Contacts of the helix formed by residues 285 - 292 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231J ALA 4.0 4.5 - - - +
232J PHE 2.8 23.6 - - - +
233J GLY* 3.3 20.6 - - - -
234J ASN 3.3 20.4 - - - +
235J ALA* 4.0 1.1 - - + +
245J ARG* 3.8 9.0 - - + +
270J LEU* 3.8 9.1 - - + +
271J GLU* 2.5 43.6 + - - +
272J MLY 5.5 0.2 - - - -
274J ARG* 3.2 24.2 - - + -
275J VAL* 3.9 20.0 - - + -
284J SER* 1.4 97.7 + - - +
286J HIS* 1.3 64.2 + - - +
287J ILE* 3.4 1.1 - - + -
288J PHE* 4.0 13.9 + + + -
289J TYR* 3.2 12.0 - - - -
434J TYR* 3.7 20.0 - + - +
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Residues in contact with HIS 286 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230J GLU* 3.3 24.9 - - + -
231J ALA* 3.2 8.8 + - - +
234J ASN 3.2 8.5 + - - -
235J ALA* 3.4 28.8 - - - -
236J MLY 3.9 2.9 - - - -
241J ASP 3.9 8.7 - - - -
242J ASN* 2.5 29.6 + - - -
283J ARG* 3.5 26.3 + - - +
285J TYR* 1.3 69.0 - - - +
287J ILE* 1.3 57.5 + - - +
288J PHE 3.0 2.5 - - - -
289J TYR* 2.6 33.6 + - - +
290J GLN* 2.7 27.8 + - - +
325J ILE* 4.7 10.4 - - + +
327J ASP* 5.4 1.6 - - - +
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Residues in contact with ILE 287 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231J ALA* 2.7 30.3 + - + +
232J PHE* 3.0 44.6 - - + -
285J TYR* 4.4 1.3 - - + -
286J HIS* 1.3 72.7 - - - +
288J PHE* 1.3 80.6 + - + +
290J GLN* 2.9 17.4 + - + +
291J ILE* 2.8 35.0 + - + +
334J THR* 4.5 7.6 - - + -
351J ILE* 5.4 0.2 - - + -
352J TYR* 4.8 15.9 - - + -
355J THR* 4.3 13.9 - - + +
434J TYR* 4.0 18.2 - - - +
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Residues in contact with PHE 288 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J VAL* 4.9 8.1 - - + -
284J SER* 4.0 17.7 - - - -
285J TYR* 4.0 22.9 - + + +
286J HIS 2.7 2.4 + - - -
287J ILE* 1.3 84.8 - - + +
289J TYR* 1.3 70.6 + - + +
291J ILE* 3.5 5.6 + - - +
292J MET* 3.2 27.6 + - - +
315J VAL* 4.0 33.2 - - + -
355J THR* 3.4 33.4 - - + -
358J VAL* 4.6 12.3 - - + -
359J MET* 3.8 29.4 - - + -
434J TYR* 3.9 32.1 - + - -
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Residues in contact with TYR 289 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278J GLN* 4.1 1.0 + - - -
283J ARG* 3.4 35.2 - - - +
284J SER* 3.3 31.2 + - - -
285J TYR 3.2 23.8 - - - -
286J HIS 2.6 10.2 + - - +
288J PHE* 1.3 72.7 - - + +
290J GLN* 1.3 67.4 + - - +
292J MET* 4.0 5.8 - - - +
293J SER* 3.3 18.0 + - - -
309J PRO* 4.7 9.6 - - + -
315J VAL* 2.3 46.3 + - + -
319J GLU 3.5 10.9 + - - -
320J ILE* 3.5 35.4 - - + +
327J ASP* 3.7 13.2 - - - +
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Residues in contact with GLN 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231J ALA* 3.5 17.2 - - - +
286J HIS* 2.7 27.6 + - - +
287J ILE* 3.0 17.6 - - + +
289J TYR* 1.3 77.2 - - - +
291J ILE* 1.3 52.1 + - + +
293J SER* 2.6 38.3 + - - -
327J ASP* 3.3 18.1 + - + +
330J GLU* 3.5 17.2 - - + +
331J LEU* 2.8 36.8 - - + +
334J THR* 2.4 39.8 + - - +
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Residues in contact with ILE 291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287J ILE* 2.8 26.2 + - + +
288J PHE* 3.6 5.8 - - - +
290J GLN* 1.3 75.2 - - + +
292J MET* 1.3 59.4 + - + +
293J SER 3.0 1.1 + - - -
294J ASN* 3.8 2.9 + - - -
299J LEU* 4.9 9.9 - - + +
300J ILE* 3.1 20.7 - - + +
303J LEU* 3.6 26.0 - - + -
305J ILE* 4.0 24.2 - - + -
331J LEU* 3.1 13.2 - - + +
352J TYR* 3.7 32.3 - - + -
355J THR* 4.7 18.2 - - + -
359J MET* 4.6 6.5 - - + -
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Residues in contact with MET 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288J PHE 3.2 21.0 + - - +
289J TYR* 4.0 6.7 - - - +
290J GLN 3.3 0.2 - - - -
291J ILE* 1.3 79.8 - - + +
293J SER* 1.3 63.8 + - - +
294J ASN* 3.2 2.8 + - - -
300J ILE* 4.2 7.4 - - - -
305J ILE* 4.3 12.3 - - + -
306J THR 3.8 13.7 - - - +
307J THR* 3.5 31.4 - - - +
308J ASN 3.4 6.3 - - - +
309J PRO* 3.0 58.1 - - + -
312J TYR* 4.4 8.5 - - + -
315J VAL* 4.8 6.3 - - - -
359J MET* 4.2 20.2 - - + +
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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