Contacts of the strand formed by residues 254 - 258 (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 VAL 254 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 3.8 23.1 - - + -
55D ILE 3.9 0.2 - - - +
56D PHE* 3.4 5.1 - - - +
57D PHE* 2.8 38.6 + - + +
60D GLN* 3.7 27.1 - - + -
63D LEU* 3.9 18.4 - - + -
68D GLN* 6.3 0.2 - - - -
122D ILE* 3.9 23.6 - - + -
123D LEU 3.2 9.6 - - - +
124D ARG* 4.1 11.2 - - + -
249D TRP* 4.3 2.2 - - - -
252D GLY 4.0 0.7 - - - +
253D ASP* 1.3 80.3 - - - +
255D ALA* 1.3 65.8 + - - +
256D ILE* 4.4 3.6 - - + -
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Residues in contact with ALA 255 (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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54D VAL* 4.3 1.8 - - + -
55D ILE 3.3 4.3 - - - +
56D PHE* 3.8 20.2 - - + -
121D SER 3.8 0.7 - - - +
122D ILE* 3.4 1.9 - - - -
123D LEU* 2.8 33.7 + - - +
137D TRP* 3.9 20.4 - - + -
249D TRP* 3.5 24.0 - - + -
254D VAL* 1.3 73.9 - - - +
256D ILE* 1.3 63.3 + - - +
257D TRP* 4.1 6.0 - - + -
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Residues in contact with ILE 256 (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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33D LEU* 4.9 0.7 - - + -
45D ILE* 4.5 1.3 - - + -
49D LEU* 3.3 25.0 - - + +
54D VAL* 3.4 1.4 - - - +
55D ILE* 2.8 43.9 + - + -
57D PHE* 3.6 32.1 - - + -
71D PHE* 3.7 33.4 - - + -
75D LEU* 4.0 13.0 - - + -
120D ALA* 4.8 4.7 - - + -
121D SER 3.3 12.3 - - - +
122D ILE* 3.9 15.5 - - + -
254D VAL* 4.4 5.8 - - + -
255D ALA* 1.3 79.9 - - - +
257D TRP* 1.3 65.3 + - - +
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Residues in contact with TRP 257 (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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49D LEU* 3.6 5.8 - - - -
53D LYS 3.3 11.2 - - - +
54D VAL* 3.8 5.6 - - + -
110D ASP* 3.4 16.7 + - - -
120D ALA* 3.2 26.3 - - - +
121D SER* 3.2 37.3 + - - -
123D LEU* 3.6 39.0 - - + -
137D TRP* 3.2 47.8 - + + +
255D ALA* 4.1 8.7 - - + -
256D ILE* 1.3 77.0 - - - +
258D ASP* 1.3 59.5 + - - +
259D ASN* 3.7 13.1 + - + +
262D THR* 3.6 19.1 - - - +
264D HIS* 3.6 24.1 - + - -
279D ARG* 5.1 0.7 - - - -
1300D AKG 3.6 17.9 - - + -
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Residues in contact with ASP 258 (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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49D LEU* 3.6 22.5 - - + +
50D VAL* 4.0 18.6 - - - +
53D LYS* 2.8 20.9 + - + +
119D LYS 3.4 5.1 - - - +
120D ALA* 4.6 1.1 - - - -
202D HIS* 2.8 26.3 + - - -
257D TRP* 1.3 68.5 - - - +
259D ASN* 1.3 52.7 + - - +
260D ARG* 3.0 41.9 + - - +
261D ALA* 3.2 13.2 + - - +
262D THR* 2.9 24.5 + - - +
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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