Contacts of the helix formed by residues 161 - 177 (chain B) in PDB entry 3VAG
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 161 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLY 4.2 8.1 - - - +
160B ILE* 1.3 85.5 - - - +
162B GLU* 1.3 64.9 + - - +
163B GLU* 3.7 19.6 - - + +
164B ALA* 3.3 22.3 + - - +
165B MET* 3.2 18.2 + - - +
191B ILE* 3.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B THR* 1.3 73.5 - - - +
163B GLU* 1.3 65.9 + - - +
165B MET* 3.4 3.2 + - - +
166B MET* 3.0 29.1 + - - +
189B VAL* 3.5 34.4 - - + +
190B GLN* 4.0 2.5 - - - +
191B ILE* 3.4 45.1 + - + +
193B GLN* 5.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B THR* 3.7 17.1 - - + +
162B GLU* 1.3 91.5 + - - +
164B ALA* 1.3 58.9 + - - +
166B MET* 3.4 15.2 + - + +
167B ASP* 3.1 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE* 3.5 22.4 - - + -
161B THR* 3.3 19.6 + - - +
162B GLU 3.3 0.6 - - - -
163B GLU* 1.3 78.6 - - - +
165B MET* 1.3 61.7 + - - +
167B ASP* 3.5 7.8 + - - +
168B PHE* 3.2 22.9 + - - +
219B PHE* 4.0 6.2 - - + -
220B GLN* 5.7 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 4.5 4.5 - - + -
156B ILE* 4.1 25.8 - - + -
157B PRO* 5.1 0.2 - - + -
160B ILE* 4.5 7.3 - - + +
161B THR 3.2 13.4 + - - +
162B GLU* 3.9 4.5 - - - +
164B ALA* 1.3 74.7 - - - +
166B MET* 1.3 65.3 + - - +
168B PHE* 3.5 1.1 + - - +
169B PHE* 3.2 50.7 + - + -
189B VAL* 4.4 8.7 - - + -
191B ILE* 4.8 6.1 - - + -
198B ALA* 4.1 25.1 - - - -
200B LEU* 4.1 11.2 - - + -
219B PHE* 3.6 40.6 - - + -
224B LEU* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLU 3.0 17.7 + - - +
163B GLU* 3.7 13.7 - - + +
164B ALA 3.3 0.2 - - - -
165B MET* 1.3 76.1 - - - +
167B ASP* 1.3 73.8 + - - +
169B PHE* 4.1 1.7 - - - +
170B ASN* 3.0 43.6 + - - +
186B VAL* 4.0 25.2 - - + +
187B LEU 4.1 21.1 - - - +
188B ALA* 4.5 5.8 - - - -
189B VAL* 4.0 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLU* 3.1 21.5 + - - +
164B ALA* 3.8 6.8 - - - +
166B MET* 1.3 87.0 - - - +
168B PHE* 1.3 65.7 + - - +
170B ASN* 3.7 6.2 + - - +
171B ALA* 3.1 24.8 + - - +
174B ARG* 4.9 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ALA 3.2 14.6 + - - +
165B MET 3.6 4.0 - - - +
167B ASP* 1.3 79.1 - - - +
169B PHE* 1.3 80.7 + + - +
171B ALA* 3.4 5.1 + - - +
172B GLN* 3.1 61.0 + - + +
217B ILE* 4.1 24.0 - - + -
218B ILE 3.6 21.5 - - - -
219B PHE* 3.4 47.6 - + + -
224B LEU* 4.2 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 4.3 3.1 - - + -
165B MET* 3.2 53.8 + - + +
166B MET* 4.3 1.1 - - - +
168B PHE* 1.3 96.4 - + - +
170B ASN* 1.3 65.4 - - - +
172B GLN* 3.4 4.1 + - + +
173B MET* 3.1 30.9 + - + +
186B VAL* 3.9 19.7 - - + -
200B LEU* 3.9 29.4 - - + -
202B PHE* 5.6 3.6 - + + -
211B ALA* 5.7 1.3 - - + -
214B PHE* 4.1 29.6 - + + -
217B ILE* 5.0 0.9 - - + -
224B LEU* 3.9 20.0 - - + -
226B ILE* 4.0 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 3.0 39.9 + - - +
167B ASP* 4.0 6.4 + - - +
169B PHE* 1.3 76.3 - - - +
171B ALA* 1.3 57.7 + - - +
173B MET* 3.5 2.7 + - - +
174B ARG* 3.1 40.3 + - - +
184B ASN* 3.6 38.3 - - - +
185B PRO* 3.3 13.8 - - + +
186B VAL* 3.1 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP 3.1 19.1 + - - +
168B PHE* 3.7 5.6 - - - +
170B ASN* 1.3 73.6 - - - +
172B GLN* 1.3 61.8 + - + +
174B ARG* 3.6 23.6 + - - +
175B LEU* 3.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 3.1 57.0 + - + +
169B PHE* 3.8 6.1 - - + +
170B ASN 3.4 0.2 - - - -
171B ALA* 1.3 77.3 - - + +
173B MET* 1.3 57.0 + - - +
175B LEU* 3.3 21.3 + - - +
176B GLY* 2.9 27.2 + - - -
214B PHE* 3.7 30.5 - - + -
217B ILE* 4.0 24.6 - - + +
218B ILE 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 3.1 22.8 + - + +
170B ASN* 3.7 5.4 - - - +
171B ALA 3.4 0.2 - - - -
172B GLN* 1.3 77.5 - - - +
174B ARG* 1.3 60.2 + - - +
176B GLY 3.6 0.2 + - - -
177B GLY 3.2 2.6 + - - -
178B LEU* 3.0 63.7 + - + +
179B THR* 3.7 11.4 - - + +
185B PRO* 4.0 29.2 - - + -
186B VAL* 5.5 0.9 - - + -
202B PHE* 4.7 6.3 - - + -
207B GLU* 3.8 25.8 - - + +
210B GLN* 4.6 0.7 - - + -
211B ALA* 4.1 17.9 - - - -
214B PHE* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP* 4.9 1.8 + - - +
170B ASN* 3.1 22.7 + - - +
171B ALA* 3.8 29.7 + - - +
173B MET* 1.3 78.6 - - - +
175B LEU* 1.3 62.3 + - - +
177B GLY* 3.4 10.6 + - - -
179B THR* 4.2 16.8 - - + +
183B GLY 4.8 6.1 - - - +
184B ASN* 3.5 22.2 + - - +
185B PRO* 5.5 0.9 - - + -
402B DIO 3.9 28.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ALA 3.0 19.1 + - - +
172B GLN* 3.3 24.0 + - - +
174B ARG* 1.3 78.7 - - - +
176B GLY* 1.3 61.2 + - - +
177B GLY 3.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLN 2.9 15.6 + - - -
173B MET 4.1 1.1 - - - -
175B LEU* 1.3 77.5 - - - +
177B GLY* 1.3 63.1 + - - +
178B LEU* 3.3 21.1 - - - +
214B PHE* 6.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B MET 3.2 5.0 + - - -
174B ARG* 3.4 8.3 + - - -
175B LEU 3.2 5.3 + - - -
176B GLY* 1.3 77.7 - - - +
178B LEU* 1.3 61.2 + - - +
179B THR* 3.4 13.0 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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