Contacts of the helix formed by residues 177 - 192 (chain B) in PDB entry 2VM8
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 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B GLN* 4.4 0.6 + - - -
176B LEU* 1.3 76.8 - - - +
178B ASP* 1.3 56.1 + - - +
179B CYS* 3.5 9.4 + - - +
180B GLN* 3.1 37.0 + - - +
181B ILE* 2.8 33.9 + - - +
203D ASP* 5.0 4.5 - - - -
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Residues in contact with ASP 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B THR* 1.3 72.3 - - - +
179B CYS* 1.3 61.0 + - - +
181B ILE* 3.2 5.1 + - - +
182B TYR* 2.9 29.1 + - - +
238B ARG* 2.9 49.0 + - - -
242B ILE* 3.6 21.0 - - + +
178D ASP* 5.6 0.9 - - - +
201D ASN* 3.3 17.0 + - - +
203D ASP* 3.3 26.4 + - + +
204D ILE* 5.5 1.9 - - + +
238D ARG* 4.6 7.6 + - - -
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Residues in contact with CYS 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B THR* 3.3 7.8 + - - +
178B ASP* 1.3 77.6 - - - +
180B GLN* 1.3 65.4 + - + +
182B TYR* 3.1 10.2 + - - +
183B GLU* 2.9 42.1 + - - +
171D LYS* 3.3 31.9 - - - +
203D ASP* 3.9 13.5 + - + +
207D GLU* 3.5 24.5 - - + -
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Residues in contact with GLN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TRP* 3.7 48.2 + - + +
175B GLN 4.5 2.1 - - - +
176B LEU* 3.4 17.8 - - + +
177B THR* 3.1 38.5 + - - +
179B CYS* 1.3 81.4 - - + +
181B ILE* 1.3 56.7 + - - +
183B GLU* 3.3 5.5 + - - +
184B VAL* 2.9 35.3 + - - +
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B VAL* 4.7 12.1 - - + -
167B TYR 4.8 1.6 - - - +
168B MET* 3.6 33.0 - - + -
176B LEU* 3.8 30.1 - - + +
177B THR 2.8 25.3 + - - +
178B ASP* 3.7 13.9 - - - +
179B CYS 3.2 0.4 - - - -
180B GLN* 1.3 69.5 - - - +
182B TYR* 1.3 62.4 + - - +
184B VAL* 3.3 6.0 + - - +
185B LEU* 2.9 54.6 + - + +
197B VAL* 5.8 1.3 - - + -
238B ARG* 5.1 0.4 - - - +
239B ALA* 5.8 4.3 - - + -
242B ILE* 3.9 17.9 - - + -
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Residues in contact with TYR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASP 2.9 13.4 + - - +
179B CYS* 3.3 11.4 - - - +
181B ILE* 1.3 77.3 - - - +
183B GLU* 1.3 63.2 + - + +
185B LEU* 4.9 0.2 - - - -
186B SER* 2.7 38.2 + - - -
242B ILE* 3.7 20.4 - - + +
245B GLN* 4.7 4.9 + - + -
246B THR* 3.8 19.7 + - - -
203D ASP 6.0 0.4 - - - +
204D ILE* 4.5 18.8 - - + -
207D GLU* 3.6 46.8 + - + +
208D GLU* 2.6 38.1 + - + +
211D ARG* 4.0 15.6 + - - +
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TRP* 2.8 37.1 + - + +
146B LYS* 5.8 1.6 + - - -
179B CYS* 2.9 37.1 + - - +
180B GLN* 3.7 4.4 - - - +
181B ILE 3.2 0.2 - - - -
182B TYR* 1.3 79.9 - - + +
184B VAL* 1.3 62.3 + - - +
186B SER* 3.4 7.2 + - - -
187B VAL* 3.3 24.1 + - - +
207D GLU* 4.5 13.8 - - - +
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE* 4.2 11.4 - - + -
144B TRP* 3.6 34.5 - - + -
152B MET* 4.2 5.8 - - + +
166B VAL* 3.7 21.1 - - + -
176B LEU* 4.0 18.4 - - + -
180B GLN 2.9 24.8 + - - +
181B ILE* 3.7 4.7 - - - +
183B GLU* 1.3 76.0 - - - +
185B LEU* 1.3 60.0 + - + +
187B VAL* 3.1 5.0 + - - +
188B ILE* 2.9 45.3 + - + +
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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
----------------------------------------------------------
166B VAL* 4.8 10.5 - - + -
181B ILE* 2.9 42.8 + - + +
182B TYR* 4.4 1.8 - - - +
184B VAL* 1.3 75.7 - - + +
186B SER* 1.3 61.0 + - - +
188B ILE* 4.0 7.4 - - + -
189B ARG* 3.0 24.4 + - - +
195B ALA* 3.5 23.6 - - + -
239B ALA* 4.7 1.6 - - - +
242B ILE* 3.9 15.3 - - + -
243B ALA* 4.2 22.9 - - + +
246B THR* 3.7 14.8 - - + -
248B CYS* 3.1 28.5 - - - +
250B LEU* 4.6 10.3 - - + -
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Residues in contact with SER 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TYR* 2.7 31.0 + - - -
183B GLU* 3.4 9.8 + - - -
184B VAL 3.2 0.6 - - - -
185B LEU* 1.3 78.3 - - - +
187B VAL* 1.3 63.1 + - - +
189B ARG* 3.5 28.7 + - - +
190B ASP* 3.1 31.2 + - - +
246B THR* 3.6 12.4 + - - +
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TRP* 4.1 7.6 - - + -
149B GLN* 3.3 50.5 - - + +
152B MET* 4.3 14.8 - - + -
153B GLU* 4.8 5.6 - - + -
183B GLU 3.3 14.6 + - - +
184B VAL* 3.1 7.7 + - - +
186B SER* 1.3 75.6 - - - +
188B ILE* 1.3 65.7 + - - +
190B ASP* 3.0 11.1 + - + +
191B ILE* 2.9 43.7 + - + +
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B MET* 3.6 18.8 - - + -
164B PHE* 4.3 18.6 - - + +
166B VAL* 5.4 1.8 - - + -
184B VAL* 2.9 37.9 + - + +
185B LEU* 3.7 8.5 - - + +
187B VAL* 1.3 75.3 - - - +
189B ARG* 1.3 57.1 + - - +
191B ILE* 3.1 8.9 + - - +
192B GLY 2.9 25.3 + - - -
193B ALA* 2.9 43.7 + - + +
194B ILE 3.7 0.4 - - - -
195B ALA* 3.7 34.5 - - + +
248B CYS* 3.7 7.4 - - - -
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Residues in contact with ARG 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU 3.0 15.1 + - - +
186B SER* 3.5 34.8 + - - +
188B ILE* 1.3 78.1 - - - +
190B ASP* 1.3 92.5 + - - +
192B GLY* 3.2 8.5 + - - -
246B THR* 2.8 30.3 + - - +
247B ASN* 3.2 36.3 - - - +
248B CYS* 3.9 6.9 - - + -
249B PRO* 4.8 0.2 - - - -
474B PHE* 4.3 4.0 - - - -
479B TYR* 3.5 20.2 + - + -
482B ILE* 4.3 11.4 - - + -
486B SER* 4.8 6.7 - - - +
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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
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186B SER* 3.1 14.0 + - - +
187B VAL* 3.0 11.0 + - + +
189B ARG* 1.3 111.8 + - - +
191B ILE* 1.3 59.9 + - - +
192B GLY 3.3 0.2 - - - -
474B PHE* 4.0 10.4 - - - -
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Residues in contact with ILE 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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152B MET* 3.6 18.2 - - + +
153B GLU* 3.4 52.0 - - + +
156B VAL* 3.5 22.4 - - + +
157B LYS* 6.4 2.5 - - + -
164B PHE* 4.6 1.8 - - + -
187B VAL* 2.9 20.0 + - + +
188B ILE* 3.1 7.6 + - - +
190B ASP* 1.3 76.9 - - + +
192B GLY* 1.3 59.0 + - - +
193B ALA* 3.2 31.4 - - + -
473B PRO* 3.5 14.7 - - - +
474B PHE* 3.8 8.0 - - - -
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Residues in contact with GLY 192 (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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162B ASN 4.5 0.3 - - - +
188B ILE 2.9 3.2 + - - -
189B ARG 3.2 4.2 + - - -
190B ASP 3.3 0.8 - - - -
191B ILE* 1.3 78.9 - - - +
193B ALA* 1.3 58.3 + - - +
473B PRO* 3.0 11.2 - - - +
474B PHE* 2.8 48.3 + - - -
475B PRO* 3.9 2.4 - - - +
479B TYR* 3.3 21.8 - - - -
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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