Contacts of the helix formed by residues 362 - 375 (chain B) in PDB entry 4WVD
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 ILE 362 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348B LEU* 6.5 0.4 - - + -
349B GLU* 6.5 1.3 - - - -
358B SER 4.0 2.8 + - - +
359B ASP* 2.6 30.1 + - + +
361B TYR* 1.3 71.9 - - - +
363B THR* 1.3 60.2 + - + +
365B MET* 3.0 7.6 + - - +
366B PHE* 2.7 45.6 + - + -
505B IVM 5.0 8.7 - - + -
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Residues in contact with THR 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B ASP* 2.9 22.2 + - + +
360B GLU* 4.9 0.7 - - - -
362B ILE* 1.3 72.9 - - + +
364B PRO* 1.3 61.7 - - - +
365B MET 2.7 5.7 + - - -
366B PHE* 2.7 29.5 + - + +
367B SER* 2.7 22.3 + - - +
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Residues in contact with PRO 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B PHE* 4.0 7.7 - - - -
360B GLU* 3.7 22.7 - - - +
361B TYR 4.8 2.2 - - - +
362B ILE 4.1 0.2 - - - -
363B THR* 1.3 97.5 - - - +
365B MET* 1.3 55.3 + - - +
367B SER* 4.6 5.8 - - - +
368B PHE* 3.1 24.5 + - - +
443B PHE* 5.6 1.1 - - + -
446B HIS* 4.1 26.7 - - + +
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Residues in contact with MET 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B PHE* 3.5 38.6 - - + +
332B SER* 3.8 16.2 - - - +
333B ALA 5.1 0.4 - - - -
336B PHE* 3.3 31.9 - - + -
361B TYR 3.3 14.3 + - - +
362B ILE* 3.0 10.4 + - - +
363B THR 2.7 5.5 + - - -
364B PRO* 1.3 76.1 - - - +
366B PHE* 1.3 72.1 + - + +
367B SER 3.5 0.2 - - - -
368B PHE* 3.7 2.8 - - + +
369B TYR* 3.0 33.4 + - - -
505B IVM 3.1 42.2 - - + +
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Residues in contact with PHE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B PHE* 4.4 17.3 - + - -
344B HIS* 4.7 3.4 - + - -
345B SER* 3.3 46.4 - - - -
348B LEU* 4.1 17.7 - - + -
349B GLU* 5.6 6.5 - - + -
362B ILE* 2.7 29.5 + - + +
363B THR* 2.7 15.7 + - + +
365B MET* 1.3 83.5 - - + +
367B SER* 1.3 67.2 + - - +
369B TYR* 3.3 23.4 - + + -
370B LYS* 3.3 19.6 + - - +
505B IVM 5.7 4.7 - - + -
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Residues in contact with SER 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B THR* 2.7 22.3 + - - +
364B PRO* 4.6 5.1 + - - +
366B PHE* 1.3 71.5 - - - +
368B PHE* 1.3 66.6 + - - +
370B LYS* 3.1 14.9 + - - +
371B SER* 3.1 13.7 + - - -
439B GLU* 4.4 7.8 + - - -
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Residues in contact with PHE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B PHE* 3.9 24.9 - + + -
330B LEU* 4.1 12.8 - - + -
333B ALA* 3.5 24.7 - - + -
364B PRO 3.1 23.7 + - - +
365B MET* 3.5 6.7 + - + +
366B PHE 3.3 0.8 - - - -
367B SER* 1.3 78.8 + - - +
369B TYR* 1.3 68.7 + - + +
371B SER* 2.6 24.0 + - - -
372B ILE* 3.0 36.4 + - + +
436B ARG* 4.2 12.6 - - + -
439B GLU* 4.1 23.3 - - + +
440B LEU* 3.2 35.7 - - + -
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Residues in contact with TYR 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ALA* 3.6 29.2 - - + -
336B PHE* 3.3 53.2 - + + -
337B ASN* 3.4 15.1 + - - +
343B GLY* 5.1 11.8 + - - -
345B SER* 5.4 4.9 + - - -
365B MET* 3.0 27.8 + - - +
366B PHE* 3.3 33.4 - + + -
368B PHE* 1.3 77.1 - - + +
370B LYS* 1.3 64.5 + - + +
372B ILE* 3.2 12.2 - - - +
373B GLY 2.8 20.8 + - - -
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Residues in contact with LYS 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B PHE 3.3 12.3 + - - +
367B SER* 3.1 11.4 + - - +
368B PHE 3.1 0.8 - - - -
369B TYR* 1.3 84.8 - - + +
371B SER* 1.3 65.5 + - - +
372B ILE 3.1 1.3 - - - -
373B GLY* 2.9 12.2 + - - -
374B GLU* 3.0 19.1 + - - +
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Residues in contact with SER 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B SER* 3.1 8.6 + - - -
368B PHE* 2.6 21.7 + - - -
370B LYS* 1.3 75.8 - - - +
372B ILE* 1.3 60.3 + - - +
374B GLU* 3.5 22.5 - - - +
375B LEU* 3.3 5.7 - - - +
436B ARG* 3.0 26.9 + - - -
439B GLU* 2.9 36.1 + - - -
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Residues in contact with ILE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B LEU* 4.7 5.8 - - + -
333B ALA* 3.6 15.5 - - + -
337B ASN* 3.2 22.4 - - - +
368B PHE* 3.0 36.5 + - + +
369B TYR* 3.2 7.2 - - - +
371B SER* 1.3 77.0 + - - +
373B GLY* 1.3 66.1 + - - +
375B LEU* 3.2 26.2 - - + +
376B LYS 3.8 1.9 + - - -
377B MET* 3.4 30.9 + - + +
382B TYR* 3.4 12.8 + - + +
385B LEU* 5.5 4.7 - - + -
433B LEU* 6.0 1.6 - - + -
436B ARG* 3.6 33.0 - - + -
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Residues in contact with GLY 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B ASN* 3.8 21.3 - - - -
369B TYR 2.8 15.5 + - - -
370B LYS* 2.9 7.0 + - - -
372B ILE* 1.3 73.9 - - - +
374B GLU* 1.3 65.9 + - - +
376B LYS* 2.9 22.4 + - - +
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Residues in contact with GLU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B LYS 3.0 15.8 + - - +
371B SER* 3.5 21.1 + - - +
373B GLY* 1.3 71.2 - - - +
375B LEU* 1.3 59.4 + - + +
376B LYS* 2.9 34.3 + - - +
436B ARG* 3.7 15.9 + - - +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B SER 3.3 22.4 - - - +
372B ILE* 3.2 23.6 - - + +
373B GLY 3.0 0.4 + - - -
374B GLU* 1.3 73.7 - - + +
376B LYS* 1.3 72.6 + - - +
377B MET* 4.1 8.1 - - + -
423B GLN* 4.0 6.7 + - - +
426B ASN* 6.0 0.7 - - - +
429B HIS* 3.2 39.1 - - + +
432B CYS* 3.5 32.3 - - + -
433B LEU* 4.3 11.7 - - + +
436B ARG* 3.3 30.7 - - + +
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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