Contacts of the strand formed by residues 341 - 348 (chain B) in PDB entry 3OVS
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A ARG* 3.2 44.8 + - + +
276A THR* 3.5 27.8 - - + -
316A LEU* 3.7 15.3 - - + -
334A GLN* 3.8 2.8 - - - -
339B SER* 2.8 21.3 + - - -
340B ARG* 1.3 77.4 - - - +
342B PHE* 1.3 60.4 - - - +
365B PHE* 4.1 6.1 - - + -
377B PHE* 4.6 8.1 - - + -
378B GLU 3.1 8.1 - - - +
379B MET* 3.3 23.6 - - - -
380B ARG* 3.1 8.4 + - - -
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Residues in contact with PHE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A LEU* 4.2 5.4 - - - -
334A GLN* 3.5 16.6 - - - +
340B ARG 4.1 0.2 - - - -
341B VAL* 1.3 74.5 - - - +
343B ARG* 1.3 77.3 + - - +
344B ARG* 4.0 28.5 - - - -
377B PHE* 3.4 7.4 - - - -
378B GLU* 3.0 68.8 + - + -
379B MET 3.9 13.9 - - - -
380B ARG* 3.6 41.3 - - + +
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Residues in contact with ARG 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A PHE* 5.4 2.8 - - - -
315A PRO 4.8 2.5 - - - +
316A LEU* 3.0 50.8 + - + +
317A ARG* 4.1 0.2 - - - +
334A GLN* 4.0 4.7 + - - +
342B PHE* 1.3 87.0 - - - +
344B ARG* 1.3 61.5 + - - +
345B MET 4.2 0.4 + - - -
368B PHE* 3.7 20.7 - - + -
370B GLU* 2.8 42.6 + - - -
375B TRP* 3.4 52.2 - - + -
376B ALA 3.4 6.3 - - - +
377B PHE* 4.8 3.4 - - + +
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Residues in contact with ARG 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B PHE* 4.0 27.0 + - + -
343B ARG* 1.3 74.8 - - - +
345B MET* 1.3 69.6 + - - +
358B PHE* 4.0 9.8 - - + -
363B ARG* 4.8 0.2 - - - +
375B TRP* 3.2 11.0 - - - +
376B ALA* 2.7 40.4 + - + +
378B GLU* 3.2 42.7 + - + +
13D U 5.1 4.9 + - - -
14D U 4.1 43.6 + - - +
15D C 4.8 2.7 - - - +
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Residues in contact with MET 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B ARG 4.3 0.4 + - - -
344B ARG* 1.3 78.6 - - - +
346B GLY* 1.3 59.4 + - - +
358B PHE* 4.2 1.7 - - - -
373B ARG* 3.5 48.9 - - - +
375B TRP* 3.5 36.8 - - + -
14D U 5.3 0.9 + - - -
15D C 3.5 34.3 + - - +
16D A 4.3 20.3 + - + +
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Residues in contact with GLY 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B ARG 3.5 3.4 + - - -
345B MET* 1.3 71.7 - - - +
347B PRO* 1.3 70.7 - - - +
358B PHE* 3.4 17.6 - - - -
373B ARG* 2.9 24.6 + - - -
374B TRP 2.7 22.5 + - - +
15D C 3.3 14.2 + - - -
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Residues in contact with PRO 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B GLY* 1.3 84.4 - - - +
348B GLN* 1.3 69.0 + - - +
351B ASP* 4.6 6.5 - - + +
354B ASN* 3.6 33.9 - - + +
355B VAL* 3.8 14.1 - - + -
358B PHE* 3.7 24.7 - - + -
373B ARG* 3.4 11.0 - - - +
374B TRP* 3.1 25.1 - - + +
15D C 3.5 25.7 - - + +
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Residues in contact with GLN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ARG* 3.6 27.2 + - - +
347B PRO* 1.3 75.5 - - - +
349B PHE* 1.3 66.5 + - - +
350B GLU* 3.1 15.0 + - + +
351B ASP* 3.2 19.2 + - + +
355B VAL* 3.7 5.6 - - - +
372B GLY 3.1 9.0 - - - +
373B ARG* 3.5 34.9 - - + +
703B EDO 3.1 35.3 + - - -
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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