Contacts of the helix formed by residues 170 - 192 (chain B) in PDB entry 3NMV
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 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B MET 3.8 22.0 - - - -
126B GLU* 4.0 16.0 + - - +
169B GLY* 1.3 71.7 - - - -
171B GLN* 1.3 68.8 + - - +
172B VAL 3.3 2.7 - - - -
173B ALA* 3.5 3.9 + - - -
174B ASN* 3.0 43.3 + - - -
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Residues in contact with GLN 171 (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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168B GLY 4.6 1.0 + - - -
169B GLY* 3.5 13.5 - - - -
170B SER* 1.3 93.6 + - - +
172B VAL* 1.3 59.1 + - - +
174B ASN* 3.5 5.5 + - - +
175B TYR* 2.9 28.8 + - - +
224B ALA* 5.8 1.6 - - + +
226B ALA* 4.2 19.5 - - + -
227B PRO* 3.7 27.7 - - + +
230B VAL* 3.9 8.4 - - + +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B SER 3.3 0.4 - - - -
171B GLN* 1.3 75.9 - - - +
173B ALA* 1.3 66.1 + - - +
175B TYR* 3.1 6.3 + - - +
176B CYS* 2.9 23.3 + - - -
220B ILE* 3.8 28.7 - - + -
226B ALA* 4.2 2.5 - - + -
230B VAL* 3.7 38.8 - - + +
231B GLY 3.8 10.3 - - - +
232B SER* 3.6 18.4 - - - -
305B ILE* 3.6 35.4 - - + +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLU 3.4 25.8 - - - +
128B SER* 3.4 17.9 - - - +
164B TYR* 3.7 16.4 - - - +
166B GLY* 3.8 5.8 - - - +
170B SER* 3.5 6.5 + - - +
171B GLN 3.4 0.2 - - - -
172B VAL* 1.3 77.7 - - - +
174B ASN* 1.3 62.2 + - - +
176B CYS* 3.3 3.1 + - - +
177B ARG 3.2 17.3 + - - -
231B GLY 4.6 1.8 + - - -
232B SER* 3.6 22.5 - - - +
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Residues in contact with ASN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLU 6.1 0.2 - - - -
127B ASP 5.1 0.9 - - - +
128B SER* 2.9 20.0 + - - -
170B SER* 3.0 41.4 + - - +
171B GLN* 3.9 5.2 - - - +
173B ALA* 1.3 72.5 - - - +
175B TYR* 1.3 66.9 + - - +
177B ARG* 3.2 29.7 + - - +
178B GLU* 2.9 30.8 + - - +
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Residues in contact with TYR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLN 2.9 18.0 + - - +
172B VAL* 3.1 8.0 + - - +
174B ASN* 1.3 79.5 - - - +
176B CYS* 1.3 60.9 + - - +
178B GLU* 3.2 6.9 + - + +
179B ARG* 3.0 51.1 + - + +
216B VAL* 4.0 20.9 - - + -
219B GLU* 2.6 51.7 + - + +
220B ILE* 4.6 7.4 - - + -
223B VAL* 3.7 22.3 - - + +
224B ALA* 3.9 26.9 - - + -
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Residues in contact with CYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B TYR* 3.4 38.9 + - + -
172B VAL* 2.9 21.9 + - - -
173B ALA 3.7 3.4 - - - +
175B TYR* 1.3 76.6 - - - +
177B ARG* 1.3 60.5 + - - +
180B MET* 2.9 39.5 + - + +
181B HIS* 4.8 0.5 + - - -
216B VAL* 4.2 14.8 - - - -
232B SER* 4.7 4.7 - - - -
234B SER* 5.1 0.9 - - - -
305B ILE* 4.0 34.5 - - - -
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Residues in contact with ARG 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASP 5.1 2.0 + - - -
128B SER* 3.6 25.5 + - - +
129B VAL 3.4 26.2 - - - +
130B SER* 3.3 16.2 + - - +
164B TYR* 3.8 12.2 - - + -
173B ALA 3.2 10.3 + - - +
174B ASN* 3.2 37.5 + - - +
176B CYS* 1.3 79.3 - - - +
178B GLU* 1.3 88.7 + - - +
181B HIS* 3.5 11.3 + - - -
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Residues in contact with GLU 178 (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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174B ASN* 2.9 30.4 + - - +
175B TYR* 3.2 7.2 + - + +
176B CYS 3.2 0.6 - - - -
177B ARG* 1.3 119.7 + - - +
179B ARG* 1.3 58.6 + - + +
181B HIS* 3.8 6.8 + - - -
182B LEU* 3.5 22.2 - - - +
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Residues in contact with ARG 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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175B TYR* 3.0 40.4 + - + +
176B CYS* 3.2 0.9 + - - -
178B GLU* 1.3 81.4 - - + +
180B MET* 1.3 61.4 + - - +
181B HIS 3.3 2.7 - - - -
182B LEU* 2.9 28.6 + - - +
183B ALA* 2.8 44.5 + - + +
186B GLU* 2.9 43.2 + - - -
215B ARG* 3.5 7.9 - - - +
216B VAL* 4.8 5.6 - - + -
219B GLU* 2.7 41.5 + - - +
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Residues in contact with MET 180 (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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160B PHE* 4.0 9.9 - - + -
164B TYR* 3.4 22.2 - - + +
176B CYS* 2.9 25.6 + - - +
178B GLU 4.0 0.2 - - - -
179B ARG* 1.3 78.3 - - - +
181B HIS* 1.3 56.9 + - - +
183B ALA* 3.3 4.4 + - + -
184B LEU* 3.0 24.8 + - + +
212B SER* 2.9 59.0 - - - +
213B PHE* 3.5 17.0 - - + +
216B VAL* 3.7 21.5 - - + -
234B SER* 4.6 6.1 - - - -
236B VAL* 4.2 9.2 - - + -
305B ILE* 5.7 0.2 - - - -
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Residues in contact with HIS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B SER* 3.9 4.0 - - - -
132B ILE* 3.6 36.8 - - + +
135B PHE* 4.0 11.7 + - + +
160B PHE* 3.7 38.3 - + + -
176B CYS 4.9 0.4 - - - -
177B ARG 3.5 25.1 + - - -
178B GLU* 3.8 8.9 + - - -
180B MET* 1.3 80.0 - - - +
182B LEU* 1.3 85.7 + - + +
184B LEU* 3.6 3.0 - - - +
185B THR* 2.8 31.9 + - - -
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Residues in contact with LEU 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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178B GLU 3.5 20.2 - - - +
179B ARG* 2.9 24.3 + - - +
181B HIS* 1.3 100.9 - - + +
183B ALA* 1.3 65.4 + - - +
185B THR* 3.4 10.7 + - + +
186B GLU* 3.1 27.5 + - - +
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Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ARG* 2.8 43.2 + - + +
180B MET* 3.8 11.7 - - + +
182B LEU* 1.3 76.8 - - - +
184B LEU* 1.3 60.1 - - - +
186B GLU* 3.4 7.3 + - - +
187B GLU* 3.1 26.2 + - - +
212B SER* 4.0 20.2 - - - +
215B ARG* 3.7 10.7 + - + +
216B VAL* 5.1 2.7 - - + +
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Residues in contact with LEU 184 (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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135B PHE* 3.7 29.4 - - + -
160B PHE* 3.8 16.2 - - + -
180B MET 3.0 16.7 + - - +
181B HIS 3.6 5.4 - - - +
183B ALA* 1.3 74.1 - - - +
185B THR* 1.3 65.3 + - - +
187B GLU* 3.1 3.0 + - - +
188B ILE* 3.0 28.6 + - + +
205B TRP* 4.3 3.4 - - + -
208B ALA* 3.8 37.2 - - + +
209B LEU* 3.7 32.3 - - + +
212B SER* 3.7 10.2 - - - +
238B VAL* 3.8 7.9 - - + -
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Residues in contact with THR 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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135B PHE* 3.8 20.0 + - - +
136B LEU* 3.8 31.6 - - + +
181B HIS 2.8 19.0 + - - -
182B LEU* 3.6 12.5 - - - +
184B LEU* 1.3 74.6 - - - +
186B GLU* 1.3 64.6 + - + +
188B ILE* 3.3 2.9 + - - +
189B VAL* 3.1 31.5 + - + +
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Residues in contact with GLU 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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179B ARG* 2.9 38.1 + - - -
182B LEU* 3.1 13.5 + - - +
183B ALA 3.6 1.6 - - - +
184B LEU 3.2 0.2 - - - -
185B THR* 1.3 80.3 - - + +
187B GLU* 1.3 58.4 + - - +
189B VAL* 3.5 8.9 + - - +
190B LYS* 3.0 35.2 + - - +
215B ARG* 2.5 39.0 + - - +
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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
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183B ALA 3.1 14.6 + - - +
184B LEU 3.1 6.3 + - - +
186B GLU* 1.3 76.3 - - - +
188B ILE* 1.3 52.6 + - - +
190B LYS* 2.6 40.9 + - - +
191B GLU* 2.8 46.2 + - + +
208B ALA* 3.8 33.4 - - + +
211B ASN* 3.7 22.8 + - + +
212B SER* 4.1 11.9 - - - +
215B ARG* 2.9 21.7 + - - +
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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
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136B LEU* 4.3 17.7 - - + -
155B HIS* 4.0 22.4 - - + +
184B LEU* 3.0 16.6 + - + +
185B THR 3.7 6.7 - - - +
186B GLU 3.3 0.2 - - - -
187B GLU* 1.3 73.3 - - - +
189B VAL* 1.3 60.2 + - + +
191B GLU* 4.4 0.9 - - + +
192B LYS* 2.9 28.2 + - - -
193B PRO* 3.4 20.2 - - + +
194B GLU* 4.5 4.2 - - - +
204B LYS 4.9 0.4 - - - +
205B TRP* 3.6 48.5 - - + -
208B ALA* 3.6 20.2 - - + -
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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
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185B THR* 3.1 26.6 + - + +
186B GLU* 3.5 11.9 + - - +
188B ILE* 1.3 76.1 - - + +
190B LYS* 1.3 58.6 + - + +
192B LYS* 2.7 44.1 + - - +
194B GLU* 6.2 0.2 - - - -
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Residues in contact with LYS 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 GLU* 3.0 18.6 + - - +
187B GLU* 2.6 43.6 + - - +
189B VAL* 1.3 82.0 - - + +
191B GLU* 1.3 66.5 + - + +
192B LYS* 4.2 7.8 + - - +
215B ARG* 3.6 22.4 - - - +
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Residues in contact with GLU 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 GLU* 2.8 30.5 + - + +
188B ILE* 3.3 1.1 + - - -
190B LYS* 1.3 74.7 - - + +
192B LYS* 1.3 71.5 + - - +
193B PRO* 3.4 11.1 - - + -
204B LYS* 2.8 71.3 + - + +
207B LYS* 3.1 45.2 + - - +
208B ALA* 4.5 7.2 - - + -
211B ASN* 4.4 6.1 + - - -
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Residues in contact with LYS 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 ILE 2.9 11.5 + - - +
189B VAL* 2.7 40.3 + - - +
190B LYS* 4.2 5.6 + - - +
191B GLU* 1.3 79.4 - - - +
193B PRO* 1.3 69.1 - - - +
194B GLU* 3.1 13.3 + - - +
195B PHE* 3.4 38.0 + - + +
196B CYS* 3.9 7.8 - - - -
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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
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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