Contacts of the strand formed by residues 341 - 346 (chain S) in PDB entry 1VYH
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 VAL 341 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280S GLU* 3.6 13.4 - - - +
281S CYS* 3.3 14.0 - - - -
314S GLY* 4.6 0.4 - - - -
315S SER 2.5 33.8 + - - +
318S LYS* 3.4 21.3 - - - +
320S ILE* 4.3 10.3 - - + -
340S TRP* 1.3 72.2 - - - +
342S ARG* 1.3 59.1 + - - +
343S GLY 4.3 5.8 - - - +
344S VAL* 4.4 8.5 - - + -
355S SER* 3.5 18.6 - - - +
356S CYS 3.2 16.8 - - - +
357S ALA* 3.3 3.8 - - + -
363S ARG* 3.3 37.2 - - - +
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Residues in contact with ARG 342 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Q LYS* 5.6 5.1 - - - +
67Q HIS* 5.6 0.4 - - - -
113S ARG* 6.0 1.0 + - - -
238S ARG* 5.9 1.8 - - - +
239S MET* 5.9 1.9 - - - +
280S GLU* 3.6 30.5 + - - +
281S CYS* 3.2 14.6 - - - -
316S ARG* 5.9 0.6 - - - +
340S TRP* 5.3 6.0 - - - -
341S VAL* 1.3 71.4 - - - +
343S GLY* 1.3 57.6 + - - +
356S CYS* 2.9 9.4 + - - -
357S ALA* 3.4 2.7 - - - +
358S ASP* 3.7 21.0 + - - +
382S PHE* 3.2 40.9 - - - -
383S VAL 3.1 20.6 - - - +
384S THR* 3.1 57.1 + - - +
400S VAL* 4.5 3.2 - - - +
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Residues in contact with GLY 343 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281S CYS* 3.4 3.9 - - - -
341S VAL* 4.8 0.2 - - - -
342S ARG* 1.3 78.0 - - - +
344S VAL* 1.3 62.7 + - - -
355S SER* 3.3 11.8 + - - -
356S CYS* 2.9 41.0 + - - -
384S THR 4.9 0.2 - - - -
385S SER* 5.3 1.3 - - - -
386S LEU* 3.8 13.3 - - - +
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Residues in contact with VAL 344 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281S CYS* 3.5 29.9 - - + +
282S ILE 5.1 1.0 - - - +
283S SER* 2.8 31.9 + - - +
312S LEU* 3.5 48.7 - - + +
314S GLY* 3.6 22.0 - - - +
320S ILE* 4.3 20.2 - - + -
341S VAL* 4.4 2.5 - - + -
343S GLY* 1.3 74.4 - - - +
345S LEU* 1.3 64.7 + - - +
353S ILE* 4.9 2.9 - - + -
354S LEU 3.8 2.0 - - - -
355S SER* 4.7 1.1 - - - +
386S LEU* 4.4 0.4 - - - +
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Residues in contact with LEU 345 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283S SER* 4.6 6.7 - - - +
312S LEU* 4.2 3.3 - - - +
344S VAL* 1.3 82.6 - - - +
346S PHE* 1.3 82.9 - - - +
353S ILE* 3.1 16.8 - - - +
354S LEU* 2.7 49.2 + - + +
386S LEU* 3.8 28.0 - - + +
387S ASP* 4.4 14.1 - - - +
388S PHE* 3.6 35.9 - - + +
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Residues in contact with PHE 346 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283S SER* 5.2 5.1 + - - -
284S TRP 3.8 11.0 - - - +
285S ALA* 3.6 24.0 - - + -
286S PRO* 3.8 27.8 - - + -
288S SER* 4.5 6.7 - - - -
291S SER* 5.9 3.4 - - - -
312S LEU* 3.3 44.9 - - + -
322S MET* 4.8 5.4 - - - -
345S LEU* 1.3 91.8 - - - +
347S HIS* 1.3 70.5 + - - +
349S GLY 4.8 4.9 - - - -
350S GLY* 4.9 0.7 - - - -
352S PHE 3.8 1.1 - - - -
353S ILE* 3.9 14.6 - - + -
354S LEU* 4.9 1.1 - - - -
367S TYR* 3.5 39.5 - + - -
388S PHE* 4.6 2.9 - - - -
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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