Contacts of the strand formed by residues 371 - 380 (chain G) in PDB entry 2OHI
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 PHE 371 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305G ILE* 4.0 20.9 - - + -
311G ILE* 4.1 28.5 - - + -
333G LEU* 4.1 24.5 - - + -
338G PHE* 4.0 22.4 - + + -
343G THR* 4.4 2.9 - - - -
344G ARG* 3.5 39.9 - - + +
345G LYS 4.5 0.9 - - - -
346G ALA* 4.1 12.1 - - + -
366G LEU* 2.9 29.0 + - + +
367G ALA* 3.7 19.2 + - - +
369G ALA* 3.8 17.5 - - + -
370G GLY* 1.3 84.6 - - - +
372G ASP* 1.3 62.0 + - - +
373G VAL* 3.6 3.4 + - - +
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Residues in contact with ASP 372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343G THR* 4.1 15.6 - - + +
344G ARG 2.8 14.2 + - - +
345G LYS* 2.8 41.3 + - + +
346G ALA* 2.8 21.9 + - - -
371G PHE* 1.3 71.1 - - - +
373G VAL* 1.3 64.3 + - - +
374G ALA* 3.2 12.6 + - - +
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Residues in contact with VAL 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346G ALA* 3.3 17.9 - - + +
348G VAL* 4.1 17.0 - - + -
363G LYS* 3.6 67.7 + - + +
366G LEU* 3.8 21.8 - - + -
367G ALA* 4.4 3.1 - - + +
371G PHE 3.6 6.8 + - - +
372G ASP* 1.3 75.7 + - - +
374G ALA* 1.3 56.9 + - - +
375G CYS 4.0 16.4 - - - +
376G GLU* 5.9 0.7 - - + -
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Residues in contact with ALA 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345G LYS* 5.8 5.2 - - + -
346G ALA 3.2 10.6 + - - +
347G LEU* 4.3 4.2 - - - +
372G ASP* 3.2 17.9 + - - +
373G VAL* 1.3 70.1 - - - +
375G CYS* 1.3 73.6 + - - +
397G LYS* 4.6 15.4 + - - +
398G LEU* 5.6 4.1 - - + +
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Residues in contact with CYS 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347G LEU* 3.6 10.9 - - + +
348G VAL 3.5 16.5 + - - -
363G LYS* 5.4 4.3 - - - +
373G VAL* 4.0 10.6 + - - +
374G ALA* 1.3 81.0 - - - +
376G GLU* 1.3 71.7 + - - +
377G GLU* 5.5 4.7 - - - +
394G ALA* 6.2 1.8 - - + -
397G LYS* 4.6 15.9 - - + +
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Residues in contact with GLU 376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347G LEU* 4.0 2.2 - - - -
348G VAL* 2.8 23.6 - - + +
359G THR* 2.6 36.3 + - - +
360G GLY* 4.7 1.2 + - - -
363G LYS* 5.3 15.1 + - + +
373G VAL* 5.9 1.6 - - + -
375G CYS* 1.3 82.4 - - - +
377G GLU* 1.3 78.6 + - - +
378G GLU* 3.8 11.1 - - + +
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Residues in contact with GLU 377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273G MET* 3.3 16.9 - - + +
277G ILE* 5.3 0.9 - - + -
347G LEU* 4.3 6.7 - - + +
348G VAL 2.9 6.7 + - - -
349G PHE* 3.0 28.9 - - + -
350G GLY 3.1 6.1 + - - -
359G THR* 4.4 0.6 - - - +
375G CYS* 5.5 4.9 - - - +
376G GLU* 1.3 81.8 - - - +
378G GLU* 1.3 62.7 + - - +
379G VAL* 5.8 2.5 - - + +
387G GLU 5.3 0.2 - - - +
390G ALA* 3.9 31.4 - - - +
391G CYS* 4.5 12.1 + - - -
394G ALA* 3.8 28.1 - - + +
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Residues in contact with GLU 378 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350G GLY 3.5 6.7 - - - +
352G MET* 3.2 42.0 - - + +
355G ASN 4.5 3.1 - - - +
356G GLY* 4.4 8.3 - - - -
357G GLY 4.6 5.2 + - - -
359G THR* 2.8 36.7 + - + +
376G GLU* 3.8 11.5 + - + +
377G GLU* 1.3 75.8 + - - +
379G VAL* 1.3 70.4 + - - +
387G GLU* 5.4 0.2 - - - +
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Residues in contact with VAL 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273G MET* 3.8 31.6 - - + -
350G GLY 3.2 6.8 + - - +
351G SER* 3.2 4.3 + - - +
352G MET* 2.8 35.0 + - - +
377G GLU* 5.8 2.9 - - + +
378G GLU* 1.3 80.7 - - - +
380G TYR* 1.3 62.8 + - - +
381G TYR 3.4 21.5 - - - +
383G PRO* 3.8 19.1 - - + -
387G GLU* 3.6 37.7 - - + +
391G CYS* 5.1 4.0 - - - -
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Residues in contact with TYR 380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352G MET* 3.5 20.7 - - + +
353G GLY 3.2 28.3 - - - -
354G GLY 5.5 1.1 - - - -
379G VAL* 1.3 69.4 - - - +
381G TYR* 1.3 81.6 + + - +
382G VAL 3.6 0.2 - - - +
387G GLU* 4.2 3.6 + - - +
109H VAL* 4.4 7.6 + - - +
112H LYS* 3.8 15.7 - - + +
113H GLY* 3.3 24.6 + - - -
116H LYS* 2.9 72.1 + - + +
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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