Contacts of the strand formed by residues 265 - 271 (chain A) in PDB entry 3OEH
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 HIS 265 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU* 4.3 10.2 + - - -
163A ARG* 4.1 10.7 - - - +
197A GLU 4.2 2.9 + - - -
198A SER* 3.1 39.3 + - - -
200A LYS 3.7 15.3 + - - +
201A LEU* 3.4 15.2 - - + -
202A TYR* 2.8 26.7 + - - -
259A PHE* 4.6 1.5 - - - +
263A GLY 4.3 5.6 + - - -
264A LYS* 1.3 88.1 + - - +
266A ALA* 1.3 61.9 + - - +
313A LYS* 4.2 9.6 - - - -
320A SER 3.4 25.8 - - - -
321A GLY* 4.0 1.3 - - - -
322A SER* 2.7 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 3.6 5.7 - - - +
202A TYR 3.2 13.0 - - - +
204A VAL* 4.9 3.1 - - + -
256A GLY* 4.0 13.9 - - - +
259A PHE* 3.7 29.8 - - + -
265A HIS* 1.3 76.0 - - - +
267A LEU* 1.3 62.1 + - - +
322A SER* 3.2 6.4 + - - +
323A LEU* 3.4 13.2 - - + +
324A THR* 3.0 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 4.7 8.5 - - + -
184A THR* 3.6 28.3 - - + -
185A ILE* 4.2 13.0 - - + +
188A GLN* 5.2 0.4 - - + -
201A LEU* 3.7 21.0 - - + +
202A TYR 2.8 10.8 + - - +
203A CYS* 3.5 18.1 - - - -
204A VAL* 2.8 34.5 + - - +
266A ALA* 1.3 73.6 - - - +
268A ILE* 1.3 56.1 + - - +
269A VAL* 4.6 5.6 - - + -
324A THR* 3.4 32.8 - - + +
326A LEU* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 3.2 18.6 - - + +
206A VAL* 3.7 15.5 - - + -
252A ALA* 3.8 7.9 - - + +
253A ALA* 3.7 24.5 - - - +
256A GLY* 5.4 1.3 - - - -
267A LEU* 1.3 75.2 - - - +
269A VAL* 1.3 65.3 + - - +
270A TYR* 3.4 43.5 + - + +
323A LEU* 4.0 21.5 - - + -
324A THR 2.7 20.2 + - - +
325A ALA* 3.3 12.6 - - + +
326A LEU* 2.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA* 3.6 29.6 - - + -
185A ILE* 3.9 29.8 - - + -
204A VAL 2.8 12.5 + - - +
205A TYR* 3.9 20.9 - - + -
206A VAL* 2.8 31.5 + - - +
267A LEU* 4.6 5.8 - - + -
268A ILE* 1.3 76.4 - - - +
270A TYR* 1.3 62.7 + - - +
271A ASP* 3.7 9.3 + - + +
326A LEU* 3.4 26.0 - - + +
328A VAL* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL* 3.6 19.5 - - + -
208A VAL* 5.5 0.7 - - + -
249A PRO* 3.6 29.2 - - + -
253A ALA* 3.5 13.2 - - - +
268A ILE* 3.4 32.8 - - + +
269A VAL* 1.3 70.2 - - - +
271A ASP* 1.3 57.4 + - - +
272A ASP* 3.2 7.1 - - - -
273A LEU* 3.5 21.5 - - + -
307A LEU* 3.3 32.1 + - + +
308A LEU* 3.7 31.2 - - + -
311A ALA* 6.2 0.2 - - - +
323A LEU* 5.0 3.6 - - - +
325A ALA* 4.1 13.9 - - + +
326A LEU 3.3 7.5 + - - -
327A PRO* 4.1 12.8 - - + -
328A VAL* 2.7 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LYS* 5.8 0.2 - - - -
178A THR* 2.7 32.4 + - - +
205A TYR* 2.7 36.1 + - + +
206A VAL* 2.9 15.9 + - - +
208A VAL* 3.3 13.5 + - - +
210A GLN* 2.7 34.5 + - - +
269A VAL* 3.7 2.9 + - + +
270A TYR* 1.3 73.0 - - - +
272A ASP* 1.3 63.0 + - - +
328A VAL* 3.8 20.9 - - + +
----------------------------------------------------------
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