Contacts of the helix formed by residues 354 - 363 (chain A) in PDB entry 2WSC
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 TRP 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ILE* 4.8 14.6 - - + +
75A SER* 3.1 41.1 - - - +
78A VAL* 3.9 16.4 - - + -
79A PHE* 5.8 3.1 - - + -
82A HIS* 5.9 0.9 - - - -
196A PHE* 4.2 5.4 - + + -
353A SER* 1.3 89.7 + - - +
355A HIS* 1.3 59.5 + - + +
356A ALA 2.9 0.2 - - - -
357A GLN* 2.5 15.1 + - - +
358A LEU* 2.4 38.7 + - - +
1761A CLA 3.2 57.4 - + + -
1769A CLA 5.7 7.2 - - + -
1780A CLA 3.1 62.9 - - + +
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Residues in contact with HIS 355 (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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63A ASP 3.7 15.2 + - - -
64A PHE* 4.7 6.6 - + + -
353A SER 3.1 6.8 + - - +
354A TRP* 1.3 77.9 - - + +
356A ALA* 1.3 61.3 + - - +
358A LEU* 3.4 12.2 - - + +
359A SER* 3.4 14.6 + - - -
413A HIS* 3.1 45.0 + + - +
416A ILE* 2.4 45.2 - - + +
417A PHE* 4.5 8.5 - - - +
420A ARG* 5.2 2.0 - - - -
421A ASP* 4.8 8.7 - - + -
1761A CLA 4.2 16.7 - - + +
1785A CLA 4.0 26.1 - - - +
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Residues in contact with ALA 356 (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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350A LEU* 4.7 8.7 - - + -
353A SER* 3.4 17.5 - - - +
354A TRP 2.7 6.7 + - - +
355A HIS* 1.3 72.6 - - - +
357A GLN* 1.3 58.6 + - - +
358A LEU 2.8 6.8 + - - -
359A SER* 3.1 10.4 + - - -
360A ILE* 3.0 20.4 + - - +
417A PHE* 3.1 37.5 - - + -
1805A BCR 4.2 17.7 - - + +
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Residues in contact with GLN 357 (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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350A LEU* 3.5 30.1 - - + +
354A TRP* 2.5 24.3 + - - +
356A ALA* 1.3 71.3 - - - +
358A LEU* 1.3 53.6 + - - -
360A ILE* 3.1 48.0 + - + +
361A ASN* 4.5 5.7 - - - +
1761A CLA 3.0 17.1 - - - +
1780A CLA 3.8 80.4 + - + +
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Residues in contact with LEU 358 (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 TRP 2.4 19.2 + - - +
355A HIS* 3.4 29.8 - - + +
357A GLN* 1.3 68.0 - - - +
359A SER* 1.3 71.7 + - - +
360A ILE 2.7 15.5 - - - +
361A ASN* 3.0 8.0 - - - +
362A LEU* 3.0 36.5 + - + +
413A HIS* 2.9 63.3 - - + +
1761A CLA 3.6 39.5 - - + -
1785A CLA 4.8 7.9 - - + -
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Residues in contact with SER 359 (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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355A HIS 3.4 10.1 - - - -
356A ALA* 3.1 4.6 + - - -
358A LEU* 1.3 83.2 - - - +
360A ILE* 1.3 63.4 + - - +
362A LEU 3.4 3.1 + - - -
363A ALA* 3.4 4.0 + - - +
410A ALA* 2.5 57.3 + - - +
413A HIS* 3.6 3.1 - - - -
414A ALA* 3.1 40.1 - - - +
1805A BCR 4.3 3.0 - - - +
1806A BCR 4.2 4.2 - - - +
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Residues in contact with ILE 360 (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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350A LEU* 4.9 2.7 - - + -
356A ALA 3.0 25.3 + - - +
357A GLN* 3.1 41.2 - - + +
358A LEU 2.7 10.0 - - - +
359A SER* 1.3 74.3 + - - +
361A ASN* 1.3 77.1 + - - +
363A ALA* 5.2 4.7 - - + -
364A MET* 4.1 8.1 - - + -
1776A CLA 4.2 2.2 - - + -
1780A CLA 3.7 33.7 - - + -
1805A BCR 3.4 60.8 - - + +
1806A BCR 5.4 2.5 - - + -
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Residues in contact with ASN 361 (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 GLN* 4.2 6.8 - - - +
358A LEU 3.0 6.3 - - - +
359A SER 3.6 0.4 + - - -
360A ILE* 1.3 93.3 - - - +
362A LEU* 1.4 58.6 + - - +
363A ALA 3.2 1.7 - - - +
364A MET* 2.5 15.8 + - - +
365A LEU* 2.4 39.1 + - - +
1761A CLA 2.3 59.1 - - - +
1780A CLA 2.5 37.9 - - + +
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Residues in contact with LEU 362 (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 LEU* 3.0 34.7 + - + +
359A SER 3.4 1.9 + - - +
361A ASN* 1.4 88.6 - - - +
363A ALA* 1.3 57.0 + - - +
365A LEU* 4.4 0.4 - - - -
366A GLY* 2.7 34.7 + - - +
406A LEU* 2.9 34.9 - - + +
407A ILE* 4.2 0.3 - - - +
409A GLY 3.7 3.6 - - - -
410A ALA* 3.1 30.1 - - + +
1761A CLA 4.0 0.9 - - - +
1785A CLA 3.4 62.4 - - + -
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Residues in contact with ALA 363 (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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359A SER 3.4 3.5 + - - +
360A ILE* 5.2 2.0 - - + -
361A ASN 3.2 2.4 - - - +
362A LEU* 1.3 74.0 - - - +
364A MET* 1.3 57.9 + - + +
367A SER* 2.6 39.0 + - - -
407A ILE* 3.8 7.6 - - - +
410A ALA* 2.8 17.6 - - + +
1776A CLA 5.1 4.3 - - + -
1806A BCR 3.7 49.7 - - + +
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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