Contacts of the strand formed by residues 184 - 188 (chain B) in PDB entry 3OPY
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 ILE 184 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LYS* 4.0 7.0 - - + +
183B THR* 1.3 76.1 - - - +
185B GLY* 1.3 64.3 + - - +
203B VAL* 4.1 15.3 - - + +
207B GLY* 4.2 16.4 - - - -
212B CYS* 3.7 26.5 - - - -
213B LYS 2.9 10.6 + - - +
214B VAL* 4.6 9.2 - - + -
215B PHE* 2.9 29.8 + - - +
277B ILE* 4.5 2.5 - - - -
279B ALA* 3.6 16.4 - - + +
281B ILE* 3.8 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ILE* 1.3 75.6 - - - +
186B VAL* 1.3 55.7 + - - -
215B PHE* 3.3 10.3 - - - -
217B ILE* 3.6 16.8 - - - -
277B ILE* 4.0 8.5 - - - +
279B ALA 2.8 15.0 + - - -
280B LEU* 3.5 4.7 - - - +
281B ILE* 2.8 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLY* 1.3 72.0 - - - -
187B MET* 1.3 61.1 + - - +
199B PHE* 4.2 9.4 - - + -
200B VAL* 4.5 14.6 - - + -
203B VAL* 3.6 41.1 - - + -
204B VAL* 4.6 0.4 - - + -
214B VAL* 3.8 15.3 - - + -
215B PHE 2.9 14.1 + - - +
216B CYS* 3.6 15.8 - - - -
217B ILE* 2.7 34.4 + - - +
251B ILE* 4.0 8.5 - - + +
281B ILE* 3.5 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B VAL* 1.3 78.8 - - - +
188B THR* 1.3 64.9 + - - +
189B SER* 3.8 17.9 - - - -
217B ILE* 3.8 28.0 - - + +
220B GLY* 3.8 15.0 - - - +
221B TYR* 3.7 61.7 - - + +
224B LEU* 4.2 12.3 - - - -
251B ILE* 4.7 3.6 - - - -
280B LEU* 4.7 4.5 - - + -
281B ILE 3.0 15.1 + - - +
282B VAL* 3.8 20.0 - - + -
283B CYS* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B MET* 1.3 79.3 - - - +
189B SER* 1.3 60.1 + - - +
196B MET* 3.9 19.5 - - + -
200B VAL* 4.1 20.2 - - + -
220B GLY* 3.4 20.8 - - - -
249B THR* 3.0 37.3 - - + +
251B ILE* 3.8 5.5 - - + +
252B GLY 3.1 14.4 + - - +
253B THR* 3.4 16.1 - - - +
283B CYS* 3.1 17.7 - - + +
----------------------------------------------------------
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