Contacts of the strand formed by residues 262 - 266 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D ILE* 4.4 5.4 - - + -
53D LYS* 3.7 32.1 - - + +
109D THR* 2.7 31.9 + - - +
137D TRP* 4.5 9.4 - - + -
138D ALA 3.0 14.8 - - - +
140D THR* 3.5 5.9 + - - +
257D TRP* 3.6 18.1 - - + -
258D ASP 2.9 18.2 + - - +
259D ASN* 3.8 2.9 + - - +
260D ARG 5.2 0.2 - - - -
261D ALA* 1.3 85.9 - - - +
263D GLN* 1.3 64.8 + - - +
264D HIS* 5.0 0.2 + - - -
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Residues in contact with GLN 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D TRP* 3.5 22.4 - - + +
108D HIS 3.2 13.8 + - - +
109D THR* 3.2 17.7 - - - +
137D TRP* 3.3 4.2 - - - +
138D ALA* 2.9 27.5 + - + -
140D THR* 4.0 8.4 - - + +
210D LEU 5.1 0.2 + - - -
212D LEU* 3.7 10.1 - - - +
213D GLY* 3.4 20.2 - - - +
235D GLN* 2.8 42.4 + - - -
238D VAL* 3.7 26.3 - - + +
262D THR* 1.3 77.3 - - - +
264D HIS* 1.3 66.9 + - - +
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Residues in contact with HIS 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D SER 3.5 0.9 - - - +
107D TRP* 3.6 3.9 - - - -
108D HIS* 2.9 52.0 + + - -
110D ASP* 3.0 24.5 - - - -
135D THR* 4.5 3.4 - - + -
136D VAL 3.1 14.6 - - - +
137D TRP* 3.6 20.9 - - + +
257D TRP* 3.6 23.8 + + - -
259D ASN* 4.1 4.8 + - - -
262D THR* 5.0 0.2 + - - -
263D GLN* 1.3 79.2 - - - +
265D TYR* 1.3 64.3 + - - +
1300D AKG 2.7 34.4 + - + -
1302D FE2 2.0 27.8 - - - -
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Residues in contact with TYR 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ARG* 4.4 8.1 + - - +
241A LEU* 3.5 31.2 + - + +
242A GLU* 2.6 40.1 + - - -
104D ALA 3.8 5.8 - - - -
105D ASN* 3.5 22.9 + - + +
106D SER* 3.6 5.8 - - - -
107D TRP* 3.5 57.0 - + + -
108D HIS* 5.0 0.4 - - - -
135D THR* 3.4 5.7 - - - +
136D VAL* 2.9 29.1 + - + +
264D HIS* 1.3 79.6 - - - +
266D ALA* 1.3 72.5 + - - +
267D VAL* 3.8 6.4 + - + -
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Residues in contact with ALA 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ARG* 5.8 1.5 - - + +
104D ALA* 2.9 30.5 + - + +
105D ASN* 3.0 26.3 + - - +
108D HIS* 5.5 0.4 - - - -
134D ASP 3.8 6.3 - - - +
135D THR* 4.4 2.2 - - - +
265D TYR* 1.3 74.3 - - - +
267D VAL* 1.3 63.2 + - - +
268D ASP* 3.5 0.9 + - - +
270D TYR* 6.4 0.7 - - + -
275D ARG* 4.6 7.0 - - - +
1300D AKG 3.6 32.0 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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