Contacts of the helix formed by residues 280 - 288 (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 THR 280 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203G ALA* 3.3 17.3 - - + +
204G GLY 5.1 0.2 - - - +
226G SER* 6.5 0.7 - - - -
245G ALA 3.6 11.5 + - - -
246G GLY* 3.4 20.2 - - - +
247G VAL 3.3 20.9 - - - +
248G THR* 3.9 5.8 - - + -
249G ILE* 3.4 8.2 - - - +
278G VAL 4.2 7.0 - - - +
279G ALA* 1.3 80.2 - - - +
281G ILE* 1.3 56.0 + - - +
283G GLY 3.4 8.0 + - - -
284G ASN* 2.6 35.3 + - - +
1465G FAD 2.6 25.5 + - - +
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Residues in contact with ILE 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243G ILE* 3.4 33.0 - - + -
244G GLY 3.2 24.5 - - - +
245G ALA* 4.1 1.6 - - - +
247G VAL* 3.3 20.3 + - + +
248G THR 5.5 0.4 - - - +
249G ILE* 3.5 12.8 - - + +
252G LEU* 3.6 26.9 - - + -
280G THR* 1.3 68.0 - - - +
282G GLY* 1.3 67.8 + - - +
284G ASN* 4.2 5.2 - - + -
285G ILE* 2.9 41.7 + - + +
294G GLY* 6.2 3.8 - - - -
298G LEU* 5.0 6.7 - - + -
339G VAL* 4.1 13.0 - - + -
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Residues in contact with GLY 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245G ALA* 2.9 38.3 + - - +
281G ILE* 1.3 78.0 - - - +
283G GLY* 1.3 52.8 + - - +
285G ILE* 3.5 1.6 - - - +
286G ALA* 2.6 37.4 + - - +
336G VAL* 4.2 11.1 - - - +
1465G FAD 4.1 10.5 - - - -
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Residues in contact with GLY 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G THR* 3.4 12.7 + - - -
281G ILE 3.3 0.2 - - - -
282G GLY* 1.3 72.1 - - - +
284G ASN* 1.3 67.0 + - - +
287G ASN* 2.8 26.7 + - - +
1465G FAD 3.4 49.5 + - - +
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Residues in contact with ASN 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G ILE* 4.6 2.2 - - + -
270G PHE* 3.3 11.7 - - + -
280G THR 2.6 22.3 + - - +
281G ILE* 3.8 8.7 - - + +
283G GLY* 1.3 73.8 - - - +
285G ILE* 1.3 62.9 + - + +
287G ASN* 3.2 16.6 + - - +
288G GLY* 3.4 5.4 + - - -
289G SER 4.8 1.0 + - - -
292G GLY* 4.2 8.2 - - - -
294G GLY* 3.2 12.1 + - - -
295G PRO* 3.1 32.9 - - - +
1465G FAD 3.0 53.4 + - - +
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Residues in contact with ILE 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G ILE* 2.9 35.7 + - + +
282G GLY* 3.7 2.9 - - - +
284G ASN* 1.3 72.7 - - + +
286G ALA* 1.3 61.6 + - - +
288G GLY* 3.2 16.1 + - - -
294G GLY* 6.0 0.9 - - - -
295G PRO* 4.6 15.9 - - + -
298G LEU* 5.0 4.9 - - + -
305G LEU* 3.8 18.2 - - + -
318G LEU* 4.0 20.6 - - + -
321G PHE* 3.7 28.4 - - + -
322G PHE* 3.6 13.4 - - + -
336G VAL* 4.3 7.0 - - + -
339G VAL* 3.5 31.9 - - + -
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Residues in contact with ALA 286 (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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282G GLY 2.6 17.6 + - - +
285G ILE* 1.3 70.3 - - - +
287G ASN* 1.3 64.3 + - - +
288G GLY 3.6 0.2 + - - -
321G PHE* 4.6 7.2 - - - -
328G GLN* 4.4 7.4 - - - +
330G ARG* 4.1 13.7 + - - +
336G VAL* 4.3 9.2 - - + +
1465G FAD 3.1 58.3 + - + +
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Residues in contact with ASN 287 (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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207G ASP* 3.4 32.3 + - - +
211G TRP* 5.1 5.9 + - - -
283G GLY 2.8 20.0 + - - +
284G ASN* 3.2 7.9 + - - +
286G ALA* 1.3 79.9 - - - +
288G GLY* 1.3 60.3 + - - +
289G SER* 3.5 28.9 + - - -
326G ARG* 5.5 4.5 + - - -
328G GLN* 4.4 4.0 - - - +
1465G FAD 3.5 24.0 + - - +
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Residues in contact with GLY 288 (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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284G ASN 3.4 4.1 + - - -
285G ILE 3.2 15.7 + - - -
287G ASN* 1.3 78.8 - - - +
289G SER* 1.3 64.6 + - - +
290G PRO* 3.7 4.0 - - - +
295G PRO* 6.4 0.2 - - - -
322G PHE* 4.0 20.5 - - - -
325G TYR* 5.4 2.1 - - - -
326G ARG 5.2 5.5 + - - -
328G GLN* 4.1 20.7 + - - +
389G GLY 5.0 4.3 - - - +
390G VAL* 5.7 0.9 - - - +
391G PRO* 5.4 2.5 - - - +
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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