Contacts of the helix formed by residues 362 - 373 (chain A) in PDB entry 4WCX
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 SER 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A GLY* 4.9 1.3 - - - -
360A LYS 3.6 2.0 + - - -
361A ARG* 1.3 76.5 - - - +
363A PRO* 1.3 69.9 - - - +
364A ASN* 3.6 9.8 + - - +
365A GLU* 3.0 26.4 + - - +
366A ILE* 2.8 28.1 + - - +
368A ARG* 5.6 0.2 + - - -
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Residues in contact with PRO 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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125A MET* 3.4 55.2 - - + +
127A HIS* 4.6 4.7 - - + +
332A ALA* 4.2 17.7 - - + +
333A GLY* 4.0 7.6 - - - -
362A SER* 1.3 87.5 - - - +
364A ASN* 1.3 64.3 + - - +
366A ILE* 4.4 6.3 - - + -
367A LEU* 2.8 32.1 + - + +
379A TYR* 4.6 7.9 - - - +
417A PHE* 4.5 10.1 - - + -
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Residues in contact with ASN 364 (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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125A MET 5.8 0.8 + - - -
362A SER* 3.2 9.2 + - - +
363A PRO* 1.3 80.3 - - - +
365A GLU* 1.3 62.6 + - - +
367A LEU* 4.1 1.8 - - - +
368A ARG* 3.1 19.1 + - - +
417A PHE* 4.0 13.8 - - - -
421A TYR* 3.0 24.0 + - - +
422A GLY* 3.5 2.4 - - - -
423A ASP* 3.1 25.1 + - - +
426A THR* 2.5 53.2 + - + +
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Residues in contact with GLU 365 (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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361A ARG* 3.8 33.4 + - + +
362A SER* 3.0 21.0 + - - +
364A ASN* 1.3 74.9 - - - +
366A ILE* 1.3 63.3 + - - +
368A ARG* 3.3 26.8 + - - +
369A THR* 2.8 36.8 + - - +
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Residues in contact with ILE 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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312A THR* 5.7 0.2 - - + -
319A ARG* 4.2 4.7 - - - +
330A ILE* 4.0 24.9 - - + -
332A ALA* 3.6 30.7 - - + -
333A GLY 4.1 0.4 - - - +
359A ASP* 4.0 18.4 - - - +
361A ARG* 3.5 54.0 + - + +
362A SER 2.8 16.5 + - - +
363A PRO* 3.9 4.5 - - + +
365A GLU* 1.3 72.4 - - - +
367A LEU* 1.3 69.6 + - + +
369A THR* 3.4 2.3 + - - -
370A LEU* 3.0 31.9 + - + +
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Residues in contact with LEU 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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80A ILE* 3.9 33.0 - - + -
332A ALA* 5.3 0.2 - - + -
363A PRO* 2.8 32.4 + - + +
364A ASN* 4.1 3.4 - - - +
366A ILE* 1.3 80.2 - - + +
368A ARG* 1.3 58.8 + - - +
370A LEU* 3.4 4.7 + - + +
371A CYS* 2.9 34.1 + - - -
377A PRO* 3.9 19.4 - - + +
379A TYR* 3.5 24.2 - - + +
414A PHE* 3.7 27.8 - - + -
417A PHE* 3.7 20.4 - - + -
426A THR* 5.8 2.7 - - + -
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Residues in contact with ARG 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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364A ASN* 3.1 24.8 + - - +
365A GLU* 3.7 25.6 - - - +
367A LEU* 1.3 77.8 - - - +
369A THR* 1.3 57.2 + - - +
371A CYS* 3.3 7.6 + - - +
372A GLU* 2.9 44.6 + - - +
423A ASP* 3.5 15.0 + - - -
425A LYS* 4.0 15.2 - - - +
426A THR* 3.2 37.2 - - + +
429A ILE* 3.6 33.2 - - + -
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Residues in contact with THR 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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361A ARG* 3.1 30.3 + - - +
365A GLU* 2.8 23.8 + - - +
366A ILE 3.8 2.0 - - - -
368A ARG* 1.3 75.0 + - - +
370A LEU* 1.3 55.6 + - - +
372A GLU* 3.1 15.6 + - + +
373A GLN* 2.7 65.4 + - + +
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Residues in contact with LEU 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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78A ILE* 4.3 17.5 - - + -
80A ILE* 4.3 14.6 - - + -
320A GLU* 6.4 0.2 - - + -
323A ILE* 4.6 20.6 - - + -
330A ILE* 4.2 13.7 - - + -
366A ILE* 3.0 34.9 + - + +
367A LEU* 3.6 5.4 - - - +
369A THR* 1.3 76.7 - - - +
371A CYS* 1.3 61.0 + - - +
373A GLN* 3.1 19.8 + - - +
374A GLY 3.2 0.3 + - - -
375A TYR* 2.8 53.8 + - + +
377A PRO* 4.3 16.6 - - + -
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Residues in contact with CYS 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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367A LEU 2.9 18.0 + - - +
368A ARG* 3.4 4.3 - - - +
370A LEU* 1.3 77.2 - - - +
372A GLU* 1.3 63.7 + - - +
374A GLY* 3.0 15.2 + - - -
375A TYR 3.5 7.7 - - - +
377A PRO* 3.8 11.2 - - - -
414A PHE* 3.5 35.7 - - - -
429A ILE* 3.3 28.0 - - + -
430A GLY* 4.3 0.9 - - - -
433A ALA* 3.8 19.1 - - + +
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Residues in contact with GLU 372 (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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368A ARG* 2.9 33.9 + - - +
369A THR* 3.6 19.4 + - + +
371A CYS* 1.3 73.2 - - - +
373A GLN* 1.3 62.1 + - + +
374A GLY* 3.4 1.0 + - - -
429A ILE* 3.9 29.9 - - + +
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Residues in contact with GLN 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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316A PRO 5.6 0.6 + - - -
320A GLU* 3.6 29.4 - - - +
361A ARG* 5.4 0.7 + - - +
369A THR* 2.7 43.3 + - + +
370A LEU* 3.6 21.7 - - - +
371A CYS 3.1 0.4 - - - -
372A GLU* 1.3 75.6 - - + +
374A GLY* 1.3 58.1 + - - +
375A TYR* 3.5 21.8 + - + -
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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