +
1084C ILE* 4.3 8.5 - - + -
1127C ILE* 3.6 30.5 - - + -
1128C LYS* 5.4 1.9 - - - +
1131C TRP* 3.6 61.8 - - + -
1152C ALA 3.0 24.5 + - - +
1155C TYR* 1.3 77.8 - - + +
1157C ASN* 1.3 60.9 + - - +
1158C ASP 3.4 0.7 + - - -
1159C LEU* 3.4 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131C TRP* 2.8 31.1 + - - +
1140C PHE* 6.3 0.2 - - - -
1153C ALA* 2.9 35.1 + - - +
1154C TYR 4.6 0.9 - - - +
1156C LEU* 1.3 75.7 - - - +
1158C ASP* 1.3 65.0 - - - +
1159C LEU 3.4 1.7 + - - -
1160C ASP* 5.3 0.5 + - - +
----------------------------------------------------------
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