Contacts of the strand formed by residues 327 - 332 (chain A) in PDB entry 2OM5
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 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A ARG 4.7 2.4 + - - -
326A PRO* 1.3 72.3 - - - +
328A VAL* 1.3 69.1 + - - +
329A ARG* 3.5 6.6 + - + +
366A VAL 3.0 14.0 - - - +
367A ALA* 4.0 0.2 - - - -
368A GLU* 2.8 37.9 + - - +
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Residues in contact with VAL 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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299A TRP* 5.0 1.3 - - + -
318A CYS* 4.4 21.1 - - + +
319A ALA* 4.8 7.0 - - - -
320A ALA* 5.0 3.8 - - + +
326A PRO* 3.9 6.4 + - + +
327A THR* 1.3 78.5 - - - +
329A ARG* 1.3 72.8 - - - +
330A TRP* 4.1 4.3 - - - +
347A ALA* 3.0 31.7 - - + +
348A GLY* 3.6 22.9 - - - +
365A CYS* 4.2 15.7 - - + -
366A VAL 3.4 5.8 - - - +
367A ALA* 4.3 15.0 - - + +
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Residues in contact with ARG 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A THR* 4.6 8.3 - - + +
328A VAL* 1.3 76.8 - - - +
330A TRP* 1.3 77.6 + - - +
331A LEU* 4.2 22.4 - - - +
336A PRO* 4.3 23.8 - - - +
365A CYS* 3.6 1.0 - - - -
366A VAL* 2.6 54.0 + - + +
368A GLU* 3.2 27.1 + - - +
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Residues in contact with TRP 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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303A ILE* 3.9 37.0 - - + -
316A TRP* 4.4 4.7 - + + -
317A GLY 4.6 0.2 - - - -
318A CYS* 4.3 4.3 - - - -
328A VAL* 4.1 0.9 - - + +
329A ARG* 1.3 93.8 + - - +
331A LEU* 1.3 66.2 + - - +
336A PRO* 3.8 4.7 - - - +
337A LEU* 2.8 48.7 + - + +
345A VAL* 4.6 17.7 - - + -
347A ALA 3.5 22.9 + - - -
348A GLY* 3.9 14.9 - - - -
349A ASP 3.7 9.3 + - - +
350A LEU* 3.6 57.4 - - + -
363A TYR* 4.8 3.8 - + + -
364A GLN 3.3 24.5 - - - -
365A CYS* 4.1 16.4 - - + -
366A VAL 4.9 0.2 - - - +
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Residues in contact with LEU 331 (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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91A VAL* 3.7 30.1 - - + -
329A ARG* 4.2 10.5 - - - +
330A TRP* 1.3 78.0 - - - +
332A ARG* 1.3 60.7 + - - +
333A ASN 4.1 0.4 + - - -
334A GLY* 4.1 9.0 - - - +
335A GLU* 3.5 13.2 - - - +
336A PRO* 3.4 33.7 - - + -
337A LEU* 4.5 2.7 - - - -
363A TYR* 3.3 7.9 - - - +
364A GLN* 2.7 50.8 + - + +
366A VAL* 3.7 26.5 - - + -
375A TYR* 4.3 3.6 - - + -
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Residues in contact with ARG 332 (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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331A LEU* 1.3 71.7 - - - +
333A ASN* 1.3 89.1 + - - +
334A GLY 3.2 0.2 - - - -
335A GLU* 3.1 28.3 + - - +
337A LEU* 4.2 20.3 - - + +
358A GLU* 2.6 38.7 + - - +
359A ASP* 3.7 12.9 + - - +
360A SER 4.3 7.7 + - - +
361A GLY* 4.6 2.8 - - - +
362A MET 3.6 8.1 - - - +
363A TYR* 3.5 41.2 + - + -
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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