Contacts of the helix formed by residues 386 - 390 (chain A) in PDB entry 1VDV
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 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A MET* 3.6 20.5 - - - +
384A PRO* 3.3 13.4 + - + +
385A MET* 1.3 75.1 - - - +
387A HIS* 1.3 72.7 + - + +
388A THR* 2.6 53.2 + - - +
389A PHE* 3.1 17.5 + - - +
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Residues in contact with HIS 387 (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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366A MET* 3.8 18.6 - - - +
386A ASP* 1.3 82.8 - - + +
388A THR* 1.3 82.5 + - + +
389A PHE 3.6 0.3 + - - -
390A PHE* 3.8 16.2 + - - +
462A ARG* 4.0 9.5 + - - -
463A THR 5.1 1.8 - - - +
464A ILE* 5.6 0.9 - - - -
465A SER* 4.1 25.1 - - - +
467A LEU* 3.5 34.3 - - + +
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Residues in contact with THR 388 (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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386A ASP* 2.6 32.9 + - - +
387A HIS* 1.3 97.0 - - + +
389A PHE* 1.3 62.8 + - - -
390A PHE* 3.1 4.6 + - - -
391A PRO* 3.8 9.2 - - - +
397A LEU* 3.1 27.4 - - - +
462A ARG* 5.8 0.4 - - - +
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Residues in contact with PHE 389 (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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352A ILE* 3.9 16.6 - - + -
353A ILE* 4.5 6.5 - - + -
372A LEU* 3.5 35.9 - - + -
374A ILE* 4.3 17.9 - - + -
383A VAL* 5.0 8.1 - - + -
385A MET* 4.1 11.2 - - + -
386A ASP* 3.1 18.9 + - - +
388A THR* 1.3 79.5 + - - +
390A PHE* 1.3 77.4 + + + +
391A PRO* 3.0 10.4 - - - +
396A THR* 3.1 33.1 - - + -
397A LEU* 3.1 36.9 + - + -
398A LEU* 4.3 12.8 - - + -
404A LEU* 5.9 1.3 - - + -
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Residues in contact with PHE 390 (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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352A ILE 3.7 7.2 - - - -
355A ALA* 3.7 33.2 - - + -
362A ASN* 3.4 38.6 - - + -
366A MET* 3.5 26.5 - - + -
385A MET* 3.6 25.4 - - + -
387A HIS 3.8 4.2 + - - +
388A THR 3.1 2.8 - - - -
389A PHE* 1.3 98.6 - + + +
391A PRO* 1.3 56.4 - - - +
392A SER 3.4 2.5 - - - +
395A LYS 3.5 6.1 - - - +
396A THR* 4.0 4.3 - - + -
462A ARG* 2.8 43.5 + - + -
463A THR* 4.3 19.5 - - - +
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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