Contacts of the helix formed by residues 187 - 196 (chain G) in PDB entry 2BM8
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 ASP 187 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160G ASN* 4.4 5.9 - - - +
162G HIS* 4.4 10.0 + - + +
185G ILE 3.6 2.2 + - - -
186G GLU* 1.3 81.2 - - - +
188G MET* 1.3 65.6 + - + +
189G ILE 3.4 2.9 + - - -
190G PRO* 3.6 12.7 - - - +
191G TYR* 3.4 23.4 - - + -
222G SER 5.0 2.4 - - - +
223G GLN* 2.9 50.2 + - - +
225G ASP 5.8 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 188 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G HIS* 3.1 47.3 - - + +
185G ILE* 4.6 0.9 - - + -
186G GLU 2.8 8.9 + - - +
187G ASP* 1.3 76.0 - - + +
189G ILE* 1.3 66.3 + - - +
190G PRO 3.5 0.2 - - - -
191G TYR* 3.1 18.4 + - + -
192G TRP* 2.9 74.8 + - + +
195G TYR* 6.0 0.9 - - + -
13K ASN* 3.6 12.6 - - - +
16K ARG* 3.8 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G PHE* 5.9 0.4 - - + -
185G ILE* 3.8 33.9 + - + +
187G ASP 3.4 0.6 - - - +
188G MET* 1.3 76.5 - - - +
190G PRO* 1.3 74.2 - - + +
192G TRP* 3.1 17.5 + - + +
193G TYR* 3.0 21.3 + - - +
200G PHE* 3.5 27.3 - - + -
204G LEU* 5.3 9.4 - - + -
225G ASP 4.7 2.5 - - - +
226G ARG* 3.5 20.4 - - + +
227G GLY* 3.8 13.7 - - - -
229G LEU* 5.4 3.8 - - + -
41H TRP* 3.4 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 190 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G ILE 6.1 0.2 - - - +
187G ASP* 3.6 15.3 - - - +
189G ILE* 1.3 98.4 - - + +
191G TYR* 1.3 66.8 + - + +
193G TYR* 3.5 8.2 + - + +
194G ARG* 3.1 22.0 + - - +
222G SER 5.5 1.1 - - - +
225G ASP* 3.7 28.7 - - + +
226G ARG* 3.6 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 191 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G ASP* 3.4 27.6 - - + -
188G MET* 3.1 24.7 + - + +
190G PRO* 1.3 78.3 - - + +
192G TRP* 1.3 61.4 + - - +
194G ARG* 3.1 11.3 + - + +
195G TYR* 2.9 66.8 + + + -
16K ARG* 4.2 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 192 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G HIS* 3.9 20.9 - - + -
165G THR* 3.4 31.9 - - + -
166G PHE* 4.2 18.2 - + - -
185G ILE* 4.2 20.2 - - + -
188G MET* 2.9 49.7 + - + +
189G ILE* 3.1 16.1 + - + +
191G TYR* 1.3 76.2 - - - +
193G TYR* 1.3 56.7 + - - +
195G TYR* 4.7 5.8 - + - +
196G ALA* 3.0 34.9 + - - +
200G PHE* 3.8 31.8 - + + +
11K ASP* 5.7 0.2 - - - -
12K LEU* 3.6 40.5 - - + +
13K ASN* 3.3 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 193 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G ILE 3.0 11.0 + - - +
190G PRO* 3.7 9.0 - - + +
191G TYR 3.2 0.2 - - - -
192G TRP* 1.3 73.0 - - - +
194G ARG* 1.3 67.0 + - - +
197G PRO* 3.2 47.7 - - + +
200G PHE* 4.1 14.7 - + + -
201G SER* 4.1 12.6 - - - -
226G ARG* 4.4 12.3 - - - -
41H TRP* 3.6 36.3 - + + -
42H ALA* 3.8 23.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G PRO 3.1 13.9 + - - +
191G TYR* 3.1 16.3 + - - +
193G TYR* 1.3 81.2 - - - +
195G TYR* 1.3 74.7 + - + +
197G PRO* 3.7 6.9 - - - +
51K SER* 4.8 6.1 + - - -
52K ASP* 2.8 29.7 + - - +
53K PHE* 3.4 56.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 195 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G MET* 6.0 0.9 - - + -
191G TYR* 2.9 47.5 + + + +
192G TRP* 4.6 6.5 - + - +
194G ARG* 1.3 89.6 - - + +
196G ALA* 1.3 61.0 + - + +
197G PRO* 3.6 3.4 - - - +
12K LEU 5.5 2.7 - - - +
15K PHE* 3.5 17.7 - - + +
16K ARG* 3.5 46.2 + - + +
17K GLY* 3.5 20.2 + - - -
19K GLY* 3.2 28.1 - - - -
20K GLU* 3.7 1.6 + - - +
53K PHE* 3.3 37.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G TRP* 3.0 18.6 + - - +
195G TYR* 1.3 81.3 - - + +
197G PRO* 1.3 67.5 - - - +
198G GLN 3.4 0.2 + - - -
199G LEU* 3.4 6.6 + - + -
200G PHE* 3.0 17.3 + - - +
12K LEU* 4.7 9.2 - - + +
15K PHE* 3.9 26.0 - - + -
20K GLU* 3.3 21.5 - - + +
----------------------------------------------------------
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