Contacts of the helix formed by residues 159 - 180 (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 THR 159 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ALA* 2.8 16.1 + - + +
158C PHE* 1.3 72.0 - - - +
160C GLU* 1.3 64.5 + - - +
161C ARG* 3.9 4.5 + - - +
162C GLU* 2.3 75.3 + - - +
163C ALA 3.3 4.5 + - - -
333C GLN* 3.5 27.8 - - + +
334C THR 3.2 11.7 - - - +
335C PRO* 4.4 6.5 - - + -
336C LEU* 4.0 1.3 - - - -
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Residues in contact with GLU 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C THR* 1.3 71.3 - - - +
161C ARG* 1.3 62.6 + - - +
163C ALA* 3.1 8.6 + - + +
164C SER* 3.0 19.2 + - - -
257C LEU* 5.4 3.4 - - + -
295C SER* 4.5 7.8 - - - -
296C GLU* 4.0 7.7 - - - +
299C LYS* 3.7 16.9 + - - +
324C TRP* 2.9 43.9 + - + -
331C VAL* 5.0 1.3 - - + -
332C PRO* 3.2 36.5 - - - +
334C THR* 2.9 27.5 + - - +
336C LEU* 4.0 15.5 - - + +
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Residues in contact with ARG 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C THR* 3.2 7.2 + - - +
160C GLU* 1.3 77.7 - - - +
162C GLU* 1.3 52.6 + - + +
164C SER* 3.2 3.0 + - - -
165C GLU* 2.8 46.8 + - + +
329C THR* 2.9 54.1 + - - +
330C LYS* 4.3 3.2 + - - +
331C VAL* 3.2 30.9 + - + -
332C PRO 3.5 8.5 + - - +
333C GLN* 3.0 34.3 + - + +
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Residues in contact with GLU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ARG* 3.8 22.3 + - - -
157C ALA 2.7 13.4 - - - +
158C PHE* 3.6 16.5 - - + -
159C THR* 2.3 56.9 + - - +
161C ARG* 1.3 72.7 - - + +
163C ALA* 1.3 66.7 + - - +
164C SER 3.0 1.3 - - - -
165C GLU* 3.1 22.7 + - - +
166C ILE* 2.9 21.4 + - + +
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Residues in contact with ALA 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C PHE* 3.0 33.9 - - + -
159C THR 3.3 1.0 + - - -
160C GLU* 3.1 15.3 + - - +
162C GLU* 1.3 78.6 - - - +
164C SER* 1.3 57.7 + - - +
166C ILE* 3.2 6.9 - - - +
167C MET* 3.1 29.5 + - - +
253C MET* 5.9 2.8 - - + +
256C LEU* 4.6 8.0 - - + +
257C LEU* 4.6 16.2 - - + -
299C LYS* 5.4 0.2 - - - +
324C TRP* 4.7 8.0 - - + -
336C LEU* 5.1 0.2 - - + -
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Residues in contact with SER 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C GLU 3.0 10.0 + - - -
161C ARG* 3.3 14.1 - - - -
162C GLU 3.0 0.2 - - - -
163C ALA* 1.3 74.6 - - - +
165C GLU* 1.3 57.8 + - - +
166C ILE 2.8 9.9 + - - -
167C MET* 3.4 2.8 + - - +
168C LYS* 3.3 24.8 + - - +
324C TRP* 2.9 51.7 + - - -
325C ILE* 4.4 2.6 - - - +
328C SER* 3.4 16.7 - - - -
331C VAL* 4.3 4.4 - - - +
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Residues in contact with GLU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ARG* 2.8 37.0 + - + +
162C GLU* 3.1 19.3 + - - +
164C SER* 1.3 70.5 - - - +
166C ILE* 1.3 58.3 + - + +
168C LYS* 4.6 7.7 - - - +
169C SER* 3.8 15.3 + - - -
328C SER* 5.6 0.4 - - - -
329C THR* 4.0 29.5 - - + +
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Residues in contact with ILE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C LEU* 4.9 14.1 - - + -
150C ILE* 4.5 7.2 - - + -
158C PHE* 3.0 43.1 - - + -
162C GLU* 2.9 14.6 - - + +
163C ALA* 3.2 6.7 - - - +
164C SER 2.8 1.8 - - - -
165C GLU* 1.3 81.2 - - + +
167C MET* 1.3 64.6 + - - +
168C LYS 3.2 1.6 - - - -
169C SER* 3.0 13.3 + - - -
170C ILE* 2.8 38.7 + - + +
194C TYR* 5.1 11.4 - - - +
203C LEU* 5.7 5.2 - - + -
252C ILE* 6.0 0.2 - - + -
256C LEU* 4.2 21.1 - - + -
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Residues in contact with MET 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ALA 3.1 10.4 + - - +
164C SER* 3.4 6.0 + - - +
166C ILE* 1.3 81.8 - - - +
168C LYS* 1.3 52.7 + - - +
170C ILE* 2.9 5.4 + - + +
171C GLY* 2.3 38.5 + - - -
249C LEU* 3.0 71.2 - - + +
252C ILE* 3.3 11.9 - - + -
253C MET* 3.8 21.3 - - + +
256C LEU* 3.6 24.2 - - - -
319C PHE* 3.7 20.4 - - + -
320C MET* 4.7 1.8 - - - -
324C TRP* 5.2 5.4 - - + -
325C ILE* 5.2 2.5 - - + -
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Residues in contact with LYS 168 (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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164C SER 3.3 13.5 + - - +
165C GLU* 4.9 5.4 - - - +
166C ILE 3.2 0.4 - - - -
167C MET* 1.3 77.8 - - - +
169C SER* 1.3 56.6 + - - +
172C GLU* 2.7 60.9 + - - +
320C MET* 3.5 16.4 - - + -
325C ILE* 3.5 24.3 + - + +
326C MET* 3.8 11.5 + - - +
328C SER* 2.6 26.6 + - - +
329C THR* 4.3 14.4 - - - +
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Residues in contact with SER 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C HIS* 3.1 42.4 + - - +
165C GLU 3.8 14.8 + - - -
166C ILE* 3.0 14.7 + - - -
168C LYS* 1.3 79.0 - - - +
170C ILE* 1.3 59.5 + - - +
172C GLU 4.2 0.2 - - - -
173C ALA* 4.1 2.3 + - - +
202C ILE* 4.7 2.6 - - - +
203C LEU* 3.1 36.5 + - - +
205C LEU* 5.0 1.7 - - - +
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Residues in contact with ILE 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C LEU* 5.5 2.9 - - + -
166C ILE* 2.8 33.2 - - + +
167C MET* 2.9 7.3 + - + +
169C SER* 1.3 81.2 - - - +
171C GLY* 1.3 55.9 + - - +
172C GLU 3.1 4.9 - - - -
173C ALA* 3.2 4.1 + - - +
174C ILE* 2.8 44.7 + - + +
187C VAL* 5.0 4.5 - - + -
192C LEU* 4.3 29.6 - - + -
203C LEU* 4.6 15.5 - - + -
205C LEU* 5.2 11.9 - - + -
249C LEU* 3.7 29.8 - - + -
252C ILE* 5.9 2.7 - - + -
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Residues in contact with GLY 171 (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 2.3 26.6 + - - -
170C ILE* 1.3 67.0 - - - +
172C GLU* 1.3 60.9 + - - +
174C ILE* 4.1 6.6 - - - +
175C GLN* 3.2 22.9 + - - +
249C LEU* 4.6 5.1 - - - +
316C ILE* 4.4 7.5 - - - +
319C PHE* 4.6 6.1 - - - -
320C MET* 3.3 27.7 - - - +
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Residues in contact with GLU 172 (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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114C CYS* 4.6 0.3 - - - -
116C HIS* 2.8 45.6 + - + +
168C LYS* 2.7 41.9 + - - +
169C SER* 4.7 0.2 - - - -
171C GLY* 1.3 77.9 - - - +
173C ALA* 1.3 64.5 + - - +
175C GLN* 3.4 14.3 + - - +
176C TYR* 3.0 21.3 + - - +
320C MET* 3.7 3.9 - - - +
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Residues in contact with ALA 173 (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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114C CYS* 4.1 11.9 - - - -
116C HIS* 3.8 9.3 - - + +
117C ILE* 3.6 12.6 - - + -
169C SER 4.1 2.8 + - - +
170C ILE 3.2 8.9 + - - +
172C GLU* 1.3 77.7 - - - +
174C ILE* 1.3 58.3 + - + +
176C TYR* 2.8 5.4 + - - +
177C LEU* 2.7 39.8 + - + +
205C LEU* 3.5 31.9 - - + -
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Residues in contact with ILE 174 (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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170C ILE* 2.8 41.2 + - + +
171C GLY* 4.1 2.7 - - - +
173C ALA* 1.3 79.3 - - + +
175C GLN* 1.3 56.0 + - - +
176C TYR 3.0 0.2 + - - -
177C LEU* 4.0 15.5 - - + -
178C HIS* 2.7 67.4 + - + +
184C HIS* 6.1 0.9 - - + -
187C VAL* 6.1 5.8 - - + -
205C LEU* 5.5 3.8 - - + -
245C ASP* 4.6 14.1 - - + +
246C MET* 4.6 2.2 - - + +
249C LEU* 5.3 10.5 - - + -
316C ILE* 2.7 39.7 - - + -
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Residues in contact with GLN 175 (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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171C GLY 3.2 16.7 + - - +
172C GLU* 3.5 14.0 - - - +
173C ALA 3.2 0.8 - - - -
174C ILE* 1.3 79.1 - - - +
176C TYR* 1.3 50.2 + - - +
178C HIS* 4.7 0.6 - - - +
179C SER* 2.6 34.7 + - - -
316C ILE* 3.8 28.9 - - + +
317C THR* 4.8 13.9 - - + +
320C MET* 4.3 19.8 - - + +
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Residues in contact with TYR 176 (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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110C ARG 5.0 4.3 - - - -
111C ALA* 5.1 4.7 - - - -
113C GLN* 2.3 51.8 + - + +
114C CYS* 3.6 41.1 - - + -
115C PRO* 6.0 0.2 - - + -
172C GLU 3.0 11.7 + - - +
173C ALA 2.8 9.8 + - - +
175C GLN* 1.3 74.3 - - - +
177C LEU* 1.3 71.6 + - + +
179C SER* 2.3 28.5 + - - -
180C ILE* 2.9 37.6 + - + +
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Residues in contact with LEU 177 (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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111C ALA* 5.0 5.2 - - + -
117C ILE* 3.2 38.6 - - + -
173C ALA* 2.7 33.3 + - + +
174C ILE* 3.8 16.2 - - + +
176C TYR* 1.3 79.6 - - + +
178C HIS* 1.3 58.4 + - + +
180C ILE* 2.8 27.9 - - + +
182C ILE* 2.8 47.2 + - + +
184C HIS* 4.1 30.7 - - + +
205C LEU* 4.8 2.2 - - + -
208C PHE* 4.6 10.8 - - + -
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Residues in contact with HIS 178 (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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174C ILE* 2.7 50.6 + - + +
175C GLN* 4.7 2.5 - - - +
177C LEU* 1.3 77.6 - - + +
179C SER* 1.3 56.0 + - - +
181C ASN* 2.9 23.7 + - - +
182C ILE 3.3 20.2 - - - +
183C ALA* 4.6 3.0 - - - -
242C LYS* 3.7 50.9 + - + +
245C ASP* 2.5 37.9 + - + -
246C MET* 4.3 4.7 - - + +
316C ILE* 4.4 11.5 - - + +
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Residues in contact with SER 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C GLN 2.6 19.5 + - - -
176C TYR* 2.3 32.6 + - - -
178C HIS* 1.3 75.8 - - - +
180C ILE* 1.3 62.5 + - - +
181C ASN* 3.2 5.3 + - - +
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Residues in contact with ILE 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ARG* 3.3 28.1 + - - +
111C ALA* 5.8 1.8 - - + -
113C GLN* 5.6 2.9 - - - +
176C TYR* 2.9 53.8 - - + +
177C LEU* 2.8 29.4 - - + +
179C SER* 1.3 81.0 - - - +
181C ASN* 1.3 68.4 + - - +
182C ILE* 3.0 29.0 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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