Contacts of the strand formed by residues 334 - 341 (chain G) in PDB entry 2W3S
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 GLU 334 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193G TYR* 3.3 6.6 + - - -
307G LEU* 3.4 27.4 - - + +
308G ARG* 3.1 15.8 + - - +
309G ARG* 3.7 19.1 + - + +
312G GLU* 4.8 3.1 - - - +
314G ARG* 2.4 51.0 + - - +
330G ARG* 3.1 27.1 + - + +
331G ARG* 3.0 43.3 + - + +
332G PRO 3.2 0.2 - - - -
333G GLY* 1.3 78.8 - - - +
335G PHE* 1.3 61.4 + - - +
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Residues in contact with PHE 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G SER* 4.5 6.5 - - - -
189G LEU* 4.2 25.1 - - + -
190G ALA* 3.7 38.8 - - + -
193G TYR* 3.6 19.3 - + + -
201G LEU* 3.9 12.6 - - + -
225G LEU* 6.3 0.2 - - + -
231G LEU* 5.0 7.0 - - + -
307G LEU* 3.4 5.8 - - - -
308G ARG* 2.8 61.3 + - + -
310G GLY 4.9 0.7 - - - -
330G ARG* 4.6 1.3 - - - +
333G GLY 4.1 3.1 - - - -
334G GLU* 1.3 74.5 - - - +
336G VAL* 1.3 84.3 + - - +
337G GLU* 3.8 20.4 - - + -
1465G FAD 3.4 24.0 - - + +
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Residues in contact with VAL 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G LEU* 4.7 0.7 - - - +
245G ALA* 3.6 15.7 - - + +
282G GLY* 4.2 9.6 - - - -
285G ILE* 4.3 22.7 - - + -
286G ALA* 4.3 18.6 - - + +
305G LEU* 3.6 24.5 - - + -
306G THR 3.8 4.7 - - - +
307G LEU* 4.0 16.6 - - + +
321G PHE* 4.5 9.4 - - + -
330G ARG* 5.4 2.0 - - - +
335G PHE* 1.3 87.3 - - - +
337G GLU* 1.3 62.5 + - - +
338G SER 4.1 5.6 - - - +
339G VAL* 5.3 0.4 - - + -
1465G FAD 3.3 27.7 + - + +
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Residues in contact with GLU 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G SER* 5.3 4.8 - - - +
231G LEU* 3.9 12.6 - - + +
244G GLY* 3.6 4.3 - - - -
245G ALA* 2.8 27.8 + - - +
306G THR* 3.0 29.7 + - - +
307G LEU 3.4 7.4 - - - +
308G ARG* 3.2 32.3 + - + +
313G ARG* 2.8 37.1 + - - +
335G PHE* 3.8 18.2 - - + +
336G VAL* 1.3 76.4 - - - +
338G SER* 1.3 67.6 + - - +
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Residues in contact with SER 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242G GLY* 5.9 0.9 - - - -
243G ILE 3.3 11.4 - - - -
244G GLY* 5.0 0.7 - - - -
245G ALA* 4.1 2.2 - - - +
305G LEU* 3.6 5.2 - - - +
306G THR* 2.8 53.1 + - - +
313G ARG* 4.1 6.3 + - - -
336G VAL* 4.1 2.4 - - - +
337G GLU* 1.3 98.1 + - - +
339G VAL* 1.3 70.2 - - - +
340G THR* 5.4 0.9 - - - -
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Residues in contact with VAL 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242G GLY* 3.3 1.9 - - - -
243G ILE* 2.5 68.4 + - + +
244G GLY 5.5 0.2 - - - -
245G ALA* 5.8 0.7 - - - +
252G LEU* 6.5 0.2 - - + -
281G ILE* 4.1 17.3 - - + -
285G ILE* 3.5 28.7 - - + -
298G LEU* 4.6 21.1 - - + -
303G ALA* 5.6 1.1 - - + -
304G SER 3.3 11.9 - - - +
305G LEU* 3.6 13.0 - - + +
318G LEU* 4.7 4.3 - - + -
336G VAL* 5.3 0.7 - - + -
338G SER* 1.3 80.0 - - - +
340G THR* 1.3 60.9 + - - +
341G LEU* 4.2 2.0 - - + -
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Residues in contact with THR 340 (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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237G THR* 4.0 19.5 - - + -
239G ASP* 5.1 5.8 - - - +
241G TYR 3.1 14.1 - - - +
242G GLY* 3.8 12.1 - - - -
303G ALA* 3.0 20.4 - - - +
304G SER* 2.7 36.8 + - - -
306G THR* 4.4 10.0 + - - -
315G ARG* 4.5 8.9 + - - +
338G SER* 5.4 0.9 - - - -
339G VAL* 1.3 74.5 - - - +
341G LEU* 1.3 61.9 + - - +
342G PRO* 4.0 0.3 - - - +
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Residues in contact with LEU 341 (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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239G ASP 5.2 0.9 - - - -
240G GLY* 3.4 1.4 - - - -
241G TYR* 2.4 51.6 + - + +
243G ILE* 3.8 34.1 - - + -
252G LEU* 4.7 5.6 - - + -
255G PHE* 5.1 3.8 - - + -
256G ALA* 5.9 1.1 - - + -
260G HIS* 4.6 10.3 - - + +
263G LEU* 4.3 19.5 - - + -
298G LEU* 3.5 36.6 - - + -
301G MET* 3.7 19.1 - - + -
303G ALA* 3.8 9.9 - - + -
339G VAL* 4.7 1.6 - - + -
340G THR* 1.3 77.7 - - - +
342G PRO* 1.3 69.9 - - + +
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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