Contacts of the helix formed by residues 382 - 387 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ASP 3.5 9.4 - - - -
295B ALA* 3.2 15.0 - - - -
297B TYR 3.5 15.9 + - - -
298B ILE* 4.2 2.2 - - - +
380B ALA 3.4 7.3 + - - -
381B LEU* 1.3 74.2 - - - +
383B ALA* 1.3 61.3 + - - -
384B THR 3.1 3.4 - - - -
385B PHE 2.8 19.1 + - - -
386B ILE* 3.0 17.9 + - - +
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Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ASP 4.5 0.2 - - - +
86B TYR* 3.9 13.9 - - + -
228B TYR* 3.7 30.5 - - + -
292B ASP 4.7 0.2 + - - -
295B ALA 2.7 14.5 + - - +
296B SER* 3.4 14.4 + - - +
382B GLY* 1.3 71.8 - - - -
384B THR* 1.3 62.4 + - - +
386B ILE* 4.2 1.6 - - - -
387B ARG* 2.9 36.8 + - - +
503B 90D 3.8 10.9 - - - -
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Residues in contact with THR 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B SER 3.4 2.7 + - - -
297B TYR* 3.4 5.0 - - - -
298B ILE* 3.4 26.6 + - + -
345B LEU* 3.9 12.4 - - + +
349B ASP* 3.8 22.7 - - - +
350B TYR* 3.9 14.8 - - + -
365B ALA* 2.9 46.7 + - + +
366B ILE* 5.2 0.2 - - + -
382B GLY 3.1 0.6 + - - -
383B ALA* 1.3 77.7 - - - +
385B PHE* 1.3 60.7 + - - +
387B ARG* 3.5 19.3 + - - +
388B LYS* 4.4 1.4 + - - +
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Residues in contact with PHE 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL* 5.8 0.2 - - + -
298B ILE* 4.0 15.8 - - + +
336B PHE* 4.1 22.4 - + - -
338B LEU* 3.9 9.2 - - + -
343B TYR* 3.8 27.1 - + + -
345B LEU* 4.5 6.5 - - + -
381B LEU* 3.7 45.8 - - + -
382B GLY 2.8 9.3 + - - +
384B THR* 1.3 77.1 - - - +
386B ILE* 1.3 69.5 + - + +
387B ARG 3.2 1.6 - - - -
388B LYS* 3.1 13.0 + - - +
389B PHE* 3.1 43.8 + + + -
402B PHE* 3.7 27.6 - + - -
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Residues in contact with ILE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE* 4.1 25.4 - - + +
227B TYR* 5.9 0.2 - - - -
228B TYR* 3.9 35.2 + - + +
291B VAL* 4.0 19.7 - - + -
293B THR* 4.6 15.5 - - + -
381B LEU 4.4 5.4 - - - +
382B GLY* 3.0 21.9 + - - +
383B ALA* 4.2 1.6 - - - +
385B PHE* 1.3 79.5 - - + +
387B ARG* 1.3 64.4 + - - +
389B PHE 3.1 28.3 + - - +
390B TYR* 3.8 1.7 + - - -
391B THR* 3.4 25.1 - - + +
405B ALA* 4.5 1.4 - - - +
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Residues in contact with ARG 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ASP* 2.5 45.8 + - - +
86B TYR* 3.1 16.7 + - - +
227B TYR* 5.6 0.3 - - - -
228B TYR* 3.6 20.7 - - + +
229B ASN 3.8 20.2 - - - +
230B ARG* 4.0 36.5 + - + +
296B SER 4.2 5.5 + - - -
349B ASP 4.2 13.5 + - - -
352B PHE* 4.6 8.7 - - - -
365B ALA* 4.9 4.6 - - - +
383B ALA* 2.9 30.0 + - - +
384B THR* 3.5 28.8 + - - +
385B PHE 3.2 0.2 - - - -
386B ILE* 1.3 77.4 - - - +
388B LYS* 1.3 60.3 + - - +
405B ALA* 3.7 12.0 - - - +
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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
------------------------------------------------------------
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