Contacts of the strand formed by residues 344 - 352 (chain J) 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 ARG 344 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250J TRP 5.6 0.2 + - - -
253J GLY* 5.1 2.8 - - - -
255J VAL* 4.0 8.5 - - - +
305J ILE* 3.0 18.3 + - - -
306J LEU* 2.8 38.8 + - - +
308J SER 2.8 25.9 + - - +
309J GLY* 3.3 14.6 - - - +
310J ALA* 4.5 1.6 - - - +
311J ILE* 5.4 0.9 - - - -
338J PHE* 3.4 19.8 + - - -
341J THR* 2.7 29.1 + - - -
342J LEU* 3.1 32.8 + - + +
343J THR* 1.3 75.3 - - - +
345J LYS* 1.3 65.7 + - - +
370J GLY 4.3 3.8 + - - -
371J PHE* 3.6 33.2 - - + +
372J ASP* 3.0 23.7 + - - -
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Residues in contact with LYS 345 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309J GLY 2.9 11.5 + - - +
310J ALA* 3.2 5.1 - - + -
311J ILE* 3.0 25.0 + - - +
343J THR* 4.5 10.6 + - - -
344J ARG* 1.3 76.3 - - - +
346J ALA* 1.3 63.3 + - - +
371J PHE* 4.3 0.2 - - - -
372J ASP* 3.3 37.5 - - - +
374J ALA* 5.5 8.1 - - + -
398J LEU* 3.9 18.8 - - + -
401J GLU* 2.9 41.6 + - + +
402J ILE* 4.3 10.6 - - + +
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Residues in contact with ALA 346 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311J ILE* 3.2 23.8 - - + -
345J LYS* 1.3 78.2 - - - +
347J LEU* 1.3 60.1 + - - +
348J VAL 4.1 0.2 - - - -
366J LEU* 3.9 22.2 - - + -
371J PHE* 4.2 11.7 - - + -
372J ASP 3.2 5.3 + - - -
373J VAL* 3.4 14.0 - - + +
374J ALA* 2.8 34.0 + - - +
398J LEU* 4.3 5.0 - - - +
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Residues in contact with LEU 347 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277J ILE* 3.7 42.2 - - + -
311J ILE 2.9 7.7 + - - +
312J ALA* 3.2 7.9 - - + +
313J LEU* 2.9 26.3 + - - +
346J ALA* 1.3 74.0 - - - +
348J VAL* 1.3 76.1 + - - +
349J PHE* 4.1 2.1 + - + -
374J ALA 4.4 6.1 - - - +
375J CYS* 3.8 15.7 - - + +
376J GLU* 4.4 1.3 - - - -
377J GLU* 4.1 14.1 - - + +
394J ALA* 4.0 31.9 - - + +
398J LEU* 3.7 21.1 - - + +
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Residues in contact with VAL 348 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313J LEU* 3.4 5.8 - - + +
346J ALA 4.1 0.4 + - - -
347J LEU* 1.3 74.4 - - - +
349J PHE* 1.3 64.6 + - - +
359J THR* 3.3 31.0 - - - +
362J MET* 3.4 27.1 - - + -
363J LYS* 4.0 12.1 - - + +
366J LEU* 3.6 30.3 - - + -
373J VAL* 3.7 19.7 - - + -
375J CYS 3.5 7.8 + - - +
376J GLU* 2.9 31.9 - - + +
377J GLU 3.0 2.4 + - - -
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Residues in contact with PHE 349 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261J VAL* 4.3 2.7 - - + -
262J ILE 4.2 0.7 - - - -
263J TYR* 4.0 5.8 - - + -
270J THR* 3.6 27.4 - - + -
273J MET* 3.8 17.5 - - + -
274J ALA* 3.6 29.8 - - + -
277J ILE* 3.4 22.0 - - + -
312J ALA* 3.8 18.6 - - + -
313J LEU 3.0 16.1 + - - +
314J GLY* 3.1 44.3 - - - -
315J ALA 3.2 4.3 + - - -
347J LEU* 4.1 7.9 - - + -
348J VAL* 1.3 76.6 - - - +
350J GLY* 1.3 60.5 + - - +
359J THR* 3.6 7.0 - - - -
362J MET* 3.6 7.1 - - - +
377J GLU* 3.1 27.4 - - + +
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Residues in contact with GLY 350 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270J THR* 4.1 7.4 - - - -
273J MET* 3.5 10.1 - - - +
315J ALA 3.5 15.3 - - - -
349J PHE* 1.3 78.4 - - - +
351J SER* 1.3 62.5 + - - -
359J THR* 3.7 5.0 - - - +
377J GLU 2.8 10.1 + - - +
378J GLU* 3.3 9.9 - - - +
379J VAL 3.0 24.4 + - - -
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Residues in contact with SER 351 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J SER* 3.5 5.2 - - - -
270J THR* 3.1 16.7 + - - -
273J MET* 3.2 17.2 - - - +
315J ALA 4.2 0.6 + - - +
316J PRO* 3.3 22.9 - - - +
317J THR* 3.6 3.6 + - - +
350J GLY* 1.3 73.4 - - - -
352J MET* 1.3 63.1 + - - +
358J ALA* 5.8 0.2 - - - +
379J VAL 3.0 9.1 + - - -
381J TYR 2.4 29.1 + - - -
3702J FMN 3.1 24.0 + - - -
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Residues in contact with MET 352 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317J THR* 3.5 19.7 - - + -
351J SER* 1.3 78.5 + - - +
353J GLY* 1.3 57.5 + - - +
354J GLY 3.5 24.0 - - - +
355J ASN 5.3 2.5 - - - +
356J GLY* 4.0 5.8 - - - -
378J GLU* 3.9 41.5 - - + +
379J VAL 3.2 5.1 + - - +
380J TYR* 3.5 32.1 - - + +
381J TYR* 2.8 31.4 + - - -
3702J FMN 3.6 16.2 - - - +
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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