Contacts of the strand formed by residues 326 - 330 (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 PRO 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A TRP* 4.3 3.4 - - + -
144A TYR* 3.3 49.8 - - + +
196A LYS* 3.7 13.9 - - + +
292A ASP 3.3 14.6 - - - +
293A GLU* 3.5 16.5 - - + +
294A VAL 3.1 24.1 + - - -
325A VAL* 1.3 92.6 - - + +
327A LEU* 1.3 62.6 + - - +
359A ASP* 3.4 18.2 - - + +
360A LYS* 5.1 3.8 - - - -
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LYS* 3.1 17.0 - - - +
294A VAL* 3.3 8.7 - - + +
296A PHE* 4.1 24.5 - - + -
316A LEU* 4.1 24.5 - - + +
319A ALA* 4.3 11.2 - - + -
320A ALA* 4.4 8.1 - - - +
323A VAL* 4.0 19.5 - - + +
325A VAL 2.8 29.8 - - - +
326A PRO* 1.3 74.6 - - - +
328A THR* 1.3 62.3 + - - +
357A GLY 3.8 19.3 - - - +
358A ALA* 4.0 4.2 - - - -
359A ASP* 2.9 32.4 + - - +
360A LYS 3.3 5.4 + - - -
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Residues in contact with THR 328 (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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293A GLU* 3.4 9.3 + - - +
294A VAL 2.8 7.2 + - - -
295A THR* 3.2 26.9 - - + +
296A PHE* 2.6 38.6 + - - -
327A LEU* 1.3 76.2 + - - +
329A VAL* 1.3 64.7 + - - +
358A ALA* 5.4 0.2 - - - -
360A LYS* 3.2 45.4 - - + +
362A SER* 4.6 12.1 - - - -
400A VAL* 4.7 10.3 - - + -
467A LEU* 6.6 0.2 - - + -
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PHE* 3.3 9.2 - - + +
298A ASN* 4.4 9.2 - - + -
312A MET* 4.1 19.7 - - + -
316A LEU* 4.3 10.5 - - + -
328A THR* 1.3 80.1 - - - +
330A GLY* 1.3 62.6 + - - +
331A GLY 5.0 1.6 - - - +
333A ILE* 4.4 5.0 - - + +
353A TYR* 3.9 33.2 - - + -
358A ALA* 3.7 24.9 - - + -
360A LYS 3.2 6.0 + - - +
361A VAL* 3.3 14.2 - - + +
362A SER 3.0 19.3 + - - -
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Residues in contact with GLY 330 (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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295A THR* 5.2 0.6 - - - +
296A PHE 2.9 9.8 + - - -
297A LEU* 3.6 13.2 - - - +
298A ASN* 2.8 25.8 + - - +
328A THR* 4.3 0.6 - - - +
329A VAL* 1.3 75.2 - - - +
331A GLY* 1.3 61.4 + - - -
362A SER* 3.5 25.5 - - - -
801A SO4 4.9 0.9 - - - -
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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