Contacts of the strand formed by residues 365 - 373 (chain A) in PDB entry 3OM0
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 GLY 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A HIS* 4.8 13.0 - - - -
361A LYS* 3.4 15.1 - - - +
362A SER* 2.9 29.2 + - - +
364A GLN* 1.3 82.3 - - - +
366A HIS* 1.3 70.7 + - - +
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Residues in contact with HIS 366 (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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231A PRO* 4.0 22.6 + - + -
357A ARG* 4.6 10.9 + - - -
359A LEU* 3.8 43.0 - - + +
360A GLU 3.2 19.3 - - - +
361A LYS* 3.7 20.7 + - + +
362A SER* 3.1 6.4 + - - -
365A GLY* 1.3 76.8 - - - +
367A ARG* 1.3 89.5 + - - +
368A GLU 4.8 0.9 - - - -
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Residues in contact with ARG 367 (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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241A ASP 4.8 3.1 - - - -
359A LEU* 3.3 6.5 - - - -
360A GLU* 2.9 37.0 + - + +
362A SER* 4.0 16.7 + - - -
363A ARG* 3.2 35.3 - - - +
366A HIS* 1.3 92.6 + - - +
368A GLU* 1.3 66.0 + - - +
369A ILE* 3.6 7.5 + - + +
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Residues in contact with GLU 368 (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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357A ARG* 2.9 44.8 + - + +
358A ILE 3.4 7.4 - - - +
359A LEU* 3.7 10.2 - - + +
366A HIS* 4.8 1.2 - - - -
367A ARG* 1.3 74.8 - - - +
369A ILE* 1.3 62.9 + - - +
370A GLY 3.6 14.7 - - - +
371A VAL* 3.5 22.5 - - - +
401A GOL 5.1 3.7 + - - -
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Residues in contact with ILE 369 (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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246A LEU* 3.9 28.0 - - + -
358A ILE* 2.8 28.8 + - + +
359A LEU 4.5 2.0 - - - -
360A GLU* 4.0 24.9 - - + +
367A ARG* 4.1 7.9 - - + +
368A GLU* 1.3 77.9 - - - +
370A GLY* 1.3 57.7 + - - +
403A GOL 3.5 22.2 - - - +
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Residues in contact with GLY 370 (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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358A ILE* 2.8 36.4 + - - +
368A GLU* 3.6 8.8 - - - +
369A ILE* 1.3 80.6 - - - +
371A VAL* 1.3 70.1 + - - +
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Residues in contact with VAL 371 (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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132A ARG* 5.0 8.5 + - - -
355A THR* 3.6 31.4 - - + +
356A LEU 3.5 8.7 - - - +
357A ARG* 4.9 5.2 - - + -
358A ILE* 3.9 9.0 - - - +
368A GLU* 3.5 18.4 - - - +
370A GLY* 1.3 81.5 - - - +
372A TRP* 1.3 63.0 + - - +
373A TYR* 3.8 40.0 - - + +
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Residues in contact with TRP 372 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A ASP* 3.5 39.7 - - + -
128A LEU* 3.8 27.0 + - + +
129A ALA* 3.7 28.9 - - + -
132A ARG* 3.9 21.5 - - + +
354A TYR* 3.8 20.2 - + - -
355A THR* 3.2 8.1 - - - -
356A LEU* 2.9 60.2 + - + +
358A ILE* 3.9 12.7 - - + +
371A VAL* 1.3 73.2 - - - +
373A TYR* 1.3 69.6 + - - +
374A SER* 3.4 34.8 - - - -
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Residues in contact with TYR 373 (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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354A TYR 3.8 4.0 - - - +
355A THR* 3.6 24.2 - - + -
371A VAL* 3.8 34.6 - - + +
372A TRP* 1.3 91.0 + - - +
374A SER* 1.3 64.8 + - - +
375A ASN* 3.2 29.2 + - - +
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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