Contacts of the helix formed by residues 285 - 292 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ALA 4.0 4.5 - - - +
232A PHE 2.8 23.8 - - - +
233A GLY* 3.3 20.9 - - - -
234A ASN 3.3 20.0 - - - +
235A ALA* 4.4 0.9 - - + -
245A ARG* 3.8 8.1 - - + +
270A LEU* 3.8 9.0 - - + +
271A GLU* 2.5 43.6 + - - +
274A ARG* 3.2 24.7 - - + -
275A VAL* 3.9 19.7 - - + -
284A SER* 1.3 97.7 + - - +
286A HIS* 1.3 65.2 + - - +
287A ILE* 3.4 0.9 - - + -
288A PHE* 4.0 14.1 + + + -
289A TYR* 3.2 11.6 - - - -
434A TYR* 3.7 20.6 - + - +
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Residues in contact with HIS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLU* 3.3 25.1 - - + -
231A ALA* 3.2 8.1 + - - +
234A ASN 3.2 8.7 + - - -
235A ALA* 3.4 28.7 + - - -
236A MLY 3.9 2.9 - - - -
241A ASP 3.9 8.7 - - - -
242A ASN* 2.5 29.8 + - - -
283A ARG* 3.5 24.3 + - - +
285A TYR* 1.3 70.6 - - - +
287A ILE* 1.3 57.9 - - - +
288A PHE 3.0 3.1 - - - -
289A TYR* 2.6 34.3 + - - +
290A GLN* 2.7 27.3 + - - +
325A ILE* 4.7 10.5 - - + +
327A ASP* 5.4 1.8 - - - +
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Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ALA* 2.7 30.5 + - + +
232A PHE* 3.0 45.3 - - + -
285A TYR* 4.4 1.1 - - + -
286A HIS* 1.3 70.7 - - - +
288A PHE* 1.3 78.7 - - + +
290A GLN* 2.9 16.9 + - + +
291A ILE* 2.8 35.9 + - + +
334A THR* 4.5 8.1 - - + -
351A ILE* 5.4 0.2 - - + -
352A TYR* 4.8 15.9 - - + -
355A THR* 4.3 13.5 - - + +
434A TYR* 4.0 18.2 - - - +
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A VAL* 4.9 9.0 - - + -
284A SER* 4.0 17.0 - - - -
285A TYR* 4.0 24.0 - + + +
286A HIS 2.7 2.4 + - - -
287A ILE* 1.3 84.4 - - + +
289A TYR* 1.3 70.7 + - + +
291A ILE* 3.5 5.3 + - - +
292A MET* 3.2 28.6 + - - +
315A VAL* 4.0 31.6 - - + -
355A THR* 3.4 34.5 - - + -
358A VAL* 4.6 12.3 - - + -
359A MET* 3.8 29.6 - - + -
434A TYR* 3.9 31.9 - + - -
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Residues in contact with TYR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLN* 4.1 1.2 + - - -
283A ARG* 3.4 36.6 - - - +
284A SER* 3.4 29.7 + - - -
285A TYR 3.2 23.8 - - - -
286A HIS 2.6 10.6 + - - +
288A PHE* 1.3 73.7 - - + +
290A GLN* 1.3 67.6 + - - +
292A MET* 3.6 6.4 + - - +
293A SER* 3.3 17.3 + - - -
309A PRO* 4.7 8.5 - - + -
315A VAL* 2.3 46.4 + - + -
319A GLU 3.5 11.1 + - - -
320A ILE* 3.5 36.6 - - + +
327A ASP* 3.7 10.9 - - - +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ALA* 3.5 17.2 - - - +
286A HIS* 2.7 28.1 + - - +
287A ILE* 2.9 18.0 + - + +
289A TYR* 1.3 76.8 - - - +
291A ILE* 1.3 51.6 + - - +
293A SER* 2.6 38.5 + - - -
327A ASP* 3.3 17.5 + - - +
330A GLU* 3.5 16.6 - - + +
331A LEU* 2.8 36.8 - - + +
334A THR* 2.4 40.9 + - - +
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Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ILE* 2.8 26.1 + - + +
288A PHE* 3.6 5.6 - - - +
290A GLN* 1.3 74.7 - - + +
292A MET* 1.3 60.1 + - + +
293A SER 3.0 1.1 + - - -
294A ASN* 3.8 2.9 + - - -
296A MLY 5.5 0.2 - - - +
299A LEU* 4.9 10.1 - - + +
300A ILE* 3.1 19.3 - - + +
303A LEU* 3.6 26.2 - - + -
305A ILE* 4.0 24.0 - - + -
331A LEU* 3.2 13.4 - - + +
352A TYR* 3.7 32.1 - - + -
355A THR* 4.7 17.9 - - + -
359A MET* 4.6 6.1 - - + -
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Residues in contact with MET 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A PHE 3.2 20.1 + - - +
289A TYR* 4.0 7.2 - - + +
290A GLN 3.3 0.2 - - - -
291A ILE* 1.3 79.6 - - + +
293A SER* 1.3 62.6 + - - +
294A ASN* 3.2 3.0 + - - -
300A ILE* 4.2 6.7 - - - -
305A ILE* 4.3 12.3 - - + -
306A THR 3.8 13.0 - - - +
307A THR* 3.5 32.3 - - - +
308A ASN 3.4 7.0 - - - +
309A PRO* 3.0 57.2 - - + -
312A TYR* 4.4 7.9 - - + -
315A VAL* 4.8 6.5 - - - -
359A MET* 4.2 21.1 - - + +
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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