Contacts of the helix formed by residues 180 - 197 (chain B) in PDB entry 1V0O
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 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B HIS* 3.3 51.2 + - + +
122B LEU* 3.5 21.8 - - + -
178B TYR* 4.6 12.3 - - + +
179B SER* 1.3 68.6 + - - +
181B THR* 1.3 68.9 + - - +
182B ILE 3.1 3.5 + - - -
183B ASP 3.2 11.5 + - - -
184B ILE* 3.7 5.7 + - - +
274B THR* 5.8 3.8 - - - +
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Residues in contact with THR 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ASP* 4.5 3.5 + - - -
179B SER* 2.4 27.1 + - - +
180B THR* 1.3 82.4 + - - +
182B ILE* 1.3 62.5 + - - +
184B ILE* 3.2 20.7 + - - +
185B TRP 3.3 5.4 + - - -
269B PRO* 3.2 48.3 - - + +
270B ASN* 5.3 1.3 - - - +
272B ARG* 3.1 26.7 + - + +
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Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 4.5 4.9 - - + -
124B ARG* 4.3 32.5 - - + +
157B TYR* 3.8 29.6 - - + +
166B TYR 4.8 0.7 - - - +
167B ARG* 6.1 1.3 - - - -
168B ALA* 4.8 9.4 - - + +
170B ASP* 5.9 1.1 - - - +
171B VAL* 3.8 27.8 - - + -
179B SER* 3.1 25.3 + - - +
180B THR 3.1 1.0 - - - +
181B THR* 1.3 83.2 + - - +
183B ASP* 1.3 78.4 + - - +
185B TRP* 3.7 5.0 + - - +
186B SER* 3.5 20.8 + - - +
272B ARG* 4.5 4.9 - - - +
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Residues in contact with ASP 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 4.3 5.6 - - + +
116B CYS* 5.8 0.7 - - - +
117B HIS* 2.8 35.0 + - + +
122B LEU* 3.6 3.6 - - - +
123B HIS* 3.0 24.9 + - - +
124B ARG* 2.8 30.3 + - - -
126B LEU* 3.8 20.2 + - + +
180B THR 3.2 1.6 + - - -
182B ILE* 1.3 85.2 - - - +
184B ILE* 1.3 60.4 + - - +
186B SER* 3.2 8.1 + - - -
187B VAL* 3.0 29.5 + - - +
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Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 5.0 4.9 - - + -
113B ILE* 4.5 4.7 - - + -
117B HIS* 4.2 12.3 - - + -
180B THR* 3.9 11.9 - - - +
181B THR* 3.2 12.9 + - - +
183B ASP* 1.3 76.2 - - - +
185B TRP* 1.3 65.7 + - - +
187B VAL* 3.2 10.6 + - + +
188B GLY 3.0 18.0 + - - -
264B MET* 3.9 35.7 - - + +
272B ARG* 4.4 5.2 - - - -
273B ILE* 3.3 28.3 - - + +
274B THR* 4.2 1.6 - - - -
275B ALA* 3.6 36.8 - - + +
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Residues in contact with TRP 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B TRP 5.2 0.4 + - - -
166B TYR 3.5 19.5 - - - -
167B ARG 3.3 11.3 + - - -
168B ALA* 3.5 25.8 - - + -
169B PRO* 3.8 20.4 - - + -
181B THR 3.3 3.6 + - - -
182B ILE 3.8 5.4 - - - +
184B ILE* 1.3 78.2 - - - +
186B SER* 1.3 61.8 + - - +
188B GLY 3.1 3.1 + - - -
189B CYS* 3.0 32.1 + - - -
201B PHE* 3.9 20.3 - + - -
209B GLN* 6.0 0.2 - - - +
213B ILE* 3.8 20.5 - - + +
217B LEU* 3.5 23.6 - - + -
264B MET 4.1 5.6 - - - -
265B LEU* 3.4 33.7 - - + +
266B LYS 3.6 15.3 - - - -
267B LEU* 3.9 6.7 - - + -
272B ARG* 3.6 28.8 - - - +
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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
----------------------------------------------------------
124B ARG 5.6 3.5 + - - -
126B LEU* 4.0 28.1 + - - +
166B TYR* 2.6 37.3 + - - +
182B ILE* 3.5 10.9 + - - +
183B ASP* 3.2 12.4 + - - -
185B TRP* 1.3 80.0 - - - +
187B VAL* 1.3 57.0 + - - +
189B CYS* 3.2 4.0 + - - +
190B ILE* 3.0 34.1 + - - +
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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
----------------------------------------------------------
106B LEU* 3.6 26.0 - - + +
109B LEU* 4.0 10.1 - - + -
110B LEU* 4.1 13.5 - - + -
113B ILE* 3.0 35.0 - - + -
126B LEU* 4.2 2.7 - - + -
183B ASP 3.0 20.6 + - - +
184B ILE* 3.2 12.5 + - + +
186B SER* 1.3 75.3 - - - +
188B GLY* 1.3 58.4 + - - +
190B ILE* 3.4 8.4 + - - +
191B PHE* 2.8 27.7 + - - +
264B MET* 3.9 16.8 - - + -
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Residues in contact with GLY 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ILE 3.0 10.3 + - - -
185B TRP 3.1 4.4 + - - -
187B VAL* 1.3 77.1 - - - +
189B CYS* 1.3 56.6 + - - +
191B PHE* 3.2 0.9 + - - -
192B ALA* 2.9 26.3 + - - +
261B LEU* 3.3 27.1 - - - +
264B MET* 3.8 19.0 - - - -
265B LEU* 3.9 7.4 - - - -
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Residues in contact with CYS 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B TRP 4.0 10.3 - - - +
166B TYR* 3.5 26.2 - - + -
185B TRP* 3.0 44.8 + - - -
186B SER 3.5 4.3 - - - +
188B GLY* 1.3 76.5 - - - +
190B ILE* 1.3 56.7 + - - +
192B ALA* 3.4 7.5 + - - +
193B GLU* 3.0 27.9 + - - +
200B LEU* 4.9 7.6 + - + +
201B PHE* 3.8 26.5 - - + -
265B LEU* 3.9 4.4 - - - +
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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
----------------------------------------------------------
86B LEU* 3.8 28.7 - - + -
109B LEU* 4.2 15.5 - - + -
126B LEU* 4.0 28.0 - - + -
127B LYS* 4.0 12.1 - - - +
128B PRO* 4.6 4.7 - - + -
131B LEU* 4.0 20.9 - - + -
166B TYR* 4.0 17.5 - - + -
186B SER 3.0 23.4 + - - +
187B VAL* 3.8 4.5 - - - +
189B CYS* 1.3 72.6 - - - +
191B PHE* 1.3 66.3 + - - +
193B GLU* 3.2 7.9 + - + +
194B MET* 3.0 29.9 + - + +
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Residues in contact with PHE 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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102B ALA* 5.4 4.5 - - + -
106B LEU* 3.7 30.7 - - + +
187B VAL 2.8 18.8 + - - +
188B GLY* 3.3 5.8 - - - +
190B ILE* 1.3 75.4 - - - +
192B ALA* 1.3 63.6 + - - +
194B MET* 3.1 27.7 + - + +
195B VAL* 2.9 31.2 + - + +
253B LEU* 4.3 11.2 - - + -
257B GLY 3.6 24.9 - - - -
260B LEU* 4.5 6.1 - - + -
261B LEU* 3.7 28.7 - - + -
264B MET* 4.3 6.7 - - - -
283B TYR* 3.6 37.2 - + - -
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Residues in contact with ALA 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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188B GLY 2.9 17.5 + - - +
189B CYS 3.6 5.8 - - - +
190B ILE 3.3 0.2 - - - -
191B PHE* 1.3 76.8 - - - +
193B GLU* 1.3 56.3 + - - +
195B VAL* 3.2 9.7 + - - +
196B ASN* 3.0 36.1 + - - +
198B THR 4.8 0.7 - - - -
200B LEU* 3.7 33.9 - - + -
250B LEU* 3.9 14.6 - - + -
261B LEU* 3.9 8.7 - - + +
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Residues in contact with GLU 193 (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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90B LEU* 3.6 22.2 - - + +
128B PRO* 3.7 15.8 - - - +
165B TRP* 5.6 0.3 - - - -
166B TYR* 2.3 40.9 + - - -
189B CYS 3.0 14.5 + - - +
190B ILE* 3.5 7.9 - - + +
191B PHE 3.2 0.4 + - - -
192B ALA* 1.3 76.3 - - - +
194B MET* 1.3 57.5 + - - +
197B GLY* 2.9 27.8 + - - +
198B THR* 3.5 26.2 - - - +
199B PRO* 3.7 27.0 - - + +
200B LEU 5.0 0.7 + - - +
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Residues in contact with MET 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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86B LEU* 4.1 22.2 - - + -
90B LEU* 4.0 10.3 - - + -
96B GLY* 3.4 0.2 - - - -
97B LEU* 3.0 51.9 + - + +
102B ALA* 3.2 37.9 - - + +
105B PHE* 3.8 23.6 - - + -
106B LEU* 4.0 22.2 - - + +
109B LEU* 6.1 0.9 - - + -
190B ILE* 3.0 17.5 + - + +
191B PHE* 3.1 23.1 + - + +
193B GLU* 1.3 75.4 - - - +
195B VAL* 1.3 61.9 + - + +
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Residues in contact with VAL 195 (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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95B GLY 3.3 17.2 - - - +
96B GLY* 3.7 0.9 - - - -
97B LEU 5.3 2.2 - - - +
102B ALA* 5.6 2.9 - - + -
191B PHE* 2.9 40.8 - - + +
192B ALA* 3.2 7.6 + - - +
194B MET* 1.3 78.2 - - - +
196B ASN* 1.3 77.3 + - - +
250B LEU* 3.9 18.8 - - + -
251B LYS* 4.2 18.2 - - - +
252B GLY 5.4 2.2 - - - +
253B LEU* 4.2 24.7 - - + -
261B LEU* 4.5 0.4 - - + -
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Residues in contact with ASN 196 (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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176A LYS* 5.8 1.4 + - - -
95B GLY* 3.3 18.0 - - - -
96B GLY 3.6 3.1 - - - -
192B ALA* 3.0 19.5 + - - +
195B VAL* 1.3 90.8 - - - +
197B GLY* 1.3 58.6 + - - +
198B THR* 3.4 25.3 + - + +
200B LEU* 4.6 12.5 - - - +
249B PHE 2.8 28.6 + - - +
250B LEU* 4.1 6.5 - - - +
251B LYS* 3.8 33.3 + - - +
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Residues in contact with GLY 197 (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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156A LYS* 5.9 1.9 + - - -
90B LEU* 4.4 18.1 - - - +
93B CYS* 4.1 9.3 - - - +
95B GLY* 4.7 2.0 - - - -
96B GLY* 3.4 22.1 - - - -
193B GLU* 2.9 18.3 + - - +
196B ASN* 1.3 76.0 - - - +
198B THR* 1.3 59.9 + - - +
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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