Contacts of the helix formed by residues 159 - 180 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D GLN* 5.2 3.8 - - - +
157D ALA 3.8 9.2 - - - +
158D PHE* 1.3 101.5 - - - -
160D GLU* 1.3 57.8 + - - +
161D ARG* 2.9 22.3 + - - +
162D GLU* 2.2 49.2 + - + +
333D GLN* 3.7 31.5 - - + +
334D THR 3.4 5.2 - - - -
335D PRO* 5.0 1.3 - - + -
336D LEU* 3.1 0.2 - - - -
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Residues in contact with GLU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D THR* 1.3 71.5 - - - +
161D ARG* 1.3 59.9 + - - +
163D ALA* 3.6 5.9 - - - +
164D SER* 3.2 16.1 + - - -
257D LEU* 5.2 6.1 - - + -
295D SER* 5.6 7.2 - - - -
296D GLU* 3.8 12.8 - - - +
299D LYS* 5.2 1.3 - - + -
324D TRP* 3.1 40.1 + - + -
331D VAL* 3.4 24.2 - - - +
332D PRO* 3.3 30.0 - - - +
334D THR* 3.0 24.9 + - - +
336D LEU* 3.0 21.7 - - + +
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Residues in contact with ARG 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D THR* 2.9 10.6 + - - +
160D GLU* 1.3 74.9 - - - +
162D GLU* 1.3 56.0 + - + +
164D SER* 2.8 5.4 + - - -
165D GLU* 2.7 58.3 + - + +
329D THR* 3.5 38.6 + - - +
330D LYS* 3.8 3.2 + - - +
331D VAL* 3.0 29.6 + - + +
332D PRO 3.4 5.8 + - - +
333D GLN* 2.6 41.0 + - + +
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Residues in contact with GLU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ARG* 3.4 14.4 + - - +
156D GLN* 3.1 21.5 + - - -
158D PHE* 2.7 20.9 - - + -
159D THR* 2.2 51.8 + - + +
161D ARG* 1.3 73.1 - - + +
163D ALA* 1.3 54.9 + - - +
165D GLU* 3.0 16.8 + - - +
166D ILE* 2.7 44.0 + - + +
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Residues in contact with ALA 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D PHE* 3.3 31.7 - - + -
159D THR 3.1 2.8 + - - -
160D GLU* 3.6 10.5 - - - +
162D GLU* 1.3 77.6 - - - +
164D SER* 1.3 61.6 + - - +
166D ILE* 3.5 4.4 + - - +
167D MET* 3.1 26.5 + - - +
256D LEU* 3.9 14.2 - - + +
257D LEU* 3.7 26.5 - - + -
324D TRP* 4.4 2.2 - - - -
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Residues in contact with SER 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D GLU 3.2 8.0 + - - -
161D ARG 2.8 10.2 + - - -
163D ALA* 1.3 78.7 - - - +
165D GLU* 1.3 62.4 + - - -
167D MET* 3.1 5.4 + - - +
168D LYS* 3.0 21.8 + - - +
324D TRP* 2.8 49.3 + - - -
325D ILE* 5.5 3.0 - - - +
328D SER* 3.5 19.0 - - - -
331D VAL* 3.4 13.7 - - - +
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Residues in contact with GLU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D ARG* 2.7 42.0 + - + +
162D GLU* 3.6 18.8 + - - +
164D SER* 1.3 71.1 - - - +
166D ILE* 1.3 62.6 + - - +
168D LYS* 3.4 10.8 + - - +
169D SER* 3.3 20.1 + - - -
328D SER* 3.6 15.7 - - - +
329D THR* 3.7 19.6 - - + +
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Residues in contact with ILE 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LEU* 3.6 32.5 - - + -
150D ILE* 4.8 4.5 - - + -
158D PHE* 6.3 0.4 - - + -
162D GLU* 2.7 26.6 + - + +
163D ALA 3.7 3.4 - - - +
165D GLU* 1.3 72.4 - - - +
167D MET* 1.3 66.8 + - - +
169D SER* 2.9 17.9 + - - -
170D ILE* 2.9 35.5 + - + +
194D TYR* 3.7 15.5 - - - +
203D LEU* 4.4 3.8 - - + -
256D LEU* 3.5 33.2 - - + -
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Residues in contact with MET 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D ALA 3.1 10.6 + - - +
164D SER* 3.1 11.3 + - - +
166D ILE* 1.3 79.8 - - - +
168D LYS* 1.3 54.0 + - - +
170D ILE* 3.7 16.8 - - + -
171D GLY* 2.6 33.8 + - - -
249D LEU* 3.0 44.2 - - + +
252D ILE* 3.5 26.7 - - + -
253D MET* 4.3 23.3 - - + -
256D LEU* 3.8 11.2 - - + -
319D PHE* 4.2 18.8 - - + -
324D TRP* 4.8 8.7 - - + -
325D ILE* 5.3 2.9 - - + -
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Residues in contact with LYS 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D SER 3.0 12.2 + - - +
165D GLU* 3.6 13.7 - - - +
166D ILE 3.2 0.2 - - - -
167D MET* 1.3 75.4 - - - +
169D SER* 1.3 50.9 - - - +
171D GLY* 3.6 1.2 - - - -
172D GLU* 2.4 67.0 + - - +
320D MET* 4.7 4.5 - - + +
325D ILE* 3.4 36.6 + - + +
326D MET* 3.1 29.2 + - - +
328D SER* 4.5 11.4 + - - +
329D THR* 5.2 7.9 - - - +
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Residues in contact with SER 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D HIS* 3.6 24.9 + - - -
165D GLU 3.3 9.3 + - - -
166D ILE* 2.9 12.2 + - - -
168D LYS* 1.3 75.6 - - - +
170D ILE* 1.3 59.2 + - - +
172D GLU* 2.7 38.1 + - - +
173D ALA* 3.1 5.5 + - - +
202D ILE* 6.1 0.2 - - - +
203D LEU* 4.5 23.4 + - - +
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Residues in contact with ILE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LEU* 4.3 3.6 - - + -
166D ILE* 2.9 37.2 + - + +
167D MET* 3.7 16.6 - - + -
169D SER* 1.3 79.0 - - - +
171D GLY* 1.3 63.5 + - - +
172D GLU 3.2 0.5 + - - -
173D ALA* 3.3 13.7 + - - +
174D ILE* 3.3 16.4 + - + +
187D VAL* 4.8 5.6 - - + -
192D LEU* 3.3 38.6 - - + -
203D LEU* 3.5 10.5 - - + +
249D LEU* 3.4 35.0 - - + -
252D ILE* 4.5 8.7 - - + -
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Residues in contact with GLY 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D MET 2.6 22.6 + - - -
168D LYS 3.6 1.6 - - - -
170D ILE* 1.3 74.0 - - - +
172D GLU* 1.3 61.2 + - - +
174D ILE* 3.5 4.5 + - - +
175D GLN* 3.0 25.0 + - - +
249D LEU* 4.0 15.3 - - - -
316D ILE* 4.0 7.1 - - - +
319D PHE* 4.2 12.8 - - - -
320D MET* 4.4 6.0 - - - +
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Residues in contact with GLU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D CYS* 4.6 1.4 - - - -
116D HIS* 3.5 30.8 + - + +
168D LYS* 2.4 63.6 + - - +
169D SER* 2.7 20.3 + - - +
171D GLY* 1.3 71.0 - - - -
173D ALA* 1.3 60.7 + - - +
175D GLN* 3.2 14.5 + - - +
176D TYR* 3.2 11.6 + - - +
320D MET* 4.0 20.3 - - + +
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Residues in contact with ALA 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D CYS* 4.1 12.8 - - - -
116D HIS* 3.8 19.4 - - + +
117D ILE* 4.3 4.3 - - + +
169D SER 3.1 4.5 + - - +
170D ILE* 3.3 10.5 + - - +
172D GLU* 1.3 78.7 - - - +
174D ILE* 1.3 67.5 + - + +
176D TYR* 2.9 7.6 + - - +
177D LEU* 2.9 29.0 + - - +
205D LEU* 4.2 22.7 - - + +
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Residues in contact with ILE 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D ILE* 3.3 15.3 + - + +
171D GLY* 4.0 7.2 - - - +
173D ALA* 1.3 83.1 - - + +
175D GLN* 1.3 64.3 + - - +
177D LEU* 3.9 21.3 - - + -
178D HIS* 3.0 53.8 + - + +
187D VAL* 4.6 13.2 - - + -
205D LEU* 4.3 11.7 - - + -
245D ASP* 3.5 23.3 - - + +
246D MET* 4.2 7.4 - - + -
249D LEU* 4.7 13.7 - - + -
316D ILE* 4.2 8.3 - - + -
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Residues in contact with GLN 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D GLY 3.0 17.9 + - - +
172D GLU* 3.5 8.3 - - - +
173D ALA 3.2 0.4 - - - -
174D ILE* 1.3 77.1 - - - +
176D TYR* 1.3 58.0 + - - +
178D HIS* 4.0 1.4 - - - +
179D SER* 3.0 28.8 + - - -
316D ILE* 3.6 24.1 + - + +
317D THR* 5.3 6.6 - - + +
320D MET* 2.8 54.5 - - + +
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Residues in contact with TYR 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA* 4.3 9.0 - - - -
113D GLN* 2.5 46.8 + - + +
114D CYS* 3.7 37.0 - - + -
117D ILE* 5.1 2.9 - - + -
172D GLU 3.2 7.9 + - - +
173D ALA 2.9 10.2 + - - +
175D GLN* 1.3 75.9 - - - +
177D LEU* 1.3 63.6 + - + +
178D HIS 3.0 1.1 - - - -
179D SER* 2.5 37.9 + - - -
180D ILE* 3.0 39.1 + - + +
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA* 4.3 11.0 - - + -
117D ILE* 3.7 25.6 - - + -
173D ALA 2.9 9.0 + - - +
174D ILE* 3.9 23.6 - - + +
176D TYR* 1.3 77.9 - - + +
178D HIS* 1.3 55.6 + - + +
180D ILE* 3.6 6.6 - - + +
181D ASN 3.6 2.4 + - - -
182D ILE* 2.6 76.7 + - + +
184D HIS* 3.8 26.9 - - + +
205D LEU* 3.9 7.0 - - + -
208D PHE* 3.7 21.8 - - + -
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Residues in contact with HIS 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D ILE* 3.0 28.7 + - + +
175D GLN 4.1 2.9 - - - +
176D TYR 3.0 0.6 - - - -
177D LEU* 1.3 75.7 - - + +
179D SER* 1.3 59.6 + - - +
180D ILE 3.0 2.2 - - - -
181D ASN* 2.9 18.2 + - - +
182D ILE 3.4 17.7 + - - +
183D ALA* 4.7 1.8 - - - -
242D LYS* 3.2 62.2 + - + +
245D ASP* 3.0 22.2 + - - +
246D MET* 3.1 35.6 - - + +
313D ARG* 5.1 1.0 + - - -
316D ILE* 4.3 19.3 - - + +
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Residues in contact with SER 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D GLN* 3.0 16.0 + - - -
176D TYR* 2.5 36.9 + - - -
178D HIS* 1.3 72.6 - - - +
180D ILE* 1.3 64.4 + - - +
181D ASN* 3.4 5.4 + - - +
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Residues in contact with ILE 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ARG* 2.9 46.8 + - - +
111D ALA* 4.6 4.7 - - + -
113D GLN* 5.4 0.7 - - - +
176D TYR* 3.0 44.0 + - + +
177D LEU* 3.6 10.3 - - - +
178D HIS 3.0 0.2 - - - -
179D SER* 1.3 89.1 - - - +
181D ASN* 1.3 66.0 + - - +
182D ILE* 3.0 31.1 - - + +
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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
------------------------------------------------------------
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