Contacts of the helix formed by residues 256 - 267 (chain C) in PDB entry 1OL1
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 ASP 256 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C LYS* 4.7 6.4 + - - -
254C PRO 4.0 1.4 + - - -
255C LEU* 1.3 77.8 - - - +
257C GLU* 1.3 54.0 + - - +
258C ASP* 4.3 6.8 - - - +
259C GLY* 2.7 34.6 + - - -
260C ARG* 2.6 35.7 + - - +
285C PHE* 3.6 16.5 - - - -
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Residues in contact with GLU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C ASP* 1.3 71.5 - - - +
258C ASP* 1.3 55.6 + - - +
260C ARG* 2.9 27.3 + - - +
261C SER* 2.7 38.1 + - - -
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Residues in contact with ASP 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C ASP* 3.4 7.9 - - - +
257C GLU* 1.3 78.9 - - - +
259C GLY* 1.3 63.2 + - - +
261C SER* 3.2 3.9 + - - -
262C LEU* 3.1 7.8 + - - +
283C HIS* 2.9 28.4 - - - -
284C PRO* 3.5 32.2 - - - +
285C PHE* 3.9 20.4 - - + -
287C GLN* 5.5 0.5 + - - -
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Residues in contact with GLY 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C PHE* 3.7 6.4 - - - -
255C LEU* 3.7 13.2 - - - -
256C ASP* 2.7 26.6 + - - -
258C ASP* 1.3 75.0 - - - +
260C ARG* 1.3 56.0 + - - +
262C LEU* 3.4 1.0 + - - +
263C LEU* 3.1 28.8 + - - +
285C PHE* 3.4 24.0 - - - -
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Residues in contact with ARG 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C PHE* 4.4 14.5 - - + +
249C SER* 3.3 47.7 + - - +
252C VAL* 3.6 33.9 - - + -
253C PRO 4.5 5.7 + - - -
255C LEU* 3.3 28.1 + - + +
256C ASP* 2.6 15.3 + - - +
257C GLU* 2.9 29.3 + - - +
259C GLY* 1.3 71.0 - - - +
261C SER* 1.3 62.6 + - - +
263C LEU* 4.2 3.7 - - - +
264C SER* 3.4 22.2 + - - -
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Residues in contact with SER 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C GLU 2.7 18.4 + - - -
258C ASP* 3.7 7.0 - - - -
260C ARG* 1.3 74.7 - - - +
262C LEU* 1.3 63.9 + - - +
264C SER* 3.4 6.0 + - - -
265C GLN* 3.1 35.5 + - - +
283C HIS* 2.9 18.6 + - - -
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Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LEU* 4.3 11.2 - - + -
112C LEU* 5.1 0.4 - - + -
193C PHE* 4.6 1.6 - - + -
258C ASP 3.1 6.0 + - - +
259C GLY 3.9 2.2 - - - +
261C SER* 1.3 79.0 + - - +
263C LEU* 1.3 64.3 + - - +
265C GLN* 3.1 6.7 + - + +
266C MET* 3.1 33.1 + - + +
275C ILE* 4.8 6.7 - - + -
280C ALA* 3.6 28.7 - - + -
283C HIS* 3.4 33.7 - - + +
285C PHE* 3.8 18.6 - - + -
286C PHE* 3.7 34.8 - - + -
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Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C GLY* 3.3 30.7 - - - +
193C PHE* 3.7 19.3 - - + -
194C ALA* 4.1 9.6 - - + -
202C LEU* 5.8 0.4 - - + -
248C PHE* 3.3 28.9 - - + -
252C VAL* 3.7 28.7 - - + -
255C LEU* 4.5 6.1 - - + -
259C GLY 3.1 17.8 + - - +
260C ARG* 4.5 2.7 - - - +
261C SER 3.4 0.2 - - - -
262C LEU* 1.3 75.7 - - - +
264C SER* 1.3 65.0 + - - +
266C MET* 3.0 14.7 + - - +
267C LEU* 3.2 29.2 + - + +
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Residues in contact with SER 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ARG* 4.4 19.9 + - - +
248C PHE* 4.3 20.4 - - - -
260C ARG 3.4 18.2 + - - -
261C SER* 3.4 8.4 + - - -
262C LEU 3.3 0.6 - - - -
263C LEU* 1.3 80.6 - - - +
265C GLN* 1.3 66.5 + - - +
267C LEU* 3.4 4.1 + - - +
268C HIS* 3.3 21.3 + - - +
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Residues in contact with GLN 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C SER* 3.1 32.2 + - - +
262C LEU* 3.1 8.6 + - - +
264C SER* 1.3 83.4 + - - +
266C MET* 1.3 61.6 + - - +
267C LEU 3.6 0.2 + - - -
268C HIS* 3.6 17.6 - - - +
273C LYS 4.9 0.6 - - - +
274C ARG* 3.7 1.0 - - - +
275C ILE* 3.4 53.7 + - + +
283C HIS* 3.9 15.7 - - - -
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Residues in contact with MET 266 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C LEU* 4.3 13.0 - - + -
112C LEU* 4.9 12.6 - - + -
186C ILE* 3.8 20.3 - - + +
187C TRP* 3.8 12.6 - - - -
189C LEU* 3.5 33.7 - - + +
190C GLY* 3.6 18.6 - - - +
193C PHE* 4.5 6.3 - - + -
262C LEU* 3.1 38.1 + - + +
263C LEU* 3.0 12.3 + - - +
265C GLN* 1.3 77.9 - - - +
267C LEU* 1.3 58.1 + - - +
268C HIS 3.3 1.3 - - - -
274C ARG* 3.3 21.1 - - - -
275C ILE* 3.8 17.9 - - + -
280C ALA* 5.2 1.8 - - + -
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C TRP* 3.1 55.2 - - + +
190C GLY 4.3 1.8 - - - -
191C CYS* 4.3 13.2 - - - +
202C LEU* 3.7 27.1 - - + -
203C PHE* 4.5 0.9 - - + -
219C LEU* 3.3 34.5 - - + +
245C ARG* 5.9 1.8 + - - +
248C PHE* 4.1 15.3 - - + -
263C LEU* 3.2 30.5 + - + +
264C SER* 3.7 7.2 - - - +
265C GLN 3.3 0.4 - - - -
266C MET* 1.3 78.8 - - - +
268C HIS* 1.3 63.5 + - - +
269C TYR* 3.5 2.8 + - - -
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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