Contacts of the helix formed by residues 367 - 380 (chain B) in PDB entry 1GVJ
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 ASP 367 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352B SER 5.0 1.8 - - - +
353B PHE* 3.1 25.3 + - + +
366B SER* 1.3 80.4 - - - +
368B PRO* 1.3 64.8 - - - +
369B ASP* 3.4 11.3 + - - +
370B GLU* 3.1 33.9 + - - +
371B VAL* 3.3 14.8 + - - +
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Residues in contact with PRO 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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365B LEU* 3.9 19.3 - - + +
366B SER 3.7 7.2 - - - +
367B ASP* 1.3 88.3 - - - +
369B ASP* 1.3 62.3 + - - +
371B VAL* 3.4 6.1 + - + +
372B ALA* 3.0 22.2 + - - +
386B TYR* 3.5 38.5 - - + +
389B LEU* 4.7 0.5 - - - +
410B TYR* 3.7 33.7 - - + -
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Residues in contact with ASP 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ASP* 3.2 9.2 + - - +
368B PRO* 1.3 76.4 - - - +
370B GLU* 1.3 62.6 + - - +
372B ALA* 3.2 4.9 + - - +
373B ARG* 2.7 37.6 + - - +
384B MET 5.0 1.9 - - - +
385B ASN* 4.5 19.6 - - - +
386B TYR* 4.6 5.5 + - + +
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Residues in contact with GLU 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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353B PHE* 3.8 30.3 - - + -
367B ASP* 3.1 31.9 + - - +
369B ASP* 1.3 74.9 - - - +
371B VAL* 1.3 66.5 + - - +
373B ARG* 2.8 44.7 + - - -
374B ARG* 2.8 52.6 + - - +
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Residues in contact with VAL 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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340B PHE* 4.0 3.1 - - + -
341B LEU* 3.9 27.6 - - + -
344B LEU* 3.9 10.5 - - + -
353B PHE* 3.6 31.2 - - + +
354B ILE* 4.0 18.8 - - + -
365B LEU* 4.1 11.9 - - + -
367B ASP 3.3 10.5 + - - +
368B PRO* 3.6 7.6 - - + +
369B ASP 3.2 0.6 - - - -
370B GLU* 1.3 78.6 - - - +
372B ALA* 1.3 63.0 + - - +
374B ARG* 3.4 2.5 + - - +
375B TRP* 3.0 21.1 + - - +
389B LEU* 4.2 17.3 - - + -
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B PRO 3.0 17.2 + - - +
369B ASP 3.6 4.7 - - - +
371B VAL* 1.3 78.5 - - - +
373B ARG* 1.3 56.1 + - - +
375B TRP* 3.2 0.7 + - - +
376B GLY 2.9 25.1 + - - -
384B MET* 3.1 14.0 - - + +
385B ASN* 3.3 43.3 - - - +
386B TYR* 3.6 3.4 - - - +
389B LEU* 4.1 15.4 - - + +
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Residues in contact with ARG 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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369B ASP* 2.7 30.6 + - - +
370B GLU* 2.8 43.1 + - - +
371B VAL 3.3 0.2 - - - -
372B ALA* 1.3 72.6 - - - +
374B ARG* 1.3 71.2 + - - +
376B GLY* 3.3 2.6 + - - +
377B LYS* 2.8 75.5 + - + +
384B MET* 4.4 8.2 + - - +
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Residues in contact with ARG 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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316B LYS* 5.8 8.1 - - - +
340B PHE* 3.6 17.0 - - + -
344B LEU* 4.6 6.9 - - + +
347B ASP* 5.5 0.4 + - - -
349B SER* 5.2 5.5 + - - -
350B CYS* 3.6 15.8 - - - -
353B PHE* 3.4 40.4 - - - -
370B GLU* 2.8 40.6 + - - +
371B VAL* 3.9 3.4 - - - +
373B ARG* 1.3 85.1 - - - +
375B TRP* 1.3 65.2 + - - +
377B LYS* 3.4 9.9 + - + +
378B ARG* 3.1 23.9 + - - +
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Residues in contact with TRP 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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335B ILE* 3.8 12.6 - - + -
336B GLN* 3.7 5.4 - - - -
337B LEU* 3.5 46.6 - - + +
340B PHE* 3.4 45.3 - + + -
371B VAL 3.0 14.9 + - - +
372B ALA 3.2 7.8 + - - +
374B ARG* 1.3 76.1 - - - +
376B GLY* 1.3 61.8 + - - +
378B ARG* 3.2 4.5 + - + -
379B LYS* 3.1 63.4 + - + +
384B MET* 3.5 38.9 - - + +
389B LEU* 3.9 17.9 - - + +
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Residues in contact with GLY 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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372B ALA 2.9 11.3 + - - -
373B ARG* 3.7 3.4 - - - -
375B TRP* 1.3 78.2 - - - +
377B LYS* 1.3 50.8 + - - +
379B LYS* 3.2 0.6 + - - -
380B ASN* 2.8 16.5 + - - -
381B LYS* 2.7 53.5 + - - -
382B PRO* 5.4 1.1 - - - -
384B MET* 3.6 13.9 - - - +
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Residues in contact with LYS 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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373B ARG* 2.8 57.5 + - + +
374B ARG* 3.7 9.9 - - + +
375B TRP 3.3 0.2 - - - -
376B GLY* 1.3 75.9 - - - +
378B ARG* 1.3 63.2 + - - +
379B LYS 3.4 0.7 + - - -
380B ASN* 3.5 9.6 + - - +
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Residues in contact with ARG 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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323B ALA* 4.3 6.9 - - - +
324B ALA* 5.4 2.2 - - - +
335B ILE* 5.4 11.4 - - + +
340B PHE* 3.7 32.1 - - + -
343B GLU* 2.9 40.8 + - - -
344B LEU* 5.8 1.4 - - - +
374B ARG 3.1 17.2 + - - +
375B TRP* 3.2 9.6 + - + +
377B LYS* 1.3 77.7 - - - +
379B LYS* 1.3 69.0 + - + +
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Residues in contact with LYS 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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334B PRO* 3.8 20.2 - - - +
335B ILE* 3.0 31.0 + - + +
375B TRP* 3.1 57.1 + - + +
376B GLY* 4.2 0.4 - - - +
378B ARG* 1.3 84.4 - - + +
380B ASN* 1.3 72.1 + - - +
381B LYS* 3.3 25.0 + - + +
384B MET* 6.0 1.1 - - + -
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Residues in contact with ASN 380 (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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334A PRO* 4.8 15.8 - - - +
376B GLY 2.8 7.8 + - - -
377B LYS* 3.5 9.9 + - - +
378B ARG 3.5 0.2 - - - -
379B LYS* 1.3 81.4 - - - +
381B LYS* 1.3 64.8 + - - +
382B PRO* 3.5 17.8 - - - +
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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