Contacts of the helix formed by residues 382 - 387 (chain A) in PDB entry 5V8V
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 GLY 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ASP 3.4 10.5 - - - -
295A ALA* 3.2 15.0 - - - -
296A SER 4.4 0.2 - - - -
297A TYR 3.8 10.7 + - - -
298A ILE* 4.3 4.2 - - - +
380A ALA 3.4 6.5 + - - -
381A LEU* 1.3 74.0 - - - +
383A ALA* 1.3 59.9 + - - -
384A THR 3.1 3.4 - - - -
385A PHE 2.8 19.1 + - - -
386A ILE* 2.9 18.1 + - - +
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Residues in contact with ALA 383 (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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83A ASP 4.3 0.7 - - - +
86A TYR* 3.9 9.0 - - + -
228A TYR* 3.9 21.5 - - + -
292A ASP 4.6 0.2 + - - -
295A ALA 2.8 8.9 + - - -
296A SER* 3.3 13.8 + - - +
382A GLY* 1.3 70.5 - - - -
384A THR* 1.3 62.8 + - - +
386A ILE* 4.3 1.3 - - - +
387A ARG* 2.9 41.6 + - - +
503A 90D 3.7 24.4 - - - -
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Residues in contact with THR 384 (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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296A SER 3.3 11.5 + - - -
297A TYR* 3.3 2.1 - - - -
298A ILE* 3.8 22.9 - - + -
345A LEU* 3.9 12.0 - - + +
349A ASP* 3.9 20.1 - - - +
350A TYR* 4.0 13.2 - - + -
365A ALA* 3.0 46.0 + - + +
382A GLY 3.1 0.6 + - - -
383A ALA* 1.3 81.0 - - - +
385A PHE* 1.3 59.3 + - - +
387A ARG* 3.7 20.4 + - - +
388A LYS* 4.4 2.1 + - - +
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Residues in contact with PHE 385 (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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291A VAL* 5.6 0.2 - - + -
298A ILE* 4.0 8.7 - - + +
336A PHE* 4.0 28.7 - + - -
338A LEU* 3.9 20.2 - - + -
343A TYR* 3.9 25.8 - + + -
345A LEU* 4.1 10.1 - - + -
381A LEU* 4.0 34.1 - - + -
382A GLY 2.8 14.2 + - - +
384A THR* 1.3 71.6 - - - +
386A ILE* 1.3 70.6 + - + +
387A ARG 3.2 1.8 - - - -
388A LYS* 3.1 12.5 + - - +
389A PHE* 3.2 40.0 + + + -
402A PHE* 3.6 31.2 - + - -
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Residues in contact with ILE 386 (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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226A PHE* 4.4 18.2 - - + +
227A TYR* 5.9 0.3 - - - -
228A TYR* 4.2 32.7 + - + +
291A VAL* 4.5 9.9 - - + -
292A ASP 4.5 0.2 - - - -
293A THR* 3.9 36.3 - - + +
381A LEU 4.0 15.0 - - - +
382A GLY 2.9 18.6 + - - +
385A PHE* 1.3 79.1 - - + +
387A ARG* 1.3 65.5 + - - +
388A LYS 3.1 0.2 - - - -
389A PHE 3.2 27.8 + - - +
390A TYR* 4.1 1.4 + - - -
391A THR* 3.8 18.8 - - - +
405A ALA* 4.7 1.7 - - - +
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Residues in contact with ARG 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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83A ASP* 2.6 46.8 + - - +
86A TYR* 3.2 18.8 + - - +
227A TYR* 5.6 0.3 - - - -
228A TYR* 3.4 27.7 - - + +
229A ASN 3.7 9.6 - - - +
230A ARG* 3.6 37.5 + - + +
296A SER 3.9 5.1 + - - -
349A ASP 4.0 15.7 + - - +
352A PHE* 4.9 9.7 - - - -
365A ALA* 5.0 4.6 - - - +
383A ALA* 2.9 34.4 + - - +
384A THR* 3.7 28.6 + - - +
385A PHE 3.2 0.2 - - - -
386A ILE* 1.3 78.9 - - - +
388A LYS* 1.3 57.8 + - + +
405A ALA* 3.6 10.6 - - - +
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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