Contacts of the helix formed by residues 276 - 289 (chain G) in PDB entry 1XFB
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 SER 276 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274G GLY 3.8 0.8 + - - -
275G GLN* 1.3 75.8 - - - +
277G GLU* 1.3 66.8 + - - +
278G GLU* 3.0 6.1 + - - +
279G GLU* 3.0 32.6 + - - +
280G ALA* 2.9 21.2 + - - +
305G ALA* 4.9 1.1 - - - -
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Residues in contact with GLU 277 (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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276G SER* 1.3 73.7 - - - +
278G GLU* 1.3 61.8 + - + +
280G ALA* 3.8 3.1 + - - +
281G SER* 2.9 13.5 + - - -
305G ALA* 3.5 24.4 - - - +
306G LEU 4.0 2.6 - - - -
308G ALA* 3.3 25.4 + - + +
309G SER* 2.8 49.5 + - - -
331G ARG* 2.8 52.3 + - - +
335G ASN* 4.9 0.2 + - - -
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Residues in contact with GLU 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G SER* 3.1 5.4 + - - +
277G GLU* 1.3 77.2 - - + +
279G GLU* 1.3 57.9 + - - +
280G ALA 3.1 1.8 - - - -
281G SER* 2.9 3.9 + - - -
282G PHE* 2.7 75.0 + - + -
331G ARG* 2.5 34.6 + - - -
343G TYR* 3.1 13.3 + - - -
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Residues in contact with GLU 279 (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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274G GLY 4.7 1.2 - - - +
275G GLN* 3.5 26.7 - - - +
276G SER* 3.0 36.1 + - - +
278G GLU* 1.3 75.6 - - - +
280G ALA* 1.3 56.7 + - - +
282G PHE* 3.9 5.3 - - - +
283G ASN* 3.0 44.3 + - - +
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Residues in contact with ALA 280 (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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272G SER* 4.4 2.7 - - - -
275G GLN* 3.6 20.8 + - + +
276G SER 2.9 15.7 + - - +
277G GLU 3.9 1.8 - - - +
279G GLU* 1.3 78.2 - - - +
281G SER* 1.3 57.4 + - - +
283G ASN* 3.9 1.0 - - - +
284G LEU* 2.8 26.7 + - - +
302G TYR* 3.1 40.6 + - + -
305G ALA* 3.8 14.6 - - + -
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Residues in contact with SER 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G GLU 2.9 14.9 + - - -
278G GLU* 2.9 8.2 + - - -
280G ALA* 1.3 78.8 - - - +
282G PHE* 1.3 57.1 + - - +
285G ASN* 2.9 31.8 + - - +
331G ARG* 3.0 17.6 + - - -
334G VAL* 3.8 19.1 - - - -
335G ASN* 2.7 26.5 + - - -
338G ALA* 3.3 7.8 - - - +
343G TYR* 4.4 8.3 - - - -
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Residues in contact with PHE 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246G PRO* 4.5 16.2 - - + +
278G GLU* 2.7 53.8 + - + +
279G GLU* 3.9 5.8 - - - +
281G SER* 1.3 71.3 - - - +
283G ASN* 1.3 63.0 + - - +
285G ASN* 3.2 7.4 + - - +
286G ALA* 2.8 30.1 + - - +
343G TYR* 3.8 21.8 - + - -
344G GLU 6.0 3.4 - - - -
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Residues in contact with ASN 283 (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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233G MET* 3.7 20.2 - - - +
235G THR* 5.2 1.0 - - - +
246G PRO* 3.1 32.7 - - - +
249G ILE* 3.8 30.5 - - + +
250G ALA* 4.6 0.5 - - - +
275G GLN* 2.7 21.3 - - - +
279G GLU* 3.0 27.8 + - - +
280G ALA 3.9 0.7 - - - +
282G PHE* 1.3 76.9 - - - +
284G LEU* 1.3 64.2 + - - +
286G ALA* 3.2 6.4 + - - +
287G ILE* 2.9 29.3 + - - +
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Residues in contact with LEU 284 (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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233G MET* 4.1 5.3 - - + +
270G PHE* 4.2 14.4 - - + -
280G ALA 2.8 21.8 + - - +
281G SER 3.8 3.8 - - - +
283G ASN* 1.3 73.3 - - - +
285G ASN* 1.3 63.4 + - - +
287G ILE* 3.1 8.1 + - + +
288G ASN* 3.0 22.4 + - - +
298G LEU 3.3 26.0 - - - +
299G THR 3.8 12.8 - - - +
300G PHE* 3.7 41.5 - - + -
302G TYR* 3.5 9.0 - - + +
335G ASN* 4.0 14.4 - - - +
338G ALA* 3.7 13.2 - - + +
339G ALA* 4.1 3.4 - - - +
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Residues in contact with ASN 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G SER 2.9 18.3 + - - +
282G PHE* 3.4 7.6 - - - +
284G LEU* 1.3 75.2 - - - +
286G ALA* 1.3 64.7 + - - +
288G ASN* 2.9 14.7 + - - +
289G ARG* 3.0 44.6 + - - +
338G ALA* 3.2 15.8 - - + +
341G GLY* 3.0 14.0 + - - -
343G TYR* 2.9 53.7 + - + +
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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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246G PRO* 3.2 39.3 - - + +
247G GLU* 4.1 13.9 - - - +
250G ALA* 3.5 7.7 - - + +
282G PHE 2.8 16.3 + - - +
283G ASN 3.5 7.2 - - - +
285G ASN* 1.3 73.2 - - - +
287G ILE* 1.3 57.4 + - - +
289G ARG* 2.9 25.5 + - - +
290G CYS* 3.0 10.7 + - - -
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Residues in contact with ILE 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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233G MET* 4.0 23.3 - - + -
249G ILE* 5.5 1.1 - - + -
250G ALA* 3.4 26.4 - - - +
253G THR* 3.8 14.4 - - + +
254G VAL* 3.8 10.1 - - + +
270G PHE* 3.8 35.9 - - + -
283G ASN* 2.9 19.2 + - + +
284G LEU* 3.1 10.5 + - + +
286G ALA* 1.3 75.0 - - - +
288G ASN* 1.3 57.7 + - - +
290G CYS* 3.0 25.4 + - - +
294G ARG* 3.6 6.6 - - - -
298G LEU* 3.4 28.9 - - + -
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Residues in contact with ASN 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G LEU* 3.0 15.0 + - - +
285G ASN 2.9 4.9 + - - +
287G ILE* 1.3 73.3 - - - +
289G ARG* 1.3 59.7 + - - +
294G ARG* 2.8 34.2 + - - +
298G LEU* 2.8 39.7 + - - +
338G ALA 2.9 20.7 + - - +
339G ALA* 3.2 21.0 - - - +
340G GLN* 3.9 4.5 - - - +
341G GLY* 3.4 22.3 - - - +
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Residues in contact with ARG 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247G GLU* 5.0 9.3 + - - -
285G ASN* 3.0 26.1 + - - +
286G ALA* 2.9 15.3 + - - +
288G ASN* 1.3 80.1 - - - +
290G CYS* 1.3 66.7 + - - +
291G PRO* 3.5 5.4 - - - +
341G GLY* 2.8 31.8 + - - +
344G GLU* 5.2 8.3 + - - -
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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