Contacts of the helix formed by residues 385 - 392 (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 SER 385 (chain B).
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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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Residues in contact with THR 386 (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* 3.4 37.0 - - - +
381B VAL* 3.1 19.1 + - - +
382B ALA* 4.0 4.7 - - - -
385B SER* 1.3 73.8 + - - +
387B ASN* 1.3 66.7 + - - +
389B ALA* 3.4 2.6 + - - +
390B LYS* 3.0 28.2 + - + +
395B TYR* 3.6 28.9 - - + -
399B GLY* 2.6 25.5 + - - +
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Residues in contact with ASN 387 (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* 4.9 3.5 - - - +
327B GLN* 2.7 44.6 + - + +
328B VAL* 3.9 5.4 - - + -
379B GLN* 5.0 3.2 - - - +
382B ALA* 2.7 39.6 + - - +
383B VAL* 4.0 7.5 - - - +
386B THR* 1.3 73.8 - - - +
388B ALA* 1.3 57.5 + - - +
390B LYS* 3.1 15.1 + - - +
391B VAL* 2.9 34.1 + - + +
477B PHE* 4.7 10.2 - - + -
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Residues in contact with ALA 388 (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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70B ILE* 4.5 12.3 - - + +
72B VAL* 3.1 36.6 - - + -
105B ILE* 5.6 0.2 - - + -
328B VAL* 3.8 16.6 - - + +
329B THR 5.9 0.2 - - - +
382B ALA 4.6 0.2 + - - -
383B VAL 6.2 0.2 - - - -
384B THR 5.5 1.3 - - - +
385B SER* 3.5 9.5 + - - +
387B ASN* 1.3 75.0 - - - +
389B ALA* 1.3 68.4 + - - +
391B VAL* 4.5 1.6 - - - +
392B PHE* 3.0 33.7 + - + +
394B LEU* 5.5 1.6 - - - -
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Residues in contact with ALA 389 (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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70B ILE* 3.9 12.9 - - + +
385B SER 3.0 18.5 + - - +
386B THR* 3.5 8.1 - - - +
388B ALA* 1.3 75.7 - - - +
390B LYS* 1.3 60.5 + - - +
393B ASN 3.3 2.6 + - - -
394B LEU* 2.7 39.6 + - - -
395B TYR* 3.1 15.2 + - + +
398B LYS 3.4 26.5 - - - +
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Residues in contact with LYS 390 (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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28A ASP* 3.6 40.2 - - - +
27B ASP* 3.5 24.0 + - - -
386B THR* 3.0 20.0 + - + +
387B ASN* 3.1 13.3 + - - +
389B ALA* 1.3 75.4 - - - +
391B VAL* 1.3 65.8 + - - +
393B ASN* 3.6 9.0 + - - +
395B TYR* 3.8 33.2 - - + -
475B PRO* 4.0 6.1 - - - +
477B PHE* 3.6 50.5 + - + +
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Residues in contact with VAL 391 (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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194B ILE* 3.8 9.8 - - + +
251B TYR* 4.5 13.5 - - + -
275B TYR* 3.9 30.7 - - + -
327B GLN* 5.9 0.7 - - + -
328B VAL* 4.4 8.5 - - + -
387B ASN* 2.9 19.8 + - + +
388B ALA* 3.3 1.1 + - - -
390B LYS* 1.3 76.3 - - - +
392B PHE* 1.3 89.3 + - + +
393B ASN 3.3 0.4 - - - -
475B PRO* 3.2 23.9 - - - +
477B PHE* 4.0 8.1 - - + -
478B VAL* 3.7 21.9 - - + +
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Residues in contact with PHE 392 (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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72B VAL* 4.0 21.8 - - + -
105B ILE* 3.9 15.7 - - + -
138B HIS* 3.7 24.0 - + - -
162B ASN* 2.9 23.4 + - - +
163B SER* 4.0 15.0 - - - -
194B ILE* 4.4 10.1 - - + -
196B GLN* 4.2 2.0 - - - -
251B TYR* 3.3 35.7 - + - -
328B VAL* 5.5 0.4 - - + -
388B ALA* 3.0 26.7 + - + +
391B VAL* 1.3 88.5 - - + +
393B ASN* 1.3 63.7 + - - +
394B LEU* 3.3 9.0 + - + +
471B ARG* 3.4 40.4 - - - +
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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