Contacts of the helix formed by residues 245 - 258 (chain C) in PDB entry 2ONL
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 245 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174C ILE* 4.6 15.0 - - + +
178C HIS* 2.5 35.2 + - + -
183C ALA* 4.3 3.2 - - - +
184C HIS* 3.5 23.4 + - - +
185C ARG* 2.9 28.0 + - - -
187C VAL* 3.8 13.3 - - + +
241C ASP 5.1 1.6 - - - -
242C LYS* 2.9 11.0 + - - +
244C CYS* 1.3 79.1 - - - +
246C MET* 1.3 60.8 + - + +
247C TRP 3.1 1.1 - - - -
248C SER* 2.8 24.3 + - - -
249C LEU* 2.8 14.7 + - - +
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Residues in contact with MET 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ILE* 4.6 2.0 - - + -
178C HIS* 4.3 9.9 - - + +
242C LYS* 3.5 15.9 + - + +
243C SER* 4.8 0.2 - - - -
245C ASP* 1.3 79.3 - - - +
247C TRP* 1.3 55.3 + - - +
249C LEU* 3.5 9.3 - - + +
250C GLY* 2.7 33.8 + - - -
306C LEU* 3.2 30.5 - - + +
313C ARG* 3.6 23.1 - - + +
314C MET* 2.8 28.5 - - + +
315C THR 4.4 0.2 - - - -
316C ILE* 3.1 52.7 - - + +
319C PHE* 4.6 3.6 - - - -
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Residues in contact with TRP 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C SER 3.6 19.3 + - - +
244C CYS* 4.4 5.6 - - - +
245C ASP 3.1 0.6 - - - -
246C MET* 1.3 77.9 - - - +
248C SER* 1.3 66.0 + - - +
251C VAL* 2.7 61.4 + - + +
262C PRO* 6.4 0.2 - - + -
263C PHE* 5.5 7.6 - + - -
306C LEU 3.7 10.4 + - - +
307C LYS* 2.9 31.4 + - - +
308C THR 5.3 2.2 - - - -
313C ARG* 5.5 0.2 - - - +
356C MET* 3.1 39.3 - - + -
359C ALA* 3.4 23.8 - - + -
360C LEU* 3.0 37.5 - - + -
363C MET* 3.8 14.1 - - + -
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Residues in contact with SER 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C VAL* 3.0 47.7 - - - +
244C CYS 2.4 31.0 + - - -
245C ASP 2.8 5.6 + - - -
247C TRP* 1.3 88.8 - - - +
249C LEU* 1.3 55.9 + - - -
251C VAL* 3.7 1.4 - - - +
252C ILE* 3.1 32.3 + - - +
356C MET* 4.0 5.7 - - - +
360C LEU* 4.3 5.5 - - - +
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Residues in contact with LEU 249 (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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167C MET* 3.0 57.2 - - + +
170C ILE* 3.7 30.3 - - + -
171C GLY* 4.6 7.0 - - - +
174C ILE* 5.3 10.5 - - + -
187C VAL* 4.6 11.0 - - + -
245C ASP 2.8 10.6 + - - +
246C MET* 3.5 16.6 - - + +
248C SER* 1.3 74.2 - - - +
250C GLY* 1.3 58.2 + - - +
251C VAL 3.1 0.9 - - - -
252C ILE* 2.5 36.1 + - + +
253C MET* 2.8 6.1 + - + -
306C LEU* 5.3 1.3 - - + -
319C PHE* 4.4 15.0 - - + -
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Residues in contact with GLY 250 (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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246C MET 2.7 16.9 + - - -
249C LEU* 1.3 74.0 - - - +
251C VAL* 1.3 57.4 + - - +
252C ILE 2.9 5.0 + - - -
253C MET* 3.0 12.8 + - - -
254C TYR* 3.2 1.0 + - - +
303C ARG* 3.1 24.0 - - - +
306C LEU* 3.0 38.0 - - - +
307C LYS* 4.4 3.1 - - - -
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Residues in contact with VAL 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C TRP* 2.7 61.4 + - + +
248C SER 3.7 1.1 - - - -
250C GLY* 1.3 69.6 - - - -
252C ILE* 1.3 56.9 + - - +
254C TYR* 4.3 5.5 - - - +
255C ILE* 2.8 30.8 + - + +
262C PRO* 4.6 13.2 - - + +
263C PHE* 5.4 3.8 - - + -
307C LYS* 3.3 28.0 - - + +
356C MET* 3.1 34.8 - - + -
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Residues in contact with ILE 252 (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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146C LEU* 5.6 3.8 - - + -
147C PHE* 4.4 22.2 - - + -
166C ILE* 6.0 0.4 - - + -
167C MET* 3.3 15.0 - - + -
170C ILE* 5.9 4.0 - - + -
187C VAL* 5.1 10.1 - - + +
189C PRO* 5.2 10.3 - - + -
192C LEU* 5.0 10.3 - - + -
248C SER 3.1 17.1 + - - +
249C LEU* 2.5 28.1 + - + +
251C VAL* 1.3 77.4 - - - +
253C MET* 1.3 53.3 + - - +
254C TYR 3.0 2.0 - - - -
255C ILE* 3.2 17.1 + - + +
256C LEU* 2.7 60.4 + - + +
356C MET* 4.7 7.9 - - + -
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Residues in contact with MET 253 (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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163C ALA* 5.9 3.6 - - + +
167C MET* 3.8 24.0 - - + -
249C LEU 2.8 5.6 + - - +
250C GLY 3.0 1.5 + - - +
252C ILE* 1.3 77.4 - - - +
254C TYR* 1.3 56.9 + - - +
256C LEU* 3.2 13.1 - - + +
257C LEU* 2.8 36.1 + - + +
299C LYS* 3.5 31.6 - - - +
302C ILE* 4.9 8.3 - - + -
303C ARG* 3.3 24.7 - - - +
306C LEU* 3.6 29.4 - - + -
319C PHE* 3.8 20.4 - - + -
324C TRP* 4.4 16.2 - - + -
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Residues in contact with TYR 254 (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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250C GLY 3.2 5.3 + - - +
251C VAL* 4.5 1.8 - - - +
252C ILE 3.0 0.4 - - - -
253C MET* 1.3 74.8 - - - +
255C ILE* 1.3 61.6 + - - +
256C LEU 2.9 5.2 + - - -
257C LEU* 3.1 11.3 + - - +
258C CYS* 3.1 26.0 + - - -
259C GLY 3.4 1.6 + - - -
260C TYR* 2.8 54.9 - - + +
261C PRO 3.1 18.5 + - - -
262C PRO* 3.7 19.3 - - + -
284C TYR* 3.4 33.2 - + - -
285C GLU 2.3 34.0 + - - -
286C PHE* 4.1 13.7 - + - -
287C PRO* 4.4 1.7 - - - +
303C ARG* 3.1 26.2 - - + +
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Residues in contact with ILE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C PHE* 3.6 18.1 - - + -
189C PRO* 6.5 1.1 - - + -
251C VAL* 2.8 32.8 - - + +
252C ILE* 3.2 17.8 + - + +
254C TYR* 1.3 77.1 - - + +
256C LEU* 1.3 56.6 + - - +
259C GLY* 2.9 26.4 - - - +
260C TYR 3.3 19.7 - - - +
261C PRO* 4.8 4.5 - - + -
262C PRO* 4.8 5.6 - - + -
263C PHE* 5.8 4.5 - - + -
338C THR* 3.9 0.2 - - - +
342C LEU* 3.6 3.4 - - + +
349C TRP* 3.5 39.9 - - + -
352C VAL* 5.2 7.6 - - + -
356C MET* 5.1 10.3 - - + -
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Residues in contact with LEU 256 (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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146C LEU* 4.6 8.7 - - + -
147C PHE* 4.5 11.0 - - + -
150C ILE* 4.6 9.9 - - + -
158C PHE* 3.7 41.2 - - + -
163C ALA* 4.6 6.1 - - + +
166C ILE* 4.2 16.8 - - + -
167C MET* 3.6 20.6 - - - -
252C ILE* 2.7 43.0 + - + +
253C MET* 3.2 11.2 - - + +
254C TYR 2.9 0.2 - - - -
255C ILE* 1.3 80.1 - - - +
257C LEU* 1.3 60.0 + - + +
338C THR* 2.7 28.5 + - - +
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Residues in contact with LEU 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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160C GLU* 5.4 3.4 - - + -
163C ALA* 4.6 12.8 - - + -
253C MET* 2.8 17.1 + - + +
254C TYR* 3.1 3.8 + - - +
256C LEU* 1.3 78.9 - - + +
258C CYS* 1.3 69.6 + - - +
292C SER* 4.1 13.9 + - - +
294C VAL 5.9 0.2 - - - +
295C SER* 3.7 22.2 - - - +
299C LYS* 3.5 24.5 - - - +
303C ARG* 2.8 32.3 - - - +
336C LEU* 4.3 26.7 - - + +
338C THR* 2.6 23.2 + - - -
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Residues in contact with CYS 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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254C TYR* 3.1 18.3 + - - +
257C LEU* 1.3 86.5 - - - +
259C GLY* 1.3 60.0 + - - +
260C TYR* 2.7 43.7 + - + +
286C PHE* 5.6 1.3 - - - -
287C PRO* 3.1 46.4 - - + -
292C SER* 4.3 11.2 - - - +
303C ARG* 6.0 0.7 - - - -
338C THR* 3.3 6.6 - - - +
341C VAL* 4.1 7.9 - - - +
342C LEU* 3.4 8.7 - - - +
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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