Contacts of the helix formed by residues 385 - 392 (chain D) 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 SER 385 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D PRO* 3.8 10.2 + - - +
68D GLY 3.4 25.1 + - - -
69D GLY* 4.1 1.1 - - - -
70D ILE* 3.8 19.5 - - - +
381D VAL* 2.9 14.6 + - - +
382D ALA 3.9 0.7 - - - -
384D THR* 1.3 83.8 + - - +
386D THR* 1.3 66.8 + - - +
387D ASN 3.4 2.0 - - - -
388D ALA* 2.9 25.4 + - - +
389D ALA 2.9 10.6 + - - -
399D GLY* 3.6 17.1 - - - -
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Residues in contact with THR 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ASP* 3.6 23.7 + - + -
381D VAL* 3.3 34.4 + - + +
382D ALA* 3.8 2.0 - - - +
385D SER* 1.3 74.9 + - - +
387D ASN* 1.3 63.2 + - - +
389D ALA* 3.2 4.2 + - - +
390D LYS* 3.0 45.8 + - - +
395D TYR* 4.0 7.8 - - - -
399D GLY* 3.1 33.2 - - - +
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Residues in contact with ASN 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASP* 5.2 1.9 - - - +
327D GLN* 2.6 50.5 + - + +
328D VAL* 4.2 2.9 - - + -
379D GLN* 5.5 1.0 + - - -
382D ALA* 3.0 34.4 + - - +
383D VAL* 4.3 3.8 - - - +
386D THR* 1.3 77.2 + - - +
388D ALA* 1.3 53.4 + - - +
390D LYS* 3.1 13.0 + - - +
391D VAL* 2.8 41.9 + - + +
477D PHE* 5.6 8.6 - - + -
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Residues in contact with ALA 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ILE* 4.2 16.2 - - + +
72D VAL* 3.3 33.2 - - + -
328D VAL* 4.2 11.9 - - + +
329D THR 5.9 0.9 - - - +
382D ALA 4.5 0.2 + - - -
383D VAL 6.1 0.9 - - - +
384D THR 5.3 0.9 - - - +
385D SER* 2.9 17.3 + - - +
387D ASN* 1.3 80.1 - - - +
389D ALA* 1.3 60.2 + - - +
390D LYS 3.2 0.7 + - - -
391D VAL* 4.6 0.9 - - - +
392D PHE* 3.2 31.4 + - + +
394D LEU* 4.7 2.2 - - - +
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Residues in contact with ALA 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ILE* 4.0 8.7 - - + +
385D SER 2.9 11.1 + - - +
386D THR* 3.2 11.6 + - - +
388D ALA* 1.3 75.4 - - - +
390D LYS* 1.3 55.3 + - - +
393D ASN 3.3 3.1 + - - -
394D LEU* 2.5 41.9 + - + -
395D TYR* 2.9 14.6 + - + +
398D LYS 2.8 37.0 - - - +
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Residues in contact with LYS 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ASP* 3.6 39.1 - - - +
27D ASP* 3.5 22.8 + - - -
386D THR* 3.0 26.3 + - - +
387D ASN* 3.4 12.6 + - - +
388D ALA 3.1 0.4 - - - -
389D ALA* 1.3 76.1 - - - +
391D VAL* 1.3 66.3 + - - +
392D PHE 3.4 0.2 + - - -
393D ASN* 3.5 8.7 + - - +
395D TYR* 3.9 33.6 + - + -
475D PRO* 3.8 6.9 - - - +
477D PHE* 3.7 47.7 - - + +
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Residues in contact with VAL 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D ILE* 3.6 10.6 - - + +
251D TYR* 4.5 13.5 - - + -
275D TYR* 4.1 20.6 - - + -
327D GLN* 5.9 0.7 - - + -
328D VAL* 4.4 9.2 - - + -
387D ASN* 2.8 22.1 + - + +
388D ALA 4.4 0.2 - - - +
390D LYS* 1.3 75.8 - - - +
392D PHE* 1.3 91.5 + - + +
475D PRO* 3.2 24.9 - - - +
477D PHE* 3.9 19.7 - - + -
478D VAL* 3.6 21.1 - - + +
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Residues in contact with PHE 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D VAL* 4.1 20.4 - - + -
105D ILE* 4.2 11.7 - - + -
138D HIS* 3.4 28.7 - + - -
162D ASN* 3.0 24.4 + - - +
163D SER* 3.9 12.1 - - - -
194D ILE* 4.1 19.1 - - + -
196D GLN* 4.6 1.3 - - - -
251D TYR* 3.5 32.1 - + - -
328D VAL* 5.8 0.4 - - + -
388D ALA* 3.2 23.2 + - - +
390D LYS 3.2 0.2 - - - -
391D VAL* 1.3 89.3 - - + +
393D ASN* 1.3 65.1 + - - +
394D LEU* 3.4 15.9 + - + +
471D ARG* 3.4 33.0 - - - +
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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