Contacts of the strand formed by residues 1173 - 1176 (chain B) in PDB entry 2O8C
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 VAL1173 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B MET* 3.2 33.0 - - + -
734B VAL 3.4 7.4 + - - +
735B LEU* 4.3 3.4 - - + -
736B ASP* 3.9 5.2 - - - +
739B THR* 2.7 44.6 + - + +
743B LEU* 4.3 8.3 - - + -
1148B GLY* 4.9 2.2 - - - +
1151B ALA* 4.8 2.0 - - + -
1152B VAL* 5.4 0.2 - - + -
1170B ILE* 4.0 11.2 - - + -
1172B ARG* 1.3 81.4 - - - +
1174B PHE* 1.3 57.0 + - - +
1175B THR* 4.1 11.9 - - + -
1209B LEU* 3.4 23.6 - - + +
1211B LEU* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B ASP* 4.6 4.7 - - - -
739B THR* 3.7 1.6 - - - -
1172B ARG* 3.3 59.9 - - + -
1173B VAL* 1.3 75.7 - - - +
1175B THR* 1.3 64.2 + - - +
1199B SER* 4.0 4.9 - - - -
1200B ILE* 3.7 48.9 - - + -
1203B HIS* 3.6 12.8 - - + -
1204B ALA* 3.6 40.4 - - + -
1208B SER* 3.9 11.7 - - - -
1209B LEU 2.8 13.4 + - - +
1210B VAL* 3.5 3.8 - - + +
1211B LEU* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738B VAL* 3.6 17.3 - - - +
739B THR* 3.2 40.8 + - + -
742B ASN* 3.1 23.6 + - - +
743B LEU* 4.0 15.3 - - + -
1173B VAL* 4.1 1.6 - - + -
1174B PHE* 1.3 79.0 - - - +
1176B ARG* 1.3 63.9 + - - +
1177B LEU* 3.9 5.8 - - + -
1196B GLU* 4.6 3.8 - - - +
1200B ILE* 4.8 6.6 - - - +
1211B LEU* 3.4 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742B ASN* 4.1 1.0 - - - +
1175B THR* 1.3 73.8 - - - +
1177B LEU* 1.3 92.4 + - - +
1178B GLY 3.5 18.4 + - - +
1189B THR 5.6 0.4 + - - -
1192B VAL* 6.3 0.6 - - - +
1193B GLU* 3.3 50.0 + - + +
1196B GLU* 3.3 30.4 + - + -
1197B THR* 3.9 13.9 - - - +
1200B ILE* 4.8 4.9 - - + -
1211B LEU 2.8 7.5 + - - -
1212B VAL* 3.9 31.9 - - + -
1213B ASP* 2.7 35.2 + - - +
1215B LEU* 5.0 2.5 - - + -
1217B ARG* 3.1 24.3 - - - +
----------------------------------------------------------
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