Contacts of the helix formed by residues 174 - 191 (chain B) in PDB entry 2ORY
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 SER 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TYR* 3.5 6.7 - - - -
91B GLY 6.0 0.4 - - - -
92B THR 5.2 2.1 + - - -
94B PRO* 3.5 8.0 - - - +
100B TRP* 3.1 17.8 - - - -
173B HIS* 1.3 84.7 - - - +
175B LYS* 1.3 66.0 + - - +
176B GLY 2.9 0.2 - - - -
177B GLY* 2.6 24.4 + - - -
178B ALA 3.5 0.7 + - - -
206B PHE 2.9 11.9 + - - -
207B ALA 3.3 16.8 + - - -
208B GLY* 3.3 12.5 - - - -
209B PRO* 3.6 4.4 - - - +
312B HIS* 2.7 27.9 + - - -
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Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 3.2 24.5 + - - +
69B ASN* 4.2 1.8 - - - +
70B ASP 2.9 22.6 + - - -
71B ALA* 5.1 0.8 - - - +
91B GLY* 3.2 24.7 - - - -
92B THR* 3.3 17.5 + - - +
100B TRP* 4.1 27.0 - - + -
104B ASP* 5.8 2.2 - - - +
128B SER* 5.5 7.2 - - - +
129B THR* 6.2 2.9 - - + -
174B SER* 1.3 82.2 + - - +
176B GLY* 1.3 58.2 + - - +
178B ALA* 3.1 8.1 + - + +
179B LEU* 2.9 48.1 + - + +
209B PRO* 4.4 11.0 - - + -
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Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 3.7 17.2 - - - +
90B ARG* 4.1 8.7 - - - -
91B GLY 3.9 5.1 - - - +
172B GLY* 3.6 7.2 - - - -
173B HIS 2.9 11.9 + - - -
174B SER 2.9 1.4 - - - -
175B LYS* 1.3 80.7 - - - +
177B GLY* 1.3 55.5 + - - +
178B ALA 3.4 0.2 - - - -
179B LEU* 3.8 8.3 - - - -
180B SER* 2.8 33.6 + - - -
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Residues in contact with GLY 177 (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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172B GLY 3.4 17.5 - - - -
173B HIS 3.5 2.8 - - - -
174B SER 2.6 20.4 + - - -
176B GLY* 1.3 71.6 - - - +
178B ALA* 1.3 56.1 + - - -
180B SER* 3.0 12.5 + - - -
181B SER* 3.0 16.6 + - - -
205B PRO* 3.1 14.8 - - - +
206B PHE 3.7 10.1 - - - -
208B GLY* 4.2 6.3 - - - -
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B THR* 4.3 21.5 - - + -
174B SER 3.5 3.2 + - - -
175B LYS* 3.1 10.0 + - + +
177B GLY* 1.3 76.1 - - - +
179B LEU* 1.3 61.3 + - - +
181B SER* 3.1 4.9 + - - -
182B THR* 2.7 33.3 + - - -
208B GLY* 4.1 2.2 - - - -
209B PRO* 3.6 35.7 - - + +
211B ALA* 4.5 7.6 - - + -
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Residues in contact with LEU 179 (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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71B ALA* 4.9 8.3 - - + -
89B ILE* 4.0 26.7 - - + -
90B ARG 4.7 5.6 - - - +
129B THR* 4.1 19.7 - - + +
132B GLY* 3.9 34.5 - - - +
133B LEU* 3.9 6.5 - - + +
136B LEU* 4.0 12.2 - - + +
175B LYS* 2.9 48.2 + - + +
176B GLY* 4.0 1.1 - - - +
178B ALA* 1.3 77.5 - - + +
180B SER* 1.3 52.5 + - - +
182B THR* 3.3 4.5 + - - -
183B LEU* 2.8 37.1 + - - +
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 3.6 15.0 - - - +
170B VAL* 3.1 20.0 - - - +
171B THR* 3.5 28.5 - - - -
172B GLY 3.6 5.2 + - - -
176B GLY 2.8 25.7 + - - -
177B GLY 3.0 8.3 + - - -
179B LEU* 1.3 74.1 - - - +
181B SER* 1.3 64.0 + - - +
183B LEU* 3.3 1.2 + - - +
184B ALA* 2.9 25.1 + - - +
203B THR* 4.2 1.7 + - - -
205B PRO* 3.6 11.4 - - - +
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Residues in contact with SER 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B GLY 3.0 17.0 + - - -
178B ALA* 3.1 9.4 + - - -
180B SER* 1.3 81.0 + - - +
182B THR* 1.3 65.8 + - - +
184B ALA* 3.5 2.3 + - - +
185B LEU* 3.3 16.1 + - - +
203B THR* 3.7 12.1 + - - -
205B PRO* 4.0 12.1 - - - -
211B ALA* 5.6 1.2 - - - +
220B PHE* 3.3 20.1 - - - -
286B ILE* 3.6 32.6 - - - +
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Residues in contact with THR 182 (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 TRP* 3.6 30.2 - - + -
125B ILE* 4.8 10.3 - - + -
129B THR* 5.0 6.5 - - - -
133B LEU* 4.1 16.2 - - + -
178B ALA 2.7 22.3 + - - -
179B LEU* 3.7 5.4 - - - -
181B SER* 1.3 78.7 + - - +
183B LEU* 1.3 64.9 + - - +
185B LEU* 3.2 7.8 + - - +
186B TRP* 3.1 18.0 + - - +
211B ALA* 3.4 21.4 - - + +
216B PHE* 4.3 13.1 - - + -
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Residues in contact with LEU 183 (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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73B MET* 4.0 18.6 - - + -
87B ILE* 4.4 10.5 - - + -
89B ILE* 4.3 5.8 - - + -
133B LEU* 3.9 19.0 - - + +
136B LEU* 4.0 30.3 - - + -
152B ILE* 5.2 3.4 - - + -
170B VAL* 4.0 16.8 - - + -
179B LEU 2.8 19.3 + - - +
180B SER 3.7 2.7 - - - +
182B THR* 1.3 73.5 - - - +
184B ALA* 1.3 58.5 + - - +
186B TRP* 3.2 25.3 + - + +
187B LEU* 3.0 50.7 + - + +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 3.7 28.0 - - + -
180B SER 2.9 17.7 + - - +
181B SER 3.6 6.5 - - - +
183B LEU* 1.3 76.8 - - - +
185B LEU* 1.3 57.7 + - - +
187B LEU* 3.4 6.9 + - - +
188B LYS* 3.1 26.3 + - - +
201B ILE* 3.9 11.1 - - + +
203B THR* 3.9 11.2 - - - -
224B LEU* 3.8 15.9 - - + -
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Residues in contact with LEU 185 (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 TRP* 3.6 18.2 - - + +
181B SER 3.3 8.9 + - - +
182B THR 3.2 9.5 + - - +
184B ALA* 1.3 77.3 - - - +
186B TRP* 1.3 60.1 + - - +
188B LYS* 3.1 3.2 + - + +
189B ASP* 2.8 32.5 + - - +
216B PHE* 3.5 35.4 - - + -
219B TYR* 4.2 17.0 - - + -
220B PHE* 3.9 31.4 - - + -
223B CYS* 4.0 24.9 - - + -
224B LEU* 3.9 10.0 - - + +
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Residues in contact with TRP 186 (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 TRP* 3.9 18.3 - - + -
115B TYR* 3.4 40.3 - + + -
133B LEU* 4.4 4.9 - - + -
137B GLN* 3.2 43.3 - - + +
152B ILE* 4.0 24.2 - - + -
153B LEU* 4.3 18.4 - - + -
182B THR 3.1 9.9 + - - +
183B LEU* 3.2 34.3 + - + +
185B LEU* 1.3 80.2 - - - +
187B LEU* 1.3 82.6 + - + +
189B ASP* 3.3 3.1 + - - +
190B ILE* 3.1 45.7 + - + +
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Residues in contact with LEU 187 (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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87B ILE* 4.0 19.3 - - + -
152B ILE* 5.7 1.1 - - + -
153B LEU* 4.6 3.8 - - + -
156B LEU* 4.2 18.2 - - + -
168B ILE* 5.3 4.7 - - + -
170B VAL* 4.5 9.9 - - + -
183B LEU* 3.0 35.4 + - + +
184B ALA* 3.6 7.4 - - - +
186B TRP* 1.3 106.1 - - + +
188B LYS* 1.3 62.6 + - - +
190B ILE* 3.2 14.0 - - + +
191B GLN* 3.2 23.9 + - - +
195B LEU* 3.8 17.5 - - + +
201B ILE* 3.8 16.8 - - + -
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Residues in contact with LYS 188 (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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184B ALA 3.1 13.6 + - - +
185B LEU* 3.1 9.6 + - - +
187B LEU* 1.3 78.9 - - - +
189B ASP* 1.3 61.9 + - - +
191B GLN* 3.2 38.2 + - - +
201B ILE* 3.8 10.8 + - + +
223B CYS* 2.9 46.7 + - - +
224B LEU* 3.8 16.7 - - + +
227B GLN* 3.3 22.8 - - - +
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Residues in contact with ASP 189 (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 TRP* 3.0 32.4 + - - -
115B TYR* 3.5 32.0 - - + +
116B ALA* 3.9 0.4 - - - +
185B LEU* 2.8 20.6 + - - +
186B TRP 3.3 2.2 + - - +
188B LYS* 1.3 76.2 - - - +
190B ILE* 1.3 60.4 + - - +
191B GLN 4.5 2.9 - - - +
193B VAL* 5.3 4.0 - - - +
219B TYR* 2.5 35.5 + - - -
223B CYS* 3.9 7.4 - - - -
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Residues in contact with ILE 190 (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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115B TYR* 4.3 13.7 - - + -
153B LEU* 3.9 27.1 - - + -
186B TRP* 3.1 52.4 + - + +
187B LEU* 3.2 20.2 - - + +
189B ASP* 1.3 78.8 - - - +
191B GLN* 1.3 65.7 - - - +
193B VAL* 2.9 9.7 + - + +
194B LYS* 2.9 44.4 + - + +
195B LEU* 3.6 6.6 + - + -
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Residues in contact with GLN 191 (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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187B LEU 3.2 17.3 + - - +
188B LYS* 3.2 32.0 + - - +
189B ASP 4.5 2.4 - - - +
190B ILE* 1.3 79.3 - - - +
192B GLY* 1.3 60.2 + - - +
193B VAL* 3.4 4.0 + - - +
195B LEU* 3.4 15.9 - - + +
196B SER 3.0 24.2 + - - +
197B GLN* 3.8 15.0 + - + -
199B ILE* 2.8 34.6 + - - +
201B ILE* 3.5 18.7 - - - +
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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
------------------------------------------------------------
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