Contacts of the helix formed by residues 285 - 292 (chain G) in PDB entry 1O1F
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 TYR 285 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231G ALA 4.0 3.8 - - - +
232G PHE 2.8 23.8 - - - +
233G GLY* 3.3 21.1 - - - -
234G ASN 3.3 20.2 - - - -
235G ALA* 4.0 1.3 - - + +
245G ARG* 3.8 8.4 - - + +
270G LEU* 3.8 8.4 - - + +
271G GLU* 2.5 43.8 + - - +
274G ARG* 3.2 24.2 - - + -
275G VAL* 3.9 20.4 - - + -
284G SER* 1.4 96.5 + - - +
286G HIS* 1.3 65.6 + - - +
287G ILE* 3.4 1.3 - - + -
288G PHE* 4.0 14.4 + + + -
289G TYR* 3.2 12.0 - - - -
434G TYR* 3.7 20.4 - + - +
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Residues in contact with HIS 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230G GLU* 3.3 25.4 - - + -
231G ALA* 3.2 8.1 + - - +
234G ASN 3.2 8.1 + - - -
235G ALA* 3.4 28.5 + - - -
236G MLY 3.9 2.9 - - - -
241G ASP 3.9 8.7 - - - -
242G ASN* 2.5 29.2 + - - -
283G ARG* 3.5 24.7 + - - +
284G SER 4.3 0.2 - - - -
285G TYR* 1.3 74.1 - - - +
287G ILE* 1.3 57.6 - - - +
289G TYR* 2.6 34.8 + - - +
290G GLN* 2.7 27.6 + - - +
325G ILE* 4.7 10.2 - - + +
327G ASP* 5.0 1.7 - - - +
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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
----------------------------------------------------------
231G ALA* 2.7 30.7 + - + +
232G PHE* 3.0 44.0 - - + -
285G TYR* 4.4 1.6 - - + -
286G HIS* 1.3 70.0 - - - +
288G PHE* 1.3 81.1 + - + +
290G GLN* 2.9 16.9 + - + +
291G ILE* 2.8 35.0 + - + +
334G THR* 4.5 7.9 - - + -
352G TYR* 4.8 15.7 - - + -
355G THR* 4.3 14.1 - - + +
434G TYR* 4.0 18.4 - - - +
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Residues in contact with PHE 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G VAL* 4.9 8.7 - - + -
284G SER* 4.0 17.7 - - - -
285G TYR* 4.0 22.4 - + + +
286G HIS 2.7 2.6 + - - -
287G ILE* 1.3 84.8 - - + +
289G TYR* 1.3 69.2 + - + +
291G ILE* 3.5 4.4 + - - +
292G MET* 3.2 28.7 + - - +
315G VAL* 4.0 33.0 - - + -
355G THR* 3.4 34.8 - - + -
358G VAL* 4.6 12.3 - - + -
359G MET* 3.8 30.7 - - + +
434G TYR* 3.9 30.7 - + - -
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Residues in contact with TYR 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G GLN* 4.1 1.0 + - - -
283G ARG* 3.4 35.2 - - - +
284G SER* 3.3 29.1 + - - -
285G TYR 3.2 23.8 - - - -
286G HIS 2.6 11.5 + - - +
288G PHE* 1.3 73.5 - - + +
290G GLN* 1.3 67.0 + - - +
292G MET* 4.0 6.6 - - - +
293G SER* 3.3 17.5 + - - -
309G PRO* 4.7 9.4 - - + -
315G VAL* 2.3 48.0 + - + +
319G GLU 3.5 12.0 + - - -
320G ILE* 3.5 36.3 - - + +
327G ASP* 3.7 13.5 - - - +
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Residues in contact with GLN 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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231G ALA* 3.5 17.9 - - - +
286G HIS* 2.7 28.1 + - - +
287G ILE* 3.0 16.8 - - + +
289G TYR* 1.3 77.4 - - - +
291G ILE* 1.3 51.4 + - + +
293G SER* 2.6 38.6 + - - -
327G ASP* 3.3 18.3 + - - +
330G GLU* 3.5 17.8 - - + +
331G LEU* 2.8 36.5 - - + +
334G THR* 2.4 39.0 + - - +
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Residues in contact with ILE 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G ILE* 2.8 27.3 + - + +
288G PHE* 3.6 5.6 - - - +
290G GLN* 1.3 74.3 - - + +
292G MET* 1.3 60.2 + - + +
293G SER 3.0 1.6 + - - -
294G ASN* 3.8 2.9 + - - -
295G MLY 5.3 0.2 + - - -
296G MLY 5.5 0.3 - - - +
299G LEU* 4.9 10.8 - - + +
300G ILE* 3.1 20.3 - - + +
303G LEU* 3.6 25.8 - - + -
305G ILE* 4.0 24.0 - - + -
331G LEU* 3.1 12.9 - - + +
352G TYR* 3.7 33.2 - - + -
355G THR* 4.7 19.1 - - + -
359G MET* 4.6 5.8 - - + -
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Residues in contact with MET 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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288G PHE 3.2 20.1 + - - +
289G TYR* 4.0 7.2 - - - +
291G ILE* 1.3 79.9 - - + +
293G SER* 1.3 63.4 + - - +
294G ASN* 3.2 2.2 - - - -
300G ILE* 4.2 7.2 - - - -
305G ILE* 4.3 12.3 - - + -
306G THR 3.8 13.5 - - - +
307G THR* 3.5 30.4 - - - +
308G ASN 3.4 6.3 - - - +
309G PRO* 3.0 58.3 - - + -
312G TYR* 4.4 7.2 - - + -
315G VAL* 4.8 7.0 - - - -
359G MET* 4.2 20.9 - - + +
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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