Contacts of the strand formed by residues 262 - 266 (chain A) in PDB entry 1OIK
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 THR 262 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 4.5 5.2 - - + -
53A LYS* 3.7 33.9 - - + +
109A THR* 2.8 32.7 + - - +
137A TRP* 4.6 6.3 - - + -
138A ALA 3.0 15.5 - - - +
140A THR* 3.5 7.6 + - - +
211A GLN* 5.5 0.7 + - - -
257A TRP* 3.5 21.4 - - + -
258A ASP 2.9 18.6 + - - +
259A ASN* 3.8 3.1 + - - +
260A ARG 3.8 0.2 - - - -
261A ALA* 1.3 85.8 - - - +
263A GLN* 1.3 65.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TRP* 3.5 23.2 - - + +
108A HIS 3.1 12.6 - - - +
109A THR* 3.3 18.2 - - - +
137A TRP* 3.2 4.0 - - - -
138A ALA* 2.8 28.5 + - + +
140A THR* 4.0 8.9 - - + +
212A LEU* 3.6 12.1 - - - +
213A GLY* 3.3 21.3 - - - +
235A GLN* 2.9 41.1 + - - -
238A VAL* 3.7 23.5 - - + +
262A THR* 1.3 76.7 - - - +
264A HIS* 1.3 67.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A SER 3.5 0.5 - - - +
107A TRP* 3.6 4.4 - - - -
108A HIS* 2.9 54.4 + + - -
110A ASP* 2.9 30.0 + - - -
135A THR* 4.5 2.7 - - + -
136A VAL 3.0 13.9 - - - +
137A TRP* 3.6 21.5 - - + +
257A TRP* 3.6 24.9 + + - -
259A ASN* 4.1 4.6 + - - -
263A GLN* 1.3 78.7 - - - +
265A TYR* 1.3 65.1 + - - +
1301A AKG 3.1 26.3 + - + -
1302A FE2 2.1 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA 3.8 5.6 - - - -
105A ASN* 3.6 29.3 + - + +
106A SER* 3.7 5.6 - - - -
107A TRP* 3.5 55.6 - + + -
108A HIS* 5.0 0.2 - - - -
135A THR* 3.3 5.9 - - - -
136A VAL* 2.9 31.3 + - + +
264A HIS* 1.3 79.9 - - - +
266A ALA* 1.3 66.5 + - - +
267A VAL* 3.8 9.0 + - + -
240D ARG* 4.5 5.9 + - - +
241D LEU* 3.6 30.3 + - + +
242D GLU* 2.7 39.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
103A ARG* 5.1 0.8 - - - -
104A ALA 2.9 27.5 + - - +
105A ASN* 3.0 26.0 + - - +
108A HIS* 5.5 0.4 - - - -
134A ASP 3.8 5.2 - - - +
135A THR* 4.5 0.4 - - - +
265A TYR* 1.3 73.4 - - - +
267A VAL* 1.4 61.5 + - - +
268A ASP* 3.5 1.0 + - - +
270A TYR* 6.5 0.9 - - + -
275A ARG* 4.7 6.3 - - - +
1301A AKG 3.7 38.0 - - + +
----------------------------------------------------------
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