Contacts of the helix formed by residues 282 - 293 (chain G) in PDB entry 1FQV
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 282 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257G GLU* 5.6 0.2 + - - -
280G ASP 5.0 2.0 - - - +
281G PHE* 1.3 81.8 - - - +
283G GLU* 1.3 70.9 + - - +
284G LYS* 3.0 25.3 + - - +
285G HIS* 3.2 23.1 + - + +
286G VAL* 3.4 12.5 + - - +
308G ASN* 3.9 11.7 - - - +
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Residues in contact with GLU 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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282G THR* 1.3 78.5 - - - +
284G LYS* 1.3 54.1 + - + +
286G VAL* 2.6 25.8 + - - +
287G GLN* 2.7 36.6 + - + +
307G LYS* 4.7 10.7 - - - +
308G ASN* 3.3 38.5 + - + +
310G GLN* 5.0 7.9 + - + -
313G ASP* 6.0 0.2 - - - +
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Residues in contact with LYS 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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257G GLU* 3.8 33.5 + - + +
282G THR* 3.0 11.4 + - - +
283G GLU* 1.3 80.9 - - + +
285G HIS* 1.3 56.6 + - - +
287G GLN* 3.6 17.9 - - - +
288G VAL* 2.8 35.0 + - + +
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Residues in contact with HIS 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G PHE* 3.0 26.6 + + - -
256G SER* 3.4 10.5 - - - -
257G GLU* 3.5 34.6 + - + -
260G LEU* 3.6 13.6 - - + +
280G ASP* 4.8 3.5 + - - -
281G PHE* 2.8 63.3 - + + +
282G THR* 3.2 21.8 + - + +
283G GLU 3.1 1.0 - - - -
284G LYS* 1.3 72.9 - - - +
286G VAL* 1.3 61.5 + - - +
289G ALA* 2.8 28.8 + - - +
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Residues in contact with VAL 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G PHE* 4.3 6.3 - - + -
282G THR 3.6 13.7 - - - +
283G GLU 2.6 12.8 + - - +
285G HIS* 1.3 72.2 - - - +
287G GLN* 1.3 56.7 + - - +
289G ALA* 3.0 8.1 - - - +
290G VAL* 3.0 31.3 + - + +
302G LEU* 4.4 10.8 - - + -
305G TYR* 3.9 33.2 - - + -
308G ASN* 3.6 21.8 - - + +
309G LEU* 3.4 33.4 - - + -
313G ASP* 4.3 8.3 - - + +
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Residues in contact with GLN 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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283G GLU* 2.7 34.0 + - + +
284G LYS* 3.6 23.8 + - - +
286G VAL* 1.3 74.0 - - - +
288G VAL* 1.3 65.7 + - - +
290G VAL* 3.3 10.5 - - - +
291G ALA* 2.9 27.1 + - - +
310G GLN* 5.7 4.4 - - - +
312G SER* 5.8 0.8 + - - -
313G ASP* 3.5 24.5 + - - +
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Residues in contact with VAL 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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257G GLU* 3.2 44.0 - - + +
260G LEU* 4.0 10.3 - - + +
261G GLN* 3.5 40.2 - - + +
264G LEU* 4.6 2.0 - - + -
284G LYS* 2.8 28.5 + - + +
285G HIS 3.7 3.8 - - - +
287G GLN* 1.3 70.5 - - + +
289G ALA* 1.3 66.7 + - - +
291G ALA* 3.0 3.0 + - - -
292G HIS* 2.9 34.5 + - + +
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Residues in contact with ALA 289 (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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260G LEU* 4.8 0.4 - - - -
264G LEU* 3.6 13.9 - - - +
275G LEU* 3.9 24.5 - - + -
281G PHE* 6.0 0.4 - - + -
285G HIS 2.8 15.6 + - - +
286G VAL* 3.0 14.6 - - - +
288G VAL* 1.3 78.1 - - - +
290G VAL* 1.3 60.3 + - - +
293G VAL* 2.7 36.3 + - + +
302G LEU* 4.2 14.8 - - + -
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Residues in contact with VAL 290 (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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286G VAL* 3.0 17.5 + - + +
287G GLN* 3.3 15.7 - - - +
289G ALA* 1.3 78.6 - - - +
291G ALA* 1.3 55.9 + - - +
293G VAL* 4.7 2.7 - - - -
300G LEU* 5.5 0.7 - - + -
302G LEU* 3.9 19.7 - - + -
309G LEU* 5.1 1.8 - - + -
313G ASP* 3.3 43.1 - - + +
316G THR* 3.5 12.5 - - + +
317G LEU* 3.7 33.5 - - + +
320G ARG* 3.2 26.2 + - - -
321G CYS* 5.0 0.5 - - - -
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Residues in contact with ALA 291 (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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287G GLN 2.9 21.4 + - - +
288G VAL* 4.4 0.4 - - - -
290G VAL* 1.3 76.5 - - - +
292G HIS* 1.3 79.0 + - + +
316G THR* 4.0 8.5 - - + -
320G ARG* 2.7 31.9 + - - +
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Residues in contact with HIS 292 (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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261G GLN* 2.8 41.1 + - + +
264G LEU* 3.2 37.6 - - + +
265G SER* 3.1 27.8 - - - +
288G VAL* 2.9 25.2 + - + +
289G ALA 3.9 0.2 - - - -
291G ALA* 1.3 96.6 - - + +
293G VAL* 1.3 63.9 + - - +
294G SER* 3.4 0.5 + - - -
320G ARG* 3.7 4.2 + - - +
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Residues in contact with VAL 293 (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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264G LEU* 4.0 11.7 - - + -
270G LEU* 5.1 3.8 - - + -
273G LEU* 3.8 28.3 - - + -
289G ALA* 2.7 31.3 + - + +
290G VAL* 4.7 2.7 - - - +
292G HIS* 1.3 76.7 - - - +
294G SER* 1.3 67.4 + - - +
297G ILE* 3.6 38.4 - - + -
300G LEU* 5.0 13.2 - - + -
302G LEU* 6.5 0.2 - - + -
317G LEU* 5.9 0.9 - - + -
320G ARG* 2.7 28.7 + - - +
321G CYS* 3.7 7.7 - - - -
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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