Contacts of the strand formed by residues 277 - 284 (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 ALA 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B THR* 1.3 72.0 - - - +
278B VAL* 1.3 60.3 + - - +
279B PHE* 4.2 6.4 - - + -
331B PHE 3.7 0.9 - - - +
332B GLU* 3.1 5.2 - - - -
333B CYS* 2.8 40.6 + - + +
335B ILE 4.1 5.6 - - - +
336B LYS* 3.9 31.1 - - + +
385B PRO* 4.2 13.2 - - + -
386B GLU* 4.3 12.8 - - - +
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B VAL* 3.8 33.3 - - + +
276B THR* 3.6 20.9 + - - +
277B ALA* 1.3 75.5 - - - +
279B PHE* 1.3 66.3 + - - +
331B PHE 3.4 9.6 - - - +
332B GLU* 3.8 14.6 - - + +
386B GLU* 4.6 1.9 + - - +
416B SER* 3.7 13.3 - - - -
417B GLY 3.9 4.5 + - - -
420B LEU* 3.8 17.9 - - + +
421B PHE* 5.4 3.0 - - + -
429B LEU* 3.8 31.4 - - + -
432B MET* 4.8 2.0 - - + -
433B MET* 4.6 2.7 - - - -
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Residues in contact with PHE 279 (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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277B ALA 4.2 6.1 - - - -
278B VAL* 1.3 78.0 - - - +
280B ALA* 1.3 70.1 + - - +
281B VAL* 5.1 1.8 - - + -
308B LEU* 4.2 5.2 - - + -
330B LEU* 3.9 1.8 - - - +
331B PHE* 3.0 67.8 + + + +
333B CYS* 4.1 9.6 - - - -
385B PRO* 3.7 26.7 - - + -
386B GLU* 3.6 35.0 - - + -
389B VAL* 4.0 34.8 - - + -
414B ILE* 4.4 7.6 - - + -
415B ILE 3.2 14.6 - - - +
416B SER* 3.7 3.8 - - - -
420B LEU* 4.0 7.0 - - - -
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Residues in contact with ALA 280 (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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279B PHE* 1.3 77.1 - - - +
281B VAL* 1.3 67.6 + - - +
282B LYS 3.9 0.2 - - - -
328B TYR* 4.6 13.2 - - + -
329B LEU 3.1 11.9 - - - +
330B LEU* 3.8 14.4 - - + -
414B ILE* 3.4 9.2 - - - +
415B ILE* 2.7 37.5 + - + +
420B LEU* 3.6 22.9 - - + +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PHE* 5.1 2.0 - - + -
280B ALA* 1.3 73.7 - - - +
282B LYS* 1.3 60.9 + - - +
283B PHE* 3.7 21.8 - - + -
304B ILE* 4.6 6.3 - - + -
327B CYS 3.4 1.4 - - - +
328B TYR* 3.2 5.4 - - - -
329B LEU* 2.8 45.1 + - + -
331B PHE* 4.4 15.5 - - + -
389B VAL* 3.9 28.7 - - + -
393B ALA* 5.5 3.6 - - + -
408B ILE* 4.7 6.7 - - + -
412B PHE* 4.1 25.1 - - + -
413B GLU 3.7 2.9 - - - -
414B ILE* 4.5 8.1 - - + -
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Residues in contact with LYS 282 (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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280B ALA 3.9 0.4 - - - -
281B VAL* 1.3 73.7 - - - +
283B PHE* 1.3 65.1 + - - +
326B PHE* 3.5 43.0 - - + -
327B CYS 3.3 5.6 - - - +
328B TYR* 3.5 28.8 + - + -
411B TYR* 5.1 3.1 - - + -
412B PHE* 3.3 4.3 - - - +
413B GLU* 2.9 65.9 + - + +
415B ILE* 4.0 20.4 - - + -
423B GLU* 2.9 30.8 + - - +
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Residues in contact with PHE 283 (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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281B VAL* 3.7 18.8 - - + -
282B LYS* 1.3 80.4 - - - +
284B ARG* 1.3 75.2 + - - +
286B PRO* 4.7 1.6 - - + -
297B LEU* 3.9 9.4 - - + -
326B PHE* 3.4 10.9 - - - -
327B CYS* 2.9 56.8 + - + -
329B LEU* 3.8 24.9 - - + -
404B VAL* 3.7 39.7 - - + -
407B SER* 3.6 10.1 - - - +
408B ILE* 3.8 17.7 - - + -
411B TYR* 3.5 24.7 - - - +
412B PHE* 4.0 5.4 - - + +
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Residues in contact with ARG 284 (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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283B PHE* 1.3 77.3 - - - +
285B LYS* 1.3 67.9 + - - +
286B PRO* 3.3 4.9 - - - +
325B GLU* 3.7 16.7 - - + +
326B PHE* 4.1 23.0 - - + -
407B SER* 2.6 29.9 + - - +
410B GLU* 5.3 12.6 + - - +
411B TYR* 4.6 30.3 + - + +
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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