Contacts of the strand formed by residues 360 - 363 (chain B) 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 LYS 360 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ILE* 4.4 5.5 - - + +
144B TYR* 4.1 16.5 + - - +
146B VAL* 5.5 1.3 - - + -
239B ARG* 4.1 1.2 - - - +
293B GLU* 2.9 29.5 + - - -
326B PRO* 5.1 5.4 - - - -
327B LEU 3.3 4.2 + - - +
328B THR* 3.2 24.1 - - + +
329B VAL* 3.2 29.1 + - - +
354B PHE* 3.9 2.7 - - - -
358B ALA* 3.6 1.2 - - - +
359B ASP* 1.3 87.0 - - + +
361B VAL* 1.3 63.5 + - - +
397B GLN 3.3 26.0 - - - +
398B ALA* 3.4 8.5 - - - +
400B VAL* 3.9 15.4 - - + +
465B GLU* 2.7 33.5 + - + +
497B ILE* 5.3 0.2 - - - +
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Residues in contact with VAL 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B THR* 4.8 0.4 - - - -
329B VAL* 3.3 12.3 - - + +
333B ILE* 4.0 34.3 - - + -
350B ALA* 4.3 7.4 - - + -
353B TYR* 4.7 2.5 - - + -
354B PHE* 3.7 29.4 - - + -
360B LYS* 1.3 75.5 - - - +
362B SER* 1.3 59.7 + - - +
363B ILE* 4.8 4.0 - - + -
390B ILE* 4.1 26.7 - - + -
398B ALA 3.0 13.2 + - - +
399B VAL* 3.8 4.6 - - + +
400B VAL* 2.8 28.3 + - - +
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Residues in contact with SER 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B THR* 6.2 1.6 - - - -
297B LEU* 6.1 1.7 - - - +
328B THR* 4.6 7.6 - - - +
329B VAL 3.0 9.9 + - - -
330B GLY* 3.5 28.6 - - - -
331B GLY 3.8 7.4 + - - -
333B ILE* 4.4 5.0 - - - +
361B VAL* 1.3 73.2 - - - +
363B ILE* 1.3 64.0 + - - +
364B GLY 4.0 1.4 + - - -
400B VAL* 3.2 17.7 - - - +
402B SER* 3.2 30.5 + - - -
467B LEU* 4.5 7.0 - - - +
804B SO4 4.5 2.4 + - - -
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Residues in contact with ILE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ILE* 3.6 37.7 - - + +
361B VAL* 4.7 3.8 - - + +
362B SER* 1.3 78.9 - - - +
364B GLY* 1.3 63.0 + - - +
366B ASP* 4.0 14.8 - - + -
367B ALA* 3.6 25.6 - - + +
386B PRO* 4.4 15.5 - - + -
387B ILE* 4.6 12.8 - - + +
390B ILE* 4.4 6.3 - - + -
399B VAL* 4.0 24.2 - - + -
400B VAL 2.7 11.2 + - - +
401B ILE* 3.5 15.1 - - + +
402B SER 2.8 23.0 + - - +
804B SO4 4.6 2.5 - - - +
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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
------------------------------------------------------------
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