Contacts of the helix formed by residues 164 - 176 (chain B) in PDB entry 2BM9
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 ASN 164 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B CYS* 3.5 29.2 - - + +
140B SER* 4.0 15.4 - - - +
142B LEU* 4.9 4.5 - - - +
162B HIS 3.7 0.4 + - - -
163B ALA* 1.3 73.3 - - + +
165B THR* 1.3 64.7 + - - +
166B PHE 3.3 2.7 - - - -
167B ASN* 3.0 47.9 + - - +
168B ILE* 3.2 12.1 + - + +
9C PHE 5.0 4.2 + - - -
11C ASP* 3.6 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ASP* 3.4 23.0 + - - +
162B HIS* 3.3 32.6 + - - -
163B ALA 2.8 4.5 + - - -
164B ASN* 1.3 76.8 - - - +
166B PHE* 1.3 62.8 + - + +
168B ILE* 2.9 9.8 + - + +
169B MET* 2.8 27.8 + - + +
183B PHE* 4.4 12.1 - - + -
185B ILE* 4.0 24.0 - - + -
192B TRP* 3.5 18.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ASN 3.1 1.2 + - - -
165B THR* 1.3 81.6 - - + +
167B ASN* 1.3 62.0 + - - +
169B MET* 3.5 15.7 + - - +
170B LYS* 3.2 17.3 + - - +
185B ILE* 5.4 5.4 - - + -
192B TRP* 3.8 28.9 - + - -
200B PHE* 3.8 27.4 - + - -
203B TYR* 3.4 55.0 - + + -
204B LEU* 4.0 13.5 - - + -
207B PHE* 3.9 10.8 - + - -
9C PHE* 3.4 36.0 - - + -
10C GLN 5.4 1.1 - - - -
12C LEU* 4.6 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 4.3 15.6 - - + +
164B ASN* 3.0 38.2 + - - +
166B PHE* 1.3 74.6 - - - +
168B ILE* 1.3 65.4 + - - +
170B LYS* 3.3 20.2 + - - +
171B TRP* 3.1 22.5 + - - +
7C GLN 4.5 0.2 - - - +
8C ASN* 3.4 26.4 + - - +
9C PHE* 3.3 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.8 15.9 - - + -
139B CYS* 3.8 13.2 - - + +
142B LEU* 4.1 14.1 - - + -
145B PHE* 3.8 35.7 - - + -
157B PHE* 4.1 30.5 - - + -
159B ASP* 5.5 0.4 - - - +
163B ALA 3.8 20.9 - - - +
164B ASN* 3.2 10.4 + - - +
165B THR* 2.9 11.3 + - + +
167B ASN* 1.3 72.0 - - - +
169B MET* 1.3 67.2 + - - +
171B TRP* 3.3 8.6 + - + +
172B ALA* 3.1 19.8 + - - +
183B PHE* 4.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B THR* 2.8 12.2 + - + +
166B PHE* 3.6 20.6 - - - +
167B ASN 3.3 0.2 - - - -
168B ILE* 1.3 77.1 - - - +
170B LYS* 1.3 57.0 + - - +
172B ALA* 3.0 5.7 + - - +
173B VAL* 2.9 30.3 + - - +
183B PHE* 3.1 43.3 - - + -
185B ILE* 4.2 12.3 - - - -
204B LEU* 5.0 6.1 - - + -
207B PHE* 3.4 31.9 - - + -
211B LEU* 3.2 32.5 - - + -
229B LEU* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PHE 3.2 12.5 + - - +
167B ASN* 3.8 14.6 + - - +
168B ILE 3.3 0.2 - - - -
169B MET* 1.3 79.5 - - - +
171B TRP* 1.3 62.3 + - - +
173B VAL* 3.7 1.9 + - - +
174B ASP* 3.2 30.1 + - - +
207B PHE* 3.9 12.3 - - + -
4C TYR* 3.7 26.5 - - + +
5C SER* 3.1 41.1 + - - +
6C ARG 4.1 2.4 + - - -
7C GLN 3.2 23.2 + - - -
9C PHE* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 4.0 30.1 - - + -
145B PHE* 3.4 57.9 - + + +
146B GLU* 3.7 22.3 + - + +
148B LEU* 4.3 5.2 - - + -
149B ARG* 4.8 7.3 - - + +
157B PHE* 4.7 7.0 - + - -
167B ASN 3.1 13.2 + - - +
168B ILE* 3.7 14.1 - - + +
169B MET 3.2 0.2 - - - -
170B LYS* 1.3 77.5 - - - +
172B ALA* 1.3 80.6 + - + +
174B ASP* 4.7 0.2 - - - -
175B HIS* 2.8 74.8 + + + +
176B LEU* 3.9 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B PHE* 5.6 1.6 - - + -
168B ILE* 3.1 12.7 + - + +
169B MET 3.0 10.2 + - - +
171B TRP* 1.3 89.9 - - + +
173B VAL* 1.3 61.8 + - - +
176B LEU* 2.8 34.1 + - + -
177B LEU* 3.0 31.7 + - + -
183B PHE* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B MET* 2.9 18.3 + - + +
170B LYS* 4.1 7.0 - - - +
172B ALA* 1.3 75.9 - - - +
174B ASP* 1.3 60.1 + - - +
176B LEU 5.0 0.2 + - - -
177B LEU* 4.2 17.3 - - + +
207B PHE* 4.2 5.8 - - + -
210B VAL* 3.5 28.5 - - + -
211B LEU* 3.8 34.5 - - + -
231B ARG* 4.0 23.1 + - - +
4C TYR* 3.5 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LYS* 3.2 21.3 + - - +
172B ALA 3.1 0.6 - - - -
173B VAL* 1.3 79.6 - - - +
175B HIS* 1.3 84.7 + - + +
176B LEU 3.8 0.2 - - - -
4C TYR* 2.9 34.1 + - - -
5C SER* 4.2 12.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG* 3.5 55.0 + - - +
171B TRP* 2.8 61.5 + + + +
172B ALA 3.8 0.2 - - - -
174B ASP* 1.3 94.6 + - + +
176B LEU* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.9 19.5 - - + +
149B ARG* 3.8 30.3 - - + +
151B MET* 5.3 0.9 - - + -
153B HIS* 3.3 29.5 + - + +
155B LEU* 4.2 27.6 - - + -
157B PHE* 4.3 14.4 - - + -
171B TRP* 3.9 24.9 - - + -
172B ALA* 2.8 17.4 + - + +
173B VAL 5.0 0.4 + - - -
174B ASP 3.8 0.8 - - - -
175B HIS* 1.3 78.9 - - - +
177B LEU* 1.3 75.3 + - + +
178B GLU* 3.3 5.4 + - - +
----------------------------------------------------------
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