Contacts of the helix formed by residues 376 - 385 (chain B) in PDB entry 2VM8
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 376 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476A ASP 4.0 8.0 - - - +
477A PHE* 3.7 21.7 - - - +
480A LYS* 3.5 35.9 - - + +
481A ARG* 3.8 14.6 + - - +
370B VAL* 4.1 5.8 - - - -
375B MET* 1.3 82.5 - - - +
377B GLU* 1.3 59.2 + - - +
378B ASN* 3.2 12.9 + - - +
379B GLN* 3.0 23.6 + - - +
380B PHE* 3.0 22.7 + - - +
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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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480A LYS* 3.1 34.3 + - + +
23B LYS* 3.1 30.9 + - - -
25B VAL* 3.4 31.1 - - + +
30B SER* 3.1 9.7 + - - -
64B MET* 3.5 15.5 - - + +
366B TRP* 3.7 22.1 - - + -
370B VAL* 4.6 3.4 - - - +
376B ASP* 1.3 71.8 - - - +
378B ASN* 1.3 59.7 + - - +
380B PHE* 3.2 12.5 - - - +
381B VAL* 3.1 22.2 + - - +
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Residues in contact with ASN 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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476A ASP* 5.2 2.8 - - - +
477A PHE* 6.0 0.7 - - - -
480A LYS* 2.6 32.2 + - - +
25B VAL* 3.4 3.4 - - - +
26B ASN 3.0 23.3 + - - -
27B ASP* 3.4 30.3 - - - +
28B ASP 4.9 0.9 - - - -
29B GLN* 3.4 17.2 - - - +
30B SER* 2.8 24.9 + - - -
376B ASP* 3.2 8.9 + - - +
377B GLU* 1.3 73.6 - - - +
379B GLN* 1.3 66.6 + - - +
380B PHE 3.2 0.2 - - - -
381B VAL 3.5 1.2 + - - -
382B ALA* 3.1 17.3 + - - +
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Residues in contact with GLN 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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321B LEU 3.3 9.7 - - - +
322B SER 2.9 23.3 - - - +
323B CYS 4.8 0.3 - - - -
324B GLY* 4.2 7.4 + - - -
375B MET* 3.5 39.0 - - + -
376B ASP* 3.0 13.8 + - - +
378B ASN* 1.3 75.0 - - - +
380B PHE* 1.3 61.4 + - - +
382B ALA* 3.0 33.5 - - - +
383B VAL* 3.0 18.0 + - + +
387B ASN* 5.0 3.0 - - - +
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Residues in contact with PHE 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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64B MET* 4.8 2.7 - - + -
66B ILE* 3.7 26.7 - - + -
362B MET* 3.3 46.7 - - + -
365B ILE* 4.1 14.8 - - + -
366B TRP* 3.4 42.0 - + - -
370B VAL* 4.0 10.5 - - + -
375B MET* 3.5 9.1 - - - -
376B ASP 3.0 14.5 + - - +
377B GLU* 3.2 15.0 - - - +
378B ASN 3.2 0.2 - - - -
379B GLN* 1.3 76.3 - - - +
381B VAL* 1.3 68.4 + - + +
383B VAL* 3.2 2.4 - - - +
384B THR* 2.9 43.9 + - + +
412B TRP* 4.0 9.6 - + - -
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Residues in contact with VAL 381 (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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25B VAL* 3.5 24.7 - - + +
26B ASN 4.3 0.2 - - - -
27B ASP 3.9 13.7 - - - +
66B ILE* 3.9 15.7 - - + -
67B PRO* 3.6 30.5 - - + +
377B GLU 3.1 15.4 + - - +
378B ASN 3.8 6.7 - - - +
380B PHE* 1.3 78.2 - - + +
382B ALA* 1.3 64.9 + - - +
384B THR* 3.6 6.5 - - - +
385B SER* 2.8 25.6 + - - +
386B THR* 3.1 20.9 + - - +
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Residues in contact with ALA 382 (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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27B ASP* 3.9 18.4 - - + +
378B ASN 3.1 10.0 + - - +
379B GLN* 3.0 33.6 + - - +
381B VAL* 1.3 80.1 - - - +
383B VAL* 1.3 57.1 + - - +
385B SER 3.8 0.3 + - - -
386B THR* 3.3 6.6 + - - -
387B ASN* 2.7 46.5 + - - +
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Residues in contact with VAL 383 (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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321B LEU* 3.8 41.7 - - + +
326B LEU 4.7 0.7 - - - +
327B GLN* 3.6 17.0 - - - +
328B VAL* 3.8 1.5 - - - -
329B THR* 2.7 38.4 + - + -
365B ILE* 4.5 8.1 - - + -
375B MET* 4.0 14.1 - - + -
379B GLN* 3.0 22.9 + - + +
380B PHE* 3.2 19.7 - - - +
382B ALA* 1.3 75.8 - - - +
384B THR* 1.3 59.6 + - + +
387B ASN* 4.0 7.4 - - - +
388B ALA 6.2 0.4 - - - -
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Residues in contact with THR 384 (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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66B ILE* 5.7 0.2 - - - +
67B PRO 5.2 1.0 + - - -
69B GLY* 3.6 0.7 - - - -
70B ILE 2.9 25.0 + - - +
361B ARG* 2.9 20.4 + - - +
362B MET* 3.7 28.8 - - + +
365B ILE* 3.9 23.6 - - + -
380B PHE* 2.9 48.7 + - + +
381B VAL* 3.4 8.7 + - - +
383B VAL* 1.3 80.5 - - + +
385B SER* 1.3 62.6 + - - +
388B ALA* 5.8 1.8 - - - -
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Residues in contact with SER 385 (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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67B PRO* 3.8 7.8 + - - +
68B GLY 3.4 24.9 - - - -
69B GLY* 4.0 3.1 - - - -
70B ILE* 3.4 20.7 - - - +
381B VAL* 2.8 27.1 + - - +
382B ALA 3.9 0.2 - - - -
383B VAL 3.8 0.6 - - - -
384B THR* 1.3 82.9 + - - +
386B THR* 1.3 61.4 + - - -
387B ASN 3.5 1.7 + - - -
388B ALA* 3.5 5.1 + - - +
389B ALA* 3.0 23.4 + - - +
399B GLY* 3.7 13.0 - - - -
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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