Contacts of the helix formed by residues 364 - 376 (chain A) in PDB entry 3CVW
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 HIS 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A LYS* 4.8 2.7 - - - -
249A THR* 3.0 35.9 + - - -
250A ALA 3.2 20.4 - - - -
251A PRO* 3.3 30.2 + - + +
257A SER* 3.2 17.1 + - - -
258A THR* 3.7 23.4 - - - +
356A GLN* 5.0 1.8 + - - -
362A TRP* 3.6 19.2 - + + -
363A ILE* 1.3 74.0 - - - +
365A ASN* 1.3 69.6 + - + +
366A LEU* 3.1 24.6 + - + -
367A ALA* 3.0 5.4 + - + +
368A ARG* 2.8 34.7 + - - +
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Residues in contact with ASN 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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246A LYS* 3.5 28.3 - - - +
364A HIS* 1.3 76.5 + - + +
366A LEU* 1.3 59.0 + - - +
368A ARG* 3.1 4.6 + - - +
369A HIS* 2.9 46.2 + - - -
521A FAD 2.9 53.6 + - - +
8C 64T 2.7 39.1 + - - +
9C 5PY 4.0 8.3 + - - -
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Residues in contact with LEU 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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246A LYS* 4.5 2.7 - - + +
247A PRO* 4.0 15.0 - - + +
249A THR 3.5 23.8 - - - +
251A PRO* 3.6 20.9 - - + -
364A HIS* 3.1 10.6 + - + +
365A ASN* 1.3 77.5 - - - +
367A ALA* 1.3 60.6 + - - +
369A HIS* 3.3 20.0 - - + +
370A ALA* 3.1 21.1 + - - +
423A TYR* 4.3 0.7 - - - +
428A PHE* 3.6 32.2 - - + -
9C 5PY 3.7 49.6 - - + +
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Residues in contact with ALA 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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251A PRO* 3.5 28.5 - - + +
349A PHE* 5.4 0.2 - - - -
353A ILE* 3.4 45.7 - - + +
363A ILE* 4.4 3.8 - - + -
364A HIS 3.0 20.3 + - - +
366A LEU* 1.3 77.8 - - - +
368A ARG* 1.3 61.2 + - - +
370A ALA* 3.6 0.4 + - - -
371A VAL* 3.4 19.1 + - - +
438A TYR* 5.0 1.6 - - - +
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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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362A TRP* 3.1 28.7 - - - +
363A ILE* 2.7 34.4 + - + +
364A HIS 2.8 14.8 + - - +
365A ASN 3.3 6.3 - - - +
367A ALA* 1.3 74.1 - - - +
369A HIS* 1.3 59.8 + - - +
371A VAL* 3.3 9.7 - - - +
372A ALA* 3.0 32.1 + - - +
391A PHE* 3.9 15.2 - - + -
395A LEU* 3.5 15.4 - - - +
397A ASP* 2.7 31.7 + - - -
521A FAD 3.1 78.5 + - + +
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Residues in contact with HIS 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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365A ASN* 2.9 38.6 + - - +
366A LEU* 3.3 18.3 - - + +
367A ALA 3.2 0.2 - - - -
368A ARG* 1.3 74.3 - - - +
370A ALA* 1.3 59.0 + - - +
372A ALA 3.3 0.3 + - - -
373A CYS* 2.9 34.6 + - - +
406A ASN* 5.7 0.8 + - - -
409A TRP* 4.6 1.1 - + - -
410A LEU* 3.5 35.3 - - + +
423A TYR* 2.8 29.5 + - + -
521A FAD 3.6 14.6 - - + +
8C 64T 3.2 25.2 + - - -
9C 5PY 3.6 27.1 - + + -
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Residues in contact with ALA 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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349A PHE* 3.7 30.7 - - + -
350A ILE* 3.6 10.2 - - + +
353A ILE* 4.0 3.6 - - + -
366A LEU 3.1 12.9 + - - +
367A ALA 3.9 5.8 - - - +
368A ARG 3.4 0.2 - - - -
369A HIS* 1.3 79.1 - - - +
371A VAL* 1.3 58.8 + - - +
373A CYS* 3.8 1.7 + - - +
374A PHE* 3.2 27.0 + - - +
423A TYR* 4.6 16.1 - - + +
425A PRO* 6.0 1.3 - - + -
428A PHE* 4.3 8.7 - - + -
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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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340A TRP* 3.2 23.6 + - + +
350A ILE* 3.8 31.2 - - + +
353A ILE* 3.7 29.6 - - + -
354A MET* 3.9 15.0 - - - -
363A ILE* 4.7 0.2 - - + -
367A ALA 3.4 8.9 + - - +
368A ARG* 3.3 17.0 - - - +
370A ALA* 1.3 76.5 - - - +
372A ALA* 1.3 62.6 + - - +
374A PHE* 3.5 4.1 + - - +
375A LEU* 3.1 24.9 + - - +
391A PHE* 3.9 18.8 - - + -
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Residues in contact with ALA 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 3.0 20.9 + - - +
369A HIS 3.8 1.1 - - - +
371A VAL* 1.3 75.4 - - - +
373A CYS* 1.3 57.3 + - - +
376A THR* 2.7 38.9 + - - +
407A TRP* 3.5 29.1 - - + -
410A LEU* 3.8 24.4 - - + +
521A FAD 3.9 12.3 - - + -
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Residues in contact with CYS 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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369A HIS 2.9 17.5 + - - +
370A ALA 4.0 3.1 - - - +
372A ALA* 1.3 75.0 - - - +
374A PHE* 1.3 60.8 + - - +
376A THR* 3.3 10.8 + - - -
377A ARG* 3.8 24.5 - - - -
378A GLY* 2.7 31.9 + - - +
410A LEU* 4.3 13.1 - - + +
422A VAL* 3.8 12.1 - - - -
423A TYR* 3.6 43.5 - - + -
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Residues in contact with PHE 374 (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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340A TRP* 4.0 14.1 - + - -
345A THR* 4.1 18.8 - - + -
347A TYR* 3.6 39.7 - + + -
350A ILE* 4.1 16.8 - - + -
370A ALA 3.2 17.2 + - - +
371A VAL* 3.7 4.5 - - - +
372A ALA 3.4 0.2 - - - -
373A CYS* 1.3 80.3 - - - +
375A LEU* 1.3 58.9 + - - +
378A GLY* 4.4 0.2 - - - -
379A ASP* 2.9 44.5 + - + +
380A LEU* 2.9 49.6 + - + -
423A TYR 5.9 1.1 + - - -
425A PRO* 4.1 16.8 - - + -
480A ILE* 5.0 1.1 - - + -
481A VAL* 4.0 13.0 - - + -
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Residues in contact with LEU 375 (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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337A LEU* 4.2 5.6 - - + -
340A TRP* 3.6 37.7 - - + +
371A VAL 3.1 16.8 + - - +
372A ALA 4.2 1.8 - - - +
374A PHE* 1.3 77.7 - - - +
376A THR* 1.3 56.8 + - + +
380A LEU* 3.3 12.7 - - + +
381A TRP 3.2 6.9 + - - -
382A ILE* 2.8 59.6 + - + +
383A SER 4.0 11.0 - - - +
387A GLY* 3.7 34.5 - - - +
407A TRP* 3.7 17.9 - - + -
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Residues in contact with THR 376 (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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330A TRP* 3.5 17.3 - - + -
372A ALA 2.7 23.2 + - - +
373A CYS* 3.3 6.4 + - - -
375A LEU* 1.3 77.4 - - + +
377A ARG* 1.3 66.1 + - - -
378A GLY 3.0 9.8 + - - -
379A ASP 3.6 2.8 + - - -
381A TRP* 3.0 23.6 + - - -
382A ILE 3.4 19.5 - - - +
384A TRP* 3.8 31.9 - - + +
407A TRP* 4.0 8.5 - - + -
410A LEU 3.9 0.3 + - - -
411A SER* 3.6 20.4 - - - -
490A ASN* 4.0 0.2 + - - -
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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