Contacts of the helix formed by residues 188 - 196 (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 MET 188 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B HIS* 3.1 46.4 - - + +
185B ILE* 4.6 2.4 - - + +
186B GLU 3.0 3.2 + - - -
187B ASP* 1.3 80.6 - - + +
189B ILE* 1.3 67.6 + - - +
190B PRO* 3.2 3.1 - - - -
191B TYR* 3.2 21.9 + - + -
192B TRP* 3.0 59.3 + - + -
195B TYR* 6.1 0.2 - - - -
13C ASN* 4.5 5.6 - - - +
16C ARG* 3.4 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TRP* 3.3 33.2 - - + +
185B ILE* 3.5 40.9 + - + +
187B ASP 5.0 0.2 - - - +
188B MET* 1.3 74.8 - - - +
190B PRO* 1.3 66.8 - - + +
192B TRP* 3.1 13.0 + - + +
193B TYR* 2.9 26.9 + - - +
200B PHE* 3.5 24.0 - - + -
204B LEU* 5.5 3.4 - - + -
226B ARG* 3.9 13.2 - - + +
227B GLY* 3.5 27.8 - - - +
229B LEU* 5.0 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TRP* 5.3 0.4 - - + -
187B ASP 3.4 17.5 - - - +
188B MET 3.2 4.5 - - - -
189B ILE* 1.3 99.6 - - + +
191B TYR* 1.3 61.8 + - + +
193B TYR* 3.6 9.7 + - + +
194B ARG* 3.2 25.6 + - - +
222B SER 5.8 0.2 - - - +
225B ASP* 4.0 20.6 - - + +
226B ARG* 3.7 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ASP* 3.3 28.7 - - + -
188B MET* 3.2 28.1 + - + +
190B PRO* 1.3 80.1 - - + +
192B TRP* 1.3 59.4 + - - +
193B TYR 3.1 1.3 - - - -
194B ARG* 3.2 8.6 + - + +
195B TYR* 3.0 66.6 + + + -
16C ARG* 5.1 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B HIS* 3.5 20.2 - - + -
165B THR* 3.5 32.1 - - + -
166B PHE* 3.8 31.0 - + - -
185B ILE* 4.3 17.9 - - + -
188B MET* 3.0 36.5 + - + +
189B ILE* 3.5 18.4 - - + +
191B TYR* 1.3 77.9 - - + +
193B TYR* 1.3 57.2 + - - +
195B TYR* 4.8 7.9 - + + -
196B ALA* 3.0 31.2 + - - +
200B PHE* 3.5 12.2 - + + +
11C ASP* 5.7 0.2 - - - -
12C LEU* 3.8 40.7 - - + +
13C ASN* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TRP* 3.5 32.3 - + + -
42A ALA* 3.8 21.0 - - + +
189B ILE 2.9 13.2 + - - +
190B PRO* 3.7 7.6 - - + +
191B TYR 3.1 0.2 - - - -
192B TRP* 1.3 75.0 - - - +
194B ARG* 1.3 66.1 + - - +
196B ALA 4.6 0.4 - - - -
197B PRO* 3.2 39.5 - - + +
200B PHE* 3.6 21.3 - + + -
201B SER* 4.1 13.9 - - - -
226B ARG* 5.0 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B PRO 3.2 14.9 + - - +
191B TYR* 3.4 17.5 - - + +
193B TYR* 1.3 81.3 - - - +
195B TYR* 1.3 70.3 - - + +
197B PRO* 3.8 5.4 - - - +
51C SER* 3.8 11.5 + - - -
52C ASP* 3.1 36.5 + - - -
53C PHE* 3.5 62.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TYR* 3.0 48.4 + + + +
192B TRP* 4.5 8.5 - + + +
194B ARG* 1.3 87.6 - - + +
196B ALA* 1.3 61.0 + - + +
197B PRO* 3.4 6.9 - - - +
12C LEU 5.6 1.6 - - - +
15C PHE* 3.5 21.3 - - + +
16C ARG* 3.6 39.9 + - + +
17C GLY* 3.5 22.1 + - - -
19C GLY* 3.2 26.0 - - - -
20C GLU* 3.8 2.6 + - - +
53C PHE* 3.5 39.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B TRP 3.0 16.1 + - - +
195B TYR* 1.3 80.2 - - + +
197B PRO* 1.3 65.7 - - - +
198B GLN 3.1 3.1 + - - -
199B LEU* 4.1 11.4 - - + -
200B PHE* 3.0 20.1 + - - +
12C LEU* 4.1 14.1 - - + -
15C PHE* 4.2 15.3 - - + -
20C GLU* 3.2 22.2 - - + +
----------------------------------------------------------
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