Contacts of the strand formed by residues 239 - 246 (chain A) in PDB entry 1OX4
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 ARG 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ILE* 3.6 33.4 + - - +
123A GLY* 4.4 9.8 - - - -
124A TRP* 4.5 17.3 - - + +
144A TYR* 5.0 3.8 - - - -
237A THR* 3.2 9.6 + - - +
238A ARG* 1.3 69.8 - - - +
240A ILE* 1.3 63.5 - - - +
241A ILE* 3.7 22.4 - - + +
292A ASP* 3.5 17.5 - - + -
293A GLU* 3.1 26.2 + - - +
465A GLU* 2.7 32.3 + - - -
495A PRO* 4.3 10.9 - - - +
497A ILE* 4.6 1.2 - - - +
512A PHE* 3.9 2.9 - - - -
518A ASP* 4.1 15.0 + - - +
519A ALA* 3.5 25.5 - - + +
520A CYS 2.9 28.2 + - - +
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ARG 3.6 13.9 - - - +
239A ARG* 1.3 79.7 - - - +
241A ILE* 1.3 62.5 + - - +
242A ALA 4.1 0.3 + - - -
291A ALA* 4.0 1.2 - - - -
292A ASP* 2.8 44.0 + - - +
293A GLU 3.8 0.3 + - - -
508A PHE* 3.8 38.8 - - + -
512A PHE* 3.8 14.6 - - + -
520A CYS 3.5 0.7 - - - -
526A PHE* 4.1 14.6 - - + -
533A VAL* 3.8 25.6 - - + -
536A VAL* 4.5 5.8 - - + -
537A LYS* 4.2 19.5 - - + -
540A LEU* 4.0 10.8 - - + -
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ARG* 3.7 34.1 - - + +
240A ILE* 1.3 78.3 - - - +
242A ALA* 1.3 62.3 + - - +
293A GLU* 3.7 33.4 - - + +
295A THR* 3.7 22.4 - - - +
497A ILE* 3.8 29.8 - - + -
519A ALA* 4.3 2.7 - - + -
520A CYS 2.7 16.0 + - - +
521A LEU* 3.2 16.9 - - + -
522A GLY 2.7 32.6 + - - +
526A PHE* 3.7 6.1 - - - -
533A VAL* 5.6 0.2 - - - -
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ILE 4.1 1.0 + - - -
241A ILE* 1.3 74.3 - - - +
243A CYS* 1.3 60.3 + - - +
286A TYR* 3.3 35.2 - - + -
291A ALA* 3.9 18.4 - - + +
293A GLU 3.1 7.0 + - - +
294A VAL* 3.3 6.7 - - + +
295A THR 2.9 23.0 + - - -
522A GLY 3.5 4.7 - - - -
526A PHE* 4.1 12.8 - - + -
533A VAL* 4.3 4.0 - - + -
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Residues in contact with CYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ALA* 1.3 74.8 - - - +
244A LEU* 1.3 67.4 + - - +
245A ASP* 6.2 0.2 - - - -
286A TYR* 3.8 9.7 + - - -
295A THR* 3.3 19.1 - - - +
297A LEU* 3.5 38.1 - - - -
467A LEU* 6.4 0.2 - - - -
521A LEU* 3.7 35.0 - - + -
522A GLY 3.0 7.8 + - - +
523A ALA* 3.5 27.6 - - + +
527A HIS* 5.5 0.5 - - - +
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A CYS* 1.3 77.1 - - - +
245A ASP* 1.3 65.6 + - - +
246A VAL* 4.6 0.2 - - + -
256A VAL* 4.0 9.0 - - + -
279A PRO* 3.6 36.6 - - + +
282A LEU* 3.8 27.6 - - + -
283A ALA* 4.5 3.8 - - + -
286A TYR* 3.9 16.2 - - + +
294A VAL* 3.5 31.2 - - + -
295A THR 2.9 11.5 + - - +
296A PHE* 3.5 21.1 - - + -
297A LEU* 2.9 24.9 + - - +
523A ALA* 5.7 0.4 - - - -
527A HIS* 6.4 0.4 - - + -
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Residues in contact with ASP 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A LEU* 1.3 77.0 - - - +
246A VAL* 1.3 64.8 + - - +
247A ARG* 3.6 17.4 + - - +
256A VAL* 3.4 46.2 - - + +
297A LEU* 3.3 33.4 - - - +
299A ILE* 3.6 22.0 - - + +
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A LEU* 4.5 1.6 - - + +
245A ASP* 1.3 78.7 - - - +
247A ARG* 1.3 61.3 + - - +
254A LEU* 4.0 19.5 - - + -
255A VAL 3.7 2.7 - - - -
279A PRO* 4.2 16.4 - - + -
296A PHE* 4.0 27.1 - - + -
297A LEU 2.9 13.6 + - - +
298A ASN* 4.4 1.1 - - - -
299A ILE* 3.0 25.1 + - - +
300A THR* 3.3 22.6 - - + +
312A MET* 3.8 31.4 - - + -
315A VAL* 4.7 2.2 - - + -
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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