Contacts of the strand formed by residues 341 - 346 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280O GLU* 3.4 26.9 - - - +
281O CYS* 3.7 2.7 - - - -
314O GLY* 4.5 7.7 - - - +
315O SER 3.4 16.7 + - - +
316O ARG* 5.9 0.2 - - - +
318O LYS 4.3 1.8 - - - +
319O THR 3.4 31.2 - - - +
320O ILE* 3.8 28.5 - - + -
339O ASN 4.0 9.2 - - - +
340O TRP* 1.3 74.9 - - - +
342O ARG* 1.3 58.5 + - - +
343O GLY 3.8 10.8 - - - +
344O VAL* 5.0 2.0 - - + -
355O SER* 4.5 2.2 - - - -
356O CYS 3.3 21.5 - - - +
357O ALA* 4.0 6.7 - - + +
363O ARG* 4.8 6.1 - - - +
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Residues in contact with ARG 342 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M HIS* 5.2 1.2 - - - -
113O ARG* 4.8 9.4 + - - -
239O MET* 6.1 0.2 - - - +
280O GLU* 2.9 37.9 + - - +
281O CYS* 3.1 12.2 - - - -
316O ARG* 4.6 1.6 - - - +
340O TRP* 3.9 19.9 - - - +
341O VAL* 1.3 74.9 - - - +
343O GLY* 1.3 54.2 + - - +
356O CYS* 2.6 13.5 + - - +
357O ALA 4.6 0.4 - - - -
358O ASP* 3.7 33.9 + - - +
382O PHE* 4.4 11.3 - - - -
383O VAL 3.0 26.9 - - - +
384O THR* 2.8 54.6 - - - +
385O SER* 4.5 1.6 - - - -
400O VAL* 5.6 0.6 - - - +
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Residues in contact with GLY 343 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239O MET* 6.3 1.1 - - - -
281O CYS* 3.2 7.1 - - - -
341O VAL* 3.8 1.9 - - - +
342O ARG* 1.3 80.4 - - - +
344O VAL* 1.3 69.3 + - - +
355O SER* 3.4 7.3 - - - -
356O CYS* 3.1 25.1 + - - +
386O LEU* 3.4 22.9 - - - -
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Residues in contact with VAL 344 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239O MET* 6.0 2.0 - - + +
281O CYS* 3.9 22.9 - - + +
282O ILE 5.0 1.9 - - - +
283O SER* 3.5 30.2 - - - +
312O LEU* 3.5 40.6 - - + +
314O GLY* 4.1 6.1 - - - +
320O ILE* 3.4 32.1 - - + -
341O VAL* 5.0 0.9 - - + -
343O GLY* 1.3 79.3 - - - +
345O LEU* 1.3 75.2 + - - +
353O ILE* 5.1 1.8 - - + -
354O LEU 3.6 4.5 - - - +
386O LEU* 3.7 1.2 - - - +
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Residues in contact with LEU 345 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283O SER* 4.5 6.1 - - - +
312O LEU* 4.2 1.2 - - - +
344O VAL* 1.3 86.5 - - - +
346O PHE* 1.3 79.2 + - - +
353O ILE* 3.4 28.9 - - - +
354O LEU* 3.2 25.7 + - + +
386O LEU* 3.9 30.7 - - + +
387O ASP* 4.7 8.1 - - - +
388O PHE* 3.2 43.3 - - + +
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Residues in contact with PHE 346 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283O SER* 4.5 7.3 + - - -
284O TRP 3.7 17.3 - - - -
285O ALA* 3.7 29.4 - - + -
286O PRO* 3.7 25.4 - - + -
288O SER* 4.5 7.4 - - - -
291O SER* 5.8 2.7 - - - -
310O PHE 5.1 0.2 - - - -
312O LEU* 3.5 42.8 - - + -
322O MET* 4.7 7.2 - - + -
345O LEU* 1.3 96.5 - - - +
347O HIS* 1.3 69.8 + - - +
349O GLY 4.8 2.9 - - - +
352O PHE 3.4 2.7 - - - -
353O ILE* 3.8 12.8 - - + -
354O LEU* 5.4 1.8 - - - -
367O TYR* 3.3 35.9 - + - -
388O PHE* 4.4 2.3 - - - +
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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