Contacts of the helix formed by residues 376 - 383 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C VAL* 4.5 3.8 - - - -
375C MET* 1.3 77.5 - - - +
377C GLU* 1.3 54.0 + - - +
378C ASN* 3.0 19.6 + - - +
379C GLN* 2.9 27.1 + - - +
380C PHE* 2.8 32.7 + - - +
476D ASP 3.8 17.0 - - - +
477D PHE* 4.0 18.4 - - - +
480D LYS* 3.7 25.5 - - + +
481D ARG* 3.9 14.9 + - + +
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Residues in contact with GLU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LYS* 2.8 33.5 + - - -
25C VAL* 3.6 13.7 - - + +
30C SER* 2.5 25.8 + - - -
64C MET* 3.5 28.1 - - + +
366C TRP* 3.9 13.2 - - + -
370C VAL* 4.6 4.2 - - + +
376C ASP* 1.3 72.8 - - - +
378C ASN* 1.3 68.8 + - - +
380C PHE* 3.1 10.9 - - - +
381C VAL* 3.0 31.9 + - - +
480D LYS* 3.2 18.0 + - + +
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Residues in contact with ASN 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 3.5 5.7 - - - +
26C ASN 2.7 28.0 + - - +
27C ASP* 3.2 36.5 - - - +
28C ASP 5.0 1.1 - - - -
29C GLN* 3.3 20.5 + - - +
30C SER* 2.8 29.4 + - - -
376C ASP* 3.0 15.2 + - - +
377C GLU* 1.3 82.1 - - - +
379C GLN* 1.3 62.3 + - - +
381C VAL* 3.7 0.9 + - - +
382C ALA* 3.3 9.9 + - - +
476D ASP* 5.3 5.2 - - - +
477D PHE* 6.2 0.2 - - - -
480D LYS* 4.4 7.6 + - - +
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Residues in contact with GLN 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASP 5.4 0.2 - - - -
321C LEU 3.1 23.6 + - - -
322C SER 4.0 12.4 + - - +
324C GLY* 4.5 10.1 - - - +
375C MET* 3.5 27.6 - - + -
376C ASP* 2.9 19.5 + - - +
378C ASN* 1.3 74.8 - - - +
380C PHE* 1.3 64.0 + - - +
382C ALA* 3.1 13.4 + - - +
383C VAL* 3.0 34.2 + - - +
387C ASN* 5.1 3.6 + - - +
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Residues in contact with PHE 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C MET* 5.5 0.2 - - + -
66C ILE* 3.9 26.9 - - + -
362C MET* 3.3 42.8 - - + -
365C ILE* 4.0 15.9 - - + -
366C TRP* 3.5 42.0 - + + -
370C VAL* 4.0 12.8 - - + -
375C MET* 3.2 10.3 - - - -
376C ASP 2.8 15.5 + - - +
377C GLU* 3.1 13.5 - - - +
379C GLN* 1.3 71.1 - - - +
381C VAL* 1.3 71.3 + - + +
383C VAL* 3.1 6.6 - - - +
384C THR* 3.0 34.8 + - + +
412C TRP* 4.1 16.4 - + - -
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Residues in contact with VAL 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 3.9 13.2 - - + +
26C ASN 4.3 2.7 - - - +
27C ASP 4.2 10.3 - - - +
66C ILE* 3.8 33.2 - - + -
67C PRO* 3.7 21.3 - - + +
377C GLU 3.0 15.0 + - - +
378C ASN 3.9 5.6 - - - +
380C PHE* 1.3 80.7 - - + +
382C ALA* 1.3 58.8 + - - +
384C THR* 3.6 6.7 - - - -
385C SER* 2.8 44.7 + - - +
386C THR* 3.7 10.5 - - - +
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Residues in contact with ALA 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASP* 3.6 26.9 - - + +
378C ASN 3.3 6.4 + - - +
379C GLN* 3.1 23.1 + - - +
381C VAL* 1.3 81.1 - - - +
383C VAL* 1.3 57.6 + - - +
384C THR 3.4 1.6 + - - -
385C SER 3.9 0.3 + - - -
386C THR* 3.4 13.1 + - - -
387C ASN* 2.7 44.9 + - - +
388C ALA 4.5 0.7 + - - -
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Residues in contact with VAL 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C LEU* 3.9 19.7 - - + +
326C LEU 4.9 1.1 - - - +
327C GLN* 3.6 21.1 - - - +
328C VAL* 4.9 1.1 - - - -
329C THR* 2.7 50.0 + - + +
365C ILE* 4.5 4.9 - - + -
375C MET* 3.9 14.1 - - + -
379C GLN* 3.0 34.0 + - - +
380C PHE* 3.1 20.2 - - - +
382C ALA* 1.3 74.8 - - - +
384C THR* 1.3 62.8 + - + +
387C ASN* 4.1 4.0 - - - +
388C ALA* 6.5 0.9 - - - -
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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