Contacts of the helix formed by residues 203 - 219 (chain B) 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 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ASN* 2.6 35.1 + - - +
202B GLN* 1.3 67.6 - - + +
204B VAL* 1.3 51.7 + - - +
205B ASP 2.8 7.7 + - - -
206B ILE* 2.4 49.2 + - + +
207B TRP 2.9 4.7 + - - -
293B SER* 2.9 22.7 + - - +
296B ARG* 3.4 48.0 + - + +
297B ILE 3.9 2.5 - - - +
298B THR* 4.7 8.3 - - + -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 3.7 25.6 - - + -
149B ARG* 5.2 4.9 - - + -
190B ALA* 4.2 18.6 + - + +
192B GLU* 3.6 23.3 - - + +
193B ILE* 4.9 8.1 - - + -
200B TYR* 3.5 29.2 - - + -
201B ASN* 2.8 29.2 + - - +
202B GLN 4.0 0.2 - - - +
203B THR* 1.3 76.4 - - - +
205B ASP* 1.3 62.3 + - - +
207B TRP* 3.6 4.6 - - - +
208B SER* 2.8 23.2 + - - -
296B ARG* 3.9 7.1 - - - +
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Residues in contact with ASP 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 3.6 12.6 - - + -
142B HIS* 2.7 28.3 + - - +
147B ILE* 3.3 13.2 - - - +
148B HIS* 3.2 26.0 + - - +
149B ARG* 2.9 30.0 + - - -
150B ASP 4.6 0.3 + - - -
151B LEU* 3.9 8.8 - - + +
202B GLN 3.5 6.4 - - - +
203B THR 2.8 0.4 - - - -
204B VAL* 1.3 76.9 - - - +
206B ILE* 1.3 63.8 + - - +
207B TRP 3.2 0.2 - - - -
208B SER* 3.2 9.8 + - - -
209B VAL* 2.9 28.7 + - - +
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Residues in contact with ILE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.8 10.3 - - + -
138B LEU* 4.7 9.4 - - + -
142B HIS* 4.8 3.1 - - + -
202B GLN 4.5 2.5 - - - +
203B THR* 2.4 45.4 + - + +
205B ASP* 1.3 68.8 - - - +
207B TRP* 1.3 60.8 + - - +
209B VAL* 2.8 23.3 + - - +
210B GLY* 3.0 6.1 + - - -
288B MET* 3.0 42.4 - - + +
296B ARG* 4.8 2.5 - - + -
297B ILE* 3.3 26.9 - - + +
298B THR* 3.9 1.6 - - - +
299B ALA* 3.5 30.7 - - + +
302B ALA* 5.5 0.2 - - + -
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Residues in contact with TRP 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TRP 5.2 0.4 + - - -
188B TYR 4.2 0.4 - - - -
189B ARG 3.6 14.3 + - - +
190B ALA* 3.4 26.9 - - + -
191B PRO* 3.6 22.9 - - + -
203B THR 2.9 7.9 + - - +
204B VAL* 3.6 10.3 - - - +
205B ASP 3.2 0.2 - - - -
206B ILE* 1.3 76.2 - - - +
208B SER* 1.3 64.3 + - - +
210B GLY* 2.9 11.4 + - - -
211B CYS* 2.9 35.2 + - - -
223B PHE* 3.8 23.7 - + - -
235B ILE* 3.5 36.1 - - + +
239B VAL* 4.4 11.2 - - + -
288B MET 4.3 8.2 + - - -
289B LEU* 3.8 31.2 - - + +
290B VAL 3.5 28.7 - - - -
291B LEU* 4.4 1.8 - - + -
296B ARG* 3.7 12.5 - - - +
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG 5.9 1.4 - - - -
150B ASP 5.8 0.3 + - - -
151B LEU* 3.6 31.5 + - - +
188B TYR* 3.2 25.8 + - - -
189B ARG* 5.2 0.2 - - - -
204B VAL 2.8 17.8 + - - -
205B ASP* 3.4 11.2 + - - -
207B TRP* 1.3 76.9 - - - +
209B VAL* 1.3 61.7 + - - +
211B CYS* 3.2 8.9 + - - +
212B ILE* 2.8 29.8 + - - +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 4.3 23.9 - - + +
134B ILE* 4.2 18.6 - - + -
135B LEU* 4.5 11.4 - - + -
138B LEU* 3.9 18.2 - - + -
151B LEU* 4.4 3.6 - - + -
205B ASP 2.9 27.6 + - - +
206B ILE* 2.8 17.4 + - - +
208B SER* 1.3 75.4 - - - +
210B GLY* 1.3 54.9 + - - +
212B ILE* 3.2 11.4 + - + +
213B MET* 2.9 26.9 + - - +
288B MET* 3.2 24.5 - - + -
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Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE 3.0 7.2 + - - -
207B TRP 2.9 6.5 + - - -
209B VAL* 1.3 76.5 - - - +
211B CYS* 1.3 62.8 + - - +
213B MET* 3.0 2.8 + - - +
214B ALA* 2.8 24.8 + - - +
285B LEU* 3.5 4.0 - - - +
288B MET* 3.5 15.2 - - - +
289B LEU* 3.4 30.7 - - - -
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Residues in contact with CYS 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TRP 4.3 5.6 - - - +
188B TYR* 3.4 36.0 - - + -
207B TRP* 2.9 53.4 + - - -
208B SER* 3.4 9.2 - - - +
210B GLY* 1.3 73.9 - - - +
212B ILE* 1.3 64.1 + - - +
214B ALA* 3.8 1.6 + - - +
215B GLU* 3.3 19.2 + - - +
222B LEU* 4.1 24.2 - - + +
223B PHE* 4.7 7.4 - - + -
289B LEU* 4.5 2.1 - - - +
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 5.8 3.1 - - + -
131B ILE* 4.0 12.1 - - + -
134B ILE* 4.7 9.6 - - + -
151B LEU* 4.0 27.8 - - + +
152B LYS* 4.4 1.8 - - - +
153B PRO* 3.6 29.6 - - + -
156B LEU* 5.2 11.0 - - + -
188B TYR* 4.3 7.2 - - + -
208B SER* 2.8 35.4 + - - +
209B VAL* 3.4 10.1 - - + +
211B CYS* 1.3 74.1 - - - +
213B MET* 1.3 68.3 + - - +
215B GLU* 2.9 16.5 + - - +
216B LEU* 3.0 39.2 + - + +
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Residues in contact with MET 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 4.6 4.0 - - + -
131B ILE* 4.1 30.7 - - + -
209B VAL 2.9 12.8 + - - +
210B GLY 3.3 7.2 - - - +
212B ILE* 1.3 76.5 - - - +
214B ALA* 1.3 64.3 + - - +
216B LEU* 3.1 23.7 + - - +
217B LEU* 3.2 30.6 + - + +
281B ALA* 4.1 4.0 - - + +
284B LEU* 3.9 18.6 - - + -
285B LEU* 3.0 47.1 - - + +
288B MET* 3.0 26.0 - - + -
307B TYR* 5.1 8.5 - - + +
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B GLY 2.8 18.5 + - - +
211B CYS 4.0 3.8 - - - +
213B MET* 1.3 73.4 - - - +
215B GLU* 1.3 59.0 + - - +
217B LEU* 3.2 4.6 + - - +
218B THR* 2.6 35.0 + - - +
222B LEU* 4.1 24.5 - - + -
274B PHE* 3.9 23.3 - - + -
285B LEU* 3.9 16.5 - - + +
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ASN* 4.8 7.1 - - - +
117B VAL* 5.5 12.0 - - + +
153B PRO* 4.7 7.5 - - + +
188B TYR* 3.0 29.9 + - - -
211B CYS 3.3 9.7 + - - +
212B ILE* 2.9 11.1 + - - +
214B ALA* 1.3 78.9 - - - +
216B LEU* 1.3 62.3 + - + +
219B GLY* 2.3 44.4 + - - +
220B ARG 3.1 21.1 + - - +
221B THR* 3.3 33.4 + - - +
222B LEU 4.4 1.3 + - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 5.0 14.1 - - + -
117B VAL* 4.5 23.6 - - + -
122B LEU* 4.9 19.1 + - + +
127B VAL* 3.9 34.0 - - + +
130B LEU* 4.9 11.9 - - + -
131B ILE* 3.9 19.1 - - + -
153B PRO* 5.6 5.6 - - + -
212B ILE* 3.0 38.3 + - + +
213B MET* 3.4 5.2 - - - +
215B GLU* 1.3 83.4 - - + +
217B LEU* 1.3 62.0 + - - +
219B GLY* 3.9 5.1 + - - -
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LYS* 5.7 2.4 + - - -
124B ASP* 3.6 25.6 - - + +
127B VAL* 4.4 20.6 - - + -
213B MET* 3.2 36.6 + - + +
214B ALA* 3.8 3.1 - - - +
216B LEU* 1.3 78.8 - - - +
218B THR* 1.3 66.3 + - + +
274B PHE* 5.8 4.3 - - + -
277B ALA* 4.6 21.5 - - + -
278B ASN 5.3 0.2 - - - +
281B ALA* 4.4 17.0 - - + -
285B LEU* 4.2 17.3 - - + -
307B TYR* 4.5 3.1 - - - +
231D ALA* 4.9 2.8 - - - +
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Residues in contact with THR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA* 2.6 22.9 + - - +
217B LEU* 1.3 78.3 - - + +
219B GLY* 1.3 57.8 + - - +
220B ARG* 3.2 25.5 + - - +
273B VAL 5.2 1.6 - - - +
274B PHE* 3.8 34.8 - - + -
229D TYR 4.2 19.3 - - - +
230D VAL 3.9 1.7 - - - +
231D ALA* 2.4 38.4 - - + +
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Residues in contact with GLY 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 5.9 6.6 - - - +
215B GLU* 2.3 33.1 + - - +
216B LEU* 4.4 4.9 - - - -
217B LEU 3.5 1.2 - - - -
218B THR* 1.3 68.9 - - - +
220B ARG* 1.3 60.3 + - - +
231D ALA* 5.9 0.2 - - - -
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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
------------------------------------------------------------
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