Contacts of the helix formed by residues 185 - 204 (chain B) in PDB entry 2E9V
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 HIS 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU* 3.1 35.6 + - - +
163B LEU* 3.1 29.3 - - + +
177B GLU* 5.0 0.7 - - - +
184B PHE* 1.3 77.9 - - - +
186B ALA* 1.3 63.6 + - - +
187B GLU* 3.6 0.7 - - - +
188B PRO* 3.2 28.8 - - + +
189B VAL* 3.5 13.9 - - - +
250B PRO* 5.9 2.5 - - + +
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Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B THR* 3.8 19.4 + - - +
155B PHE* 3.7 29.4 - - + -
161B GLU* 4.2 4.2 + - - -
162B ARG 5.2 0.6 + - - -
164B LEU* 3.6 31.8 - - + +
184B PHE* 3.7 2.6 + - - -
185B HIS* 1.3 70.9 - - - +
187B GLU* 1.3 68.1 + - - +
189B VAL* 3.0 25.1 + - - +
190B ASP* 3.5 4.0 + - - +
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Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B HIS* 3.5 36.9 + - + +
155B PHE* 3.4 23.0 - - + -
156B ARG* 2.9 33.7 + - - -
161B GLU* 4.1 9.8 + - - +
185B HIS* 4.7 0.4 - - - +
186B ALA* 1.3 76.5 - - - +
188B PRO* 1.3 68.6 - - + +
189B VAL 3.2 0.5 + - - -
190B ASP 3.4 1.9 + - - -
191B VAL* 3.3 26.0 + - + +
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Residues in contact with PRO 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B GLU* 4.3 0.7 - - - +
185B HIS* 3.2 32.8 - - + +
187B GLU* 1.3 95.7 - - + +
189B VAL* 1.3 60.0 + - - +
191B VAL* 3.5 7.6 + - + +
192B TRP* 3.0 17.8 + - - +
250B PRO* 4.1 26.7 - - + +
253B ARG* 3.3 34.5 + - + +
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B THR* 5.4 0.9 - - - +
129B ARG* 5.5 11.0 - - + +
173B TYR 5.2 0.5 - - - +
174B VAL* 5.1 4.0 - - + -
175B ALA* 4.2 17.0 - - + +
177B GLU* 3.9 9.6 - - - +
178B LEU* 3.7 40.6 - - + -
184B PHE* 4.0 11.4 - - + -
185B HIS 3.5 14.4 - - - +
186B ALA* 3.0 14.7 + - - +
188B PRO* 1.3 74.2 - - - +
190B ASP* 1.3 71.9 + - - +
192B TRP* 3.1 6.1 + - - +
193B SER* 3.0 21.5 + - - -
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Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 4.3 3.8 - - + -
121B LEU* 6.0 0.2 - - - +
122B HIS* 2.6 35.4 + - + +
127B THR* 2.4 31.3 + - - -
128B HIS* 3.4 5.7 + - - -
129B ARG* 3.1 28.4 + - - +
131B ILE* 3.7 18.3 - - + +
186B ALA 3.5 0.8 + - - +
187B GLU 3.4 2.2 + - - -
189B VAL* 1.3 77.3 - - - +
191B VAL* 1.3 62.5 + - - +
193B SER* 2.5 26.9 + - - -
194B CYS* 3.0 11.6 + - - -
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B MET* 5.8 2.0 - - - -
118B VAL* 5.9 0.7 - - - -
122B HIS* 4.9 1.6 - - + -
187B GLU* 3.3 15.8 + - + +
188B PRO* 3.6 11.4 - - + +
189B VAL 3.2 0.4 - - - -
190B ASP* 1.3 76.6 - - - +
192B TRP* 1.3 66.3 + - - +
194B CYS* 3.2 10.5 + - - +
195B GLY 3.1 14.4 + - - -
245B ILE* 3.5 20.4 - - + +
253B ARG* 4.8 5.2 - - + -
254B ILE* 3.6 24.9 - - + +
255B THR* 5.2 1.1 - - - -
256B ILE* 3.7 34.5 - - + +
259B ILE* 4.2 15.7 - - + -
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Residues in contact with TRP 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B TYR 3.2 20.7 + - - -
174B VAL 3.3 10.3 + - - -
175B ALA* 3.7 15.3 - - + -
176B PRO* 3.5 32.1 - - + -
188B PRO 3.0 13.9 + - - +
189B VAL 3.3 9.0 - - - +
191B VAL* 1.3 76.0 - - - +
193B SER* 1.3 62.4 + - - +
195B GLY* 2.9 14.0 + - - -
196B ILE* 3.2 23.7 + - + +
208B TRP* 3.5 26.0 - + - +
211B PRO* 3.7 9.9 - - + -
218B TYR* 3.8 21.8 - + - -
245B ILE* 4.2 8.7 - - - -
246B LEU* 3.7 36.1 - - + +
247B VAL 3.7 17.3 - - - -
248B GLU 4.3 0.4 - - - -
253B ARG* 3.5 22.4 - - - +
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG 6.5 0.2 - - - -
131B ILE* 3.1 42.1 - - - +
173B TYR* 3.6 22.8 - - - -
189B VAL* 3.0 13.1 + - - -
190B ASP* 2.5 22.3 + - - -
192B TRP* 1.3 77.5 - - - +
194B CYS* 1.3 59.8 + - - +
196B ILE* 3.1 14.5 + - - +
197B VAL* 3.1 16.8 + - - +
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Residues in contact with CYS 194 (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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111B PHE* 4.0 7.7 - - + -
114B LEU* 3.7 20.9 - - + -
115B MET* 3.1 37.2 - - + -
118B VAL* 3.9 15.7 - - - -
131B ILE* 4.1 4.0 - - - -
190B ASP 3.0 16.8 + - - -
191B VAL* 3.2 7.8 + - + +
193B SER* 1.3 81.7 + - - +
195B GLY* 1.3 62.3 + - - +
197B VAL* 3.1 12.2 + - - +
198B LEU* 2.8 28.8 + - - +
245B ILE* 6.2 0.7 - - + -
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Residues in contact with GLY 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 5.2 0.2 - - - -
191B VAL 3.1 6.3 + - - -
192B TRP 2.9 9.7 + - - -
194B CYS* 1.3 77.5 - - - +
196B ILE* 1.3 62.6 + - - +
198B LEU* 3.4 7.9 + - - +
199B THR* 3.0 27.0 + - - -
242B LEU* 3.7 10.2 - - - +
245B ILE* 3.9 24.4 - - - +
246B LEU* 4.4 3.8 - - - -
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Residues in contact with ILE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PRO 3.8 15.3 - - - +
173B TYR* 3.5 26.0 - - + -
192B TRP* 3.6 27.4 - - + +
193B SER 3.1 7.7 + - - +
195B GLY* 1.3 75.1 - - - +
197B VAL* 1.3 61.6 + - - +
199B THR* 3.2 4.7 + - - +
200B ALA* 3.0 27.2 + - - +
206B LEU* 3.5 19.9 - - + +
207B PRO* 4.1 13.9 - - + -
208B TRP* 3.8 23.1 - - + +
246B LEU* 3.4 28.5 - - + -
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.9 22.7 - - + -
114B LEU* 4.2 7.4 - - + -
131B ILE* 4.0 24.7 - - + +
132B LYS* 4.2 14.4 - - - -
133B PRO* 4.4 8.5 - - + -
136B LEU* 3.9 11.7 - - + -
173B TYR* 4.6 3.8 - - + -
193B SER 3.1 14.6 + - - +
194B CYS* 3.1 9.8 + - - +
196B ILE* 1.3 77.6 - - - +
198B LEU* 1.3 56.9 + - - +
200B ALA* 3.4 7.8 + - - +
201B MET* 2.9 42.1 + - + +
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ALA* 4.7 2.2 - - + +
111B PHE* 3.9 28.5 - - + -
194B CYS 2.8 14.6 + - - +
195B GLY 3.6 5.6 - - - +
197B VAL* 1.3 76.0 - - - +
199B THR* 1.3 66.6 + - - +
201B MET* 3.2 18.2 + - + -
202B LEU* 3.0 47.3 + - + +
238B PRO 4.8 3.1 - - - +
241B LEU* 4.1 9.2 - - + -
242B LEU* 3.6 24.2 - - + -
245B ILE* 5.2 0.9 - - + -
264B TRP* 3.9 31.9 - - + -
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Residues in contact with THR 199 (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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195B GLY 3.0 16.9 + - - -
196B ILE* 3.2 10.6 + - - -
198B LEU* 1.3 76.2 - - - +
200B ALA* 1.3 57.4 + - - +
202B LEU 3.2 0.9 + - - -
203B ALA* 2.7 34.1 + - - +
205B GLU 3.9 7.2 - - - +
207B PRO* 4.1 9.2 - - + -
230B PRO* 3.8 21.5 - - + -
231B TRP* 3.5 39.2 - - + -
234B ILE* 4.2 7.0 - - + -
242B LEU* 3.6 13.3 - - - +
246B LEU* 4.3 3.1 - - - +
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 3.3 23.9 - - + +
133B PRO* 4.7 6.5 - - + -
173B TYR* 5.3 0.4 - - - +
196B ILE 3.0 13.2 + - - +
197B VAL* 3.5 11.9 - - - +
199B THR* 1.3 78.6 - - - +
201B MET* 1.3 58.4 + - - +
204B GLY* 2.8 28.2 + - - -
205B GLU* 3.8 15.2 + - - +
206B LEU* 4.2 17.5 - - + +
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Residues in contact with MET 201 (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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92B LEU* 4.0 12.6 - - + -
96B ILE* 4.4 12.6 - - + -
101B GLY* 3.1 1.8 - - - -
102B MET* 3.0 63.2 + - + +
107B ALA* 3.8 26.2 - - + +
110B PHE* 3.8 22.0 - - + -
111B PHE* 4.4 15.3 - - + +
114B LEU* 5.5 1.3 - - + -
197B VAL* 2.9 36.2 + - + +
198B LEU* 3.2 20.4 + - + +
200B ALA* 1.3 76.4 - - - +
202B LEU* 1.3 59.5 + - - +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE 3.3 12.6 - - - +
102B MET 4.8 4.0 + - - +
104B GLU* 4.0 29.8 - - + +
107B ALA* 3.8 21.3 - - + -
198B LEU* 3.0 37.1 + - + +
199B THR 4.0 1.8 - - - +
201B MET* 1.3 79.5 - - - +
203B ALA* 1.3 58.7 + - - +
204B GLY 3.7 0.4 - - - -
233B LYS* 4.1 13.0 - - - +
234B ILE* 3.8 23.3 - - + -
238B PRO* 3.4 38.1 - - + -
242B LEU* 5.3 0.7 - - + -
264B TRP* 4.8 2.0 - - + -
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASP 3.6 7.1 - - - +
100B ILE 4.0 7.6 - - - -
199B THR 2.7 18.1 + - - +
202B LEU* 1.3 74.8 - - - +
204B GLY* 1.3 63.5 + - - +
205B GLU* 3.2 2.1 + - + +
230B PRO* 3.3 44.9 - - + +
233B LYS* 3.2 26.5 + - + -
234B ILE* 4.2 8.1 - - + -
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Residues in contact with GLY 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 3.8 13.0 - - - -
98B PRO* 3.8 4.0 - - - +
99B ASP* 2.8 22.0 + - - +
100B ILE 3.7 3.8 - - - -
101B GLY 3.5 20.2 - - - +
200B ALA 2.8 17.6 + - - -
203B ALA* 1.3 77.6 - - - +
205B GLU* 1.3 60.0 + - - +
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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