Contacts of the strand formed by residues 275 - 280 (chain B) in PDB entry 2OT7
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 TYR 275 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TRP* 3.7 6.0 - - + -
188B HIS* 3.3 27.4 - - - -
189B THR* 3.7 28.2 + - + +
210B SER* 3.4 5.4 + - - -
211B VAL* 2.9 35.4 + - + -
216B GLY* 3.7 33.7 - - - -
219B LEU* 3.5 29.8 - - + -
220B GLU* 2.7 35.0 + - + +
238B LEU* 3.5 28.7 - - + +
273B TYR* 3.6 11.7 + + - -
274B GLY* 1.3 71.8 - - - +
276B HIS* 1.3 58.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY 5.3 0.4 + - - -
44B LEU* 5.1 2.0 - - + -
185B PHE* 4.0 2.9 - + - -
186B ALA 3.3 3.3 - - - +
187B TRP* 3.3 6.6 - - - -
188B HIS* 3.0 48.6 + + - -
189B THR* 4.6 0.7 - - - -
190B GLU* 3.1 18.8 - - + -
208B TRP* 3.8 24.9 - + + -
209B TYR 3.0 16.6 - - - +
210B SER* 4.6 5.6 - - - +
270B THR* 3.5 24.8 - - + +
274B GLY 2.8 25.3 + - - -
275B TYR* 1.3 74.6 - - - +
277B ALA* 1.3 60.1 + - - +
500B OGA 3.2 8.1 + - - -
501B NI 2.2 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TRP* 6.4 2.0 - - + -
185B PHE* 3.2 28.2 - - - +
186B ALA* 4.5 0.4 - - - -
187B TRP* 3.5 42.5 - - + +
208B TRP* 3.4 4.2 - - - -
209B TYR* 2.8 32.2 + - + +
244B LEU* 6.0 0.9 - - + -
276B HIS* 1.3 74.3 - - - +
278B GLY* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B TYR* 4.2 3.3 + - - -
184B SER* 3.4 5.0 - - - -
185B PHE* 3.0 38.6 + - - +
207B SER 3.2 12.6 - - - -
209B TYR* 4.1 13.7 - - - -
277B ALA* 1.3 76.1 - - - +
279B PHE* 1.3 67.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 4.1 22.2 - + - -
117B LEU* 4.5 4.5 - - + -
118B GLU* 4.2 10.3 - - - -
121B TYR* 3.3 55.0 - + + +
181B TRP* 4.1 16.4 - + - -
182B LYS 5.0 0.2 - - - -
183B THR 3.1 14.1 - - - +
184B SER* 4.2 0.4 - - - +
185B PHE* 3.8 3.4 - - - -
206B LYS* 3.6 4.2 - - - +
207B SER* 2.9 42.4 + - - +
209B TYR* 3.9 24.0 - + - -
278B GLY* 1.3 79.8 - - - +
280B ASN* 1.3 74.8 + - - +
281B HIS* 3.9 18.1 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B TYR* 3.5 30.5 + - - -
179B GLY* 3.8 2.2 - - - -
180B MET 3.4 16.6 - - - +
181B TRP* 3.6 3.3 - - - -
182B LYS 3.1 26.2 + - - -
183B THR* 2.9 28.4 + - - +
185B PHE* 5.6 2.2 - - - -
205B PRO 3.8 1.8 - - - -
206B LYS* 3.0 25.5 + - - +
279B PHE* 1.3 78.9 - - - +
281B HIS* 1.3 62.0 + - - +
282B GLY 4.1 4.3 - - - +
284B ASN* 3.0 30.9 + - - +
----------------------------------------------------------
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