Contacts of the helix formed by residues 365 - 379 (chain B) in PDB entry 7NPA
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 365 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A LYS* 6.5 1.1 - - - -
383A ILE* 5.3 0.2 - - - -
364B TYR* 1.3 75.7 - - - +
366B ILE* 1.3 64.4 - - - +
367B ASP* 3.7 8.2 + - - +
368B GLU* 2.9 43.1 + - - +
369B ALA* 3.0 22.3 + - - +
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Residues in contact with ILE 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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373A LEU* 3.8 19.1 - - + +
376A ALA* 4.1 3.8 - - + -
377A GLU* 3.5 41.5 - - + +
381A GLY 3.8 17.7 - - - +
382A LYS* 5.8 1.3 - - + -
383A ILE* 4.1 17.7 - - + +
364B TYR 3.8 0.6 + - - +
365B SER* 1.3 72.2 - - - +
367B ASP* 1.3 60.4 + - - +
369B ALA* 3.3 2.9 + - - +
370B ARG* 2.9 67.6 + - - +
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Residues in contact with ASP 367 (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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377A GLU* 5.3 1.4 - - - +
365B SER* 3.2 6.9 + - - +
366B ILE* 1.3 82.4 - - - +
368B GLU* 1.3 56.7 + - - +
370B ARG* 3.3 15.7 + - - +
371B GLU* 3.0 39.0 + - + +
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Residues in contact with GLU 368 (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 LYS* 3.4 24.7 + - - -
363B TRP 4.6 1.4 - - - +
364B TYR* 3.6 17.9 - - + +
365B SER* 2.9 42.0 + - - +
367B ASP* 1.3 74.4 - - - +
369B ALA* 1.3 65.6 + - - +
371B GLU* 3.2 12.7 + - - +
372B ILE* 3.1 27.1 + - - +
413B PHE* 3.6 24.0 - - + -
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Residues in contact with ALA 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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373A LEU* 3.6 30.7 - - + -
383A ILE* 5.7 2.0 - - + -
391A PHE* 6.1 0.7 - - + -
364B TYR* 4.8 7.8 - - + +
365B SER 3.0 16.1 + - - +
366B ILE 3.7 1.1 - - - +
368B GLU* 1.3 76.9 - - - +
370B ARG* 1.3 63.3 + - - +
372B ILE* 3.3 12.0 + - - +
373B LEU* 3.0 28.2 + - + +
391B PHE* 4.4 20.1 - - + -
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Residues in contact with ARG 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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370A ARG* 5.1 11.2 + - + +
373A LEU* 3.7 23.2 + - + +
374A GLU* 3.8 27.1 - - - +
377A GLU* 2.9 42.2 + - - -
366B ILE* 2.9 34.8 + - - +
367B ASP* 3.6 13.6 + - - +
369B ALA* 1.3 77.9 - - - +
371B GLU* 1.3 57.0 + - - +
373B LEU* 3.3 7.4 + - + +
374B GLU* 2.9 28.1 + - - +
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Residues in contact with GLU 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 ASP* 3.0 20.4 + - + +
368B GLU* 3.2 17.5 + - - +
370B ARG* 1.3 73.6 - - + +
372B ILE* 1.3 65.0 + - - +
374B GLU* 3.2 10.8 + - - +
375B ILE* 3.2 29.5 + - - +
411B LYS* 3.3 43.6 + - + +
413B PHE* 3.7 24.9 - - + -
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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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356B ILE* 3.8 33.4 - - + -
364B TYR* 4.8 6.5 - - + -
368B GLU 3.1 15.9 + - - +
369B ALA* 3.5 7.9 - - - +
371B GLU* 1.3 75.6 - - - +
373B LEU* 1.3 60.8 + - + +
375B ILE* 3.4 8.8 + - - +
376B ALA* 3.0 27.0 + - - +
383B ILE* 4.6 4.9 - - + -
391B PHE* 3.7 46.2 - - + -
393B ILE* 4.1 12.3 - - + +
408B LEU* 4.8 1.8 - - + -
413B PHE* 3.7 29.4 - - + -
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Residues in contact with LEU 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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366A ILE* 4.4 14.0 - - + +
369A ALA* 3.7 31.6 - - + -
370A ARG* 3.8 32.2 + - + +
373A LEU* 3.7 27.1 - - + -
369B ALA* 3.0 17.4 + - + +
370B ARG* 3.6 5.8 - - - +
372B ILE* 1.3 78.6 - - + +
374B GLU* 1.3 61.6 + - - +
376B ALA* 3.5 4.1 + - - +
377B GLU* 3.0 24.8 + - - +
383B ILE* 3.8 32.8 - - + -
391B PHE* 5.1 8.7 - - + -
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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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370A ARG* 3.9 15.4 - - - +
370B ARG 2.9 13.5 + - - +
371B GLU* 3.2 13.8 + - - +
373B LEU* 1.3 75.9 - - - +
375B ILE* 1.3 59.7 + - + +
377B GLU* 3.3 8.6 + - - +
378B LYS* 2.9 28.3 + - + +
411B LYS* 6.0 0.2 + - - -
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Residues in contact with ILE 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 GLU 3.2 19.4 + - - +
372B ILE 3.8 3.8 - - - +
374B GLU* 1.3 75.4 - - + +
376B ALA* 1.3 64.7 + - - +
378B LYS* 3.2 10.1 + - - -
379B TYR* 3.2 33.4 - - + -
393B ILE* 5.3 0.4 - - + -
404B MET* 3.8 31.3 - - + +
407B GLU* 3.9 36.6 - - + +
408B LEU* 3.7 34.3 - - + +
411B LYS* 4.2 17.9 - - + -
413B PHE* 4.9 1.3 - - + -
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Residues in contact with ALA 376 (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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366A ILE* 4.4 3.4 - - + -
372B ILE 3.0 18.4 + - - +
373B LEU* 3.7 4.7 - - - +
375B ILE* 1.3 75.0 - - - +
377B GLU* 1.3 59.5 - - - +
379B TYR 3.3 2.4 + - - -
380B ASP 3.1 3.6 + - - -
381B GLY 2.7 35.5 + - - +
383B ILE* 3.7 26.7 - - + -
393B ILE* 3.8 24.8 - - + +
404B MET* 4.7 2.7 - - - -
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Residues in contact with GLU 377 (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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366A ILE* 3.9 20.3 - - + +
367A ASP* 5.5 0.5 - - - +
370A ARG* 2.9 37.7 + - - +
373B LEU 3.0 17.8 + - - +
374B GLU* 3.5 10.9 - - - +
375B ILE 3.3 0.2 - - - -
376B ALA* 1.3 76.0 - - - +
378B LYS* 1.3 64.6 + - - +
380B ASP* 3.2 18.6 + - - +
381B GLY 5.0 0.2 - - - +
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Residues in contact with LYS 378 (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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374B GLU* 2.9 14.9 + - + +
375B ILE* 3.2 10.7 + - - +
377B GLU* 1.3 78.0 - - - +
379B TYR* 1.3 82.1 + - + +
380B ASP* 3.7 4.3 + - - +
407B GLU* 2.9 39.6 + - - +
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Residues in contact with TYR 379 (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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375B ILE* 3.2 23.7 + - + +
376B ALA 3.3 2.6 + - - +
377B GLU 3.2 0.6 - - - -
378B LYS* 1.3 102.2 + - + +
380B ASP* 1.3 70.0 + - - +
381B GLY 3.2 1.6 + - - -
395B GLY 4.7 3.3 - - - +
396B ILE* 3.7 14.6 - - + +
397B SER 5.4 0.7 + - - -
400B ASP* 3.8 41.1 - - + +
403B ALA* 3.7 21.9 + - + +
404B MET* 3.7 51.8 - - + -
407B GLU* 2.6 32.7 + - - -
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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