Contacts of the helix formed by residues 360 - 366 (chain A) in PDB entry 2VMX
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 THR 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A VAL* 2.7 32.8 + - - +
288A ASN* 3.8 7.4 - - - -
289A ALA* 3.6 27.4 - - + +
292A LEU* 3.9 21.8 - - + -
311A HIS 3.0 9.0 + - - +
313A LEU* 6.1 0.4 - - + -
358A ILE* 5.5 0.2 - - + -
359A GLY* 1.3 75.2 - - - -
361A ALA* 1.3 63.4 + - - +
362A ALA 3.3 2.9 - - - -
363A VAL* 3.4 10.1 - - + +
364A THR* 2.6 37.8 + - - -
373A MET* 4.0 9.0 - - - -
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Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 4.9 7.6 - - - +
32A GLU 3.9 9.6 - - - +
33A ASN* 3.8 13.5 - - - +
226A LYS 5.1 0.2 - - - +
227A THR* 4.2 24.0 - - + +
281A TYR* 2.8 30.2 + - - +
285A VAL* 4.0 13.0 - - + +
311A HIS* 4.8 2.8 + - + +
359A GLY 3.6 2.2 - - - -
360A THR* 1.3 77.2 + - - +
362A ALA* 1.3 61.1 + - - +
364A THR 3.6 0.2 + - - -
365A THR* 3.1 16.8 + - - -
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Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU* 3.6 21.7 + - + +
29A ILE 5.2 3.1 + - - +
32A GLU* 3.8 20.0 + - + +
33A ASN* 4.0 13.5 - - - -
34A PHE* 3.5 31.4 - - + -
359A GLY 5.1 0.8 + - - +
360A THR 3.3 0.6 - - - -
361A ALA* 1.3 76.7 - - - +
363A VAL* 1.3 65.7 + - - +
365A THR* 3.1 14.7 + - - -
366A ARG 3.2 8.7 + - - -
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Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.9 17.9 - - + -
27A GLU* 3.6 22.6 + - + +
28A LEU* 3.9 18.8 - - + -
34A PHE* 5.3 0.7 - - + -
359A GLY 4.8 0.4 - - - +
360A THR* 3.4 23.3 - - - +
362A ALA* 1.3 74.7 - - - +
364A THR* 1.3 61.2 + - - +
366A ARG* 3.2 14.3 + - + +
367A GLY 3.4 0.5 + - - -
368A PHE* 3.1 48.2 + - + +
373A MET* 3.9 23.1 - - + -
376A ILE* 4.6 0.7 - - + -
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Residues in contact with THR 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A TYR* 3.7 17.8 - - + -
284A ARG* 3.6 26.8 + - + +
285A VAL* 3.6 36.9 - - - +
288A ASN* 3.0 19.1 + - - +
360A THR* 2.6 26.7 + - - -
361A ALA 3.8 0.4 - - - -
363A VAL* 1.3 74.4 - - - +
365A THR* 1.3 60.1 + - - +
367A GLY* 2.9 21.1 + - - -
368A PHE 4.0 8.5 - - - +
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Residues in contact with THR 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASN* 2.6 22.4 + - - +
34A PHE* 3.6 35.7 - - + +
229A ARG* 3.1 22.1 + - - +
281A TYR* 3.0 19.2 + - - -
361A ALA 3.1 4.1 + - - -
362A ALA 3.1 9.4 + - - -
364A THR* 1.3 76.5 - - - +
366A ARG* 1.3 61.4 + - + +
367A GLY* 3.3 1.6 + - - -
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Residues in contact with ARG 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG 5.4 0.4 + - - -
22A GLN* 3.5 33.5 + - - +
23A HIS* 4.1 18.1 + - - +
34A PHE* 3.5 59.0 - - + +
362A ALA 3.2 4.0 + - - +
363A VAL* 3.5 12.3 - - + +
364A THR 3.1 0.6 - - - -
365A THR* 1.3 76.5 - - - +
367A GLY* 1.3 58.0 + - - +
368A PHE* 3.6 16.6 - - + -
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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