Contacts of the strand formed by residues 345 - 352 (chain D) 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 LYS 345 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309D GLY 3.1 11.5 + - - +
310D ALA* 3.2 4.6 - - + -
311D ILE* 3.0 24.0 + - - +
343D THR* 4.1 16.8 - - - -
344D ARG* 1.3 77.5 - - - +
346D ALA* 1.3 60.5 + - - +
372D ASP* 3.3 35.9 - - + +
374D ALA* 5.2 9.2 - - + -
398D LEU* 4.3 16.4 - - + -
401D GLU* 4.0 37.1 + - + +
402D ILE* 4.8 10.0 - - + +
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Residues in contact with ALA 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D ILE* 3.1 25.8 - - + -
345D LYS* 1.3 78.3 - - - +
347D LEU* 1.3 59.8 + - - +
348D VAL 4.1 0.4 - - - -
366D LEU* 3.8 23.3 - - + -
371D PHE* 4.3 9.9 - - + -
372D ASP 3.0 6.9 + - - -
373D VAL* 3.4 12.5 - - + +
374D ALA* 2.8 33.8 + - - +
398D LEU* 4.9 4.0 - - - -
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Residues in contact with LEU 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D ILE* 3.8 42.4 - - + -
311D ILE 2.7 8.7 + - - -
312D ALA* 3.1 5.6 - - + +
313D LEU 2.9 26.7 + - - +
346D ALA* 1.3 73.3 - - - +
348D VAL* 1.3 70.5 + - - +
349D PHE* 4.1 3.7 - - + -
374D ALA 4.0 6.5 - - - +
375D CYS* 3.5 27.1 - - + +
376D GLU* 4.1 4.3 - - - +
377D GLU* 4.4 5.6 - - + +
394D ALA* 3.9 33.2 - - + +
397D LYS* 6.5 1.1 - - + -
398D LEU* 3.6 23.5 - - + +
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Residues in contact with VAL 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D LEU 3.4 6.7 - - - +
347D LEU* 1.3 73.8 - - - +
349D PHE* 1.3 64.5 + - - +
359D THR* 3.6 16.4 - - - +
362D MET* 3.5 41.1 - - + -
363D LYS* 4.3 6.7 - - + -
366D LEU* 3.4 32.8 - - + -
373D VAL* 3.4 22.4 - - + -
375D CYS 3.4 6.3 + - - -
376D GLU* 2.9 37.1 - - + +
377D GLU 3.0 1.7 + - - -
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Residues in contact with PHE 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D VAL* 4.4 3.1 - - + -
262D ILE 4.0 6.7 - - - -
263D TYR* 4.0 2.0 - - + -
270D THR* 3.6 32.3 - - + -
273D MET* 3.8 17.7 - - + -
274D ALA* 3.7 26.5 - - + -
277D ILE* 3.7 18.6 - - + -
312D ALA* 3.9 14.4 - - + -
313D LEU 3.2 18.6 + - - -
314D GLY* 3.0 40.6 - - - -
315D ALA 3.2 3.8 + - - -
347D LEU* 4.1 9.2 - - + -
348D VAL* 1.3 79.0 - - - +
350D GLY* 1.3 61.2 + - - +
359D THR* 3.7 7.9 - - - -
362D MET* 3.6 8.1 - - - +
377D GLU* 3.1 26.7 - - + +
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Residues in contact with GLY 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D THR* 4.0 7.2 - - - -
273D MET* 3.8 11.4 - - - -
315D ALA 3.7 14.1 - - - -
349D PHE* 1.3 79.7 - - - +
351D SER* 1.3 61.5 + - - -
352D MET* 5.3 0.4 - - - -
359D THR* 3.9 4.5 - - - +
377D GLU 2.8 9.8 + - - +
378D GLU* 3.2 10.1 - - - +
379D VAL 3.1 21.8 + - - -
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Residues in contact with SER 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D SER* 3.6 11.8 - - - -
270D THR* 3.4 9.6 + - - -
273D MET* 3.3 20.8 - - - +
315D ALA 4.5 0.2 - - - +
316D PRO* 3.2 26.3 - - - +
317D THR 3.5 1.4 + - - -
350D GLY* 1.3 72.9 - - - -
352D MET* 1.3 65.7 + - - +
379D VAL 3.4 5.2 - - - -
381D TYR* 2.6 26.6 + - - -
2701D FMN 3.1 21.5 + - - +
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Residues in contact with MET 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D THR* 3.1 26.2 - - + -
350D GLY 4.8 0.4 - - - +
351D SER* 1.3 74.5 + - - +
353D GLY* 1.3 59.5 + - - +
354D GLY 3.5 22.4 - - - +
355D ASN 4.0 1.6 - - - +
356D GLY* 3.7 18.6 - - - -
378D GLU* 3.8 29.2 - - + +
379D VAL 2.9 20.3 + - - +
380D TYR* 3.5 27.4 - - + +
381D TYR* 2.9 25.5 + - - -
2701D FMN 3.5 14.4 - - - +
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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