Contacts of the helix formed by residues 196 - 206 (chain J) 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 ALA 196 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192J TRP* 2.8 13.2 + - - +
195J TYR* 1.3 77.9 - - + +
197J PRO* 1.3 58.3 - - - +
198J GLN 3.5 0.4 - - - -
199J LEU* 4.5 3.1 - - + -
200J PHE* 3.0 28.9 + - - +
12L LEU* 4.2 15.7 - - + +
15L PHE* 3.8 31.2 - - + -
20L GLU* 3.4 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 197 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193J TYR* 3.4 39.6 - - + +
194J ARG 3.9 5.4 - - - +
195J TYR 3.3 8.5 - - - +
196J ALA* 1.3 86.1 - - - +
198J GLN* 1.3 67.7 + - + +
200J PHE* 4.1 0.2 - - - +
201J SER* 3.0 30.0 + - - -
20L GLU* 3.1 10.8 - - - +
51L SER* 5.3 9.9 - - - +
53L PHE* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 198 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197J PRO* 1.3 80.9 - - + +
199J LEU* 1.3 59.9 + - + +
201J SER* 3.9 3.5 - - - -
202J GLU* 3.1 28.7 + - - +
20L GLU* 3.4 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196J ALA* 4.3 3.6 - - + +
197J PRO 3.4 0.2 - - - -
198J GLN* 1.3 79.4 - - + +
200J PHE* 1.3 59.9 + - - +
202J GLU* 3.5 20.1 + - - +
203J TYR* 3.0 51.2 + - + +
10L GLN* 3.6 29.4 - - - +
12L LEU* 4.3 13.2 - - + -
15L PHE* 3.5 33.2 - - + -
20L GLU* 3.2 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 200 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166J PHE* 3.7 27.8 - + - -
189J ILE* 3.6 38.6 - - + -
192J TRP* 3.9 25.1 - + + +
193J TYR* 3.8 21.8 - + + -
196J ALA 3.0 20.7 + - - +
197J PRO 4.1 1.6 - - - +
199J LEU* 1.3 76.8 - - - +
201J SER* 1.3 68.7 + - - +
203J TYR* 3.3 1.2 + - - -
204J LEU* 2.9 47.6 + - + +
41K TRP* 3.6 37.2 - + - -
12L LEU* 4.0 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 201 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193J TYR* 4.1 16.3 - - - -
197J PRO 3.0 19.2 + - - -
198J GLN* 3.9 4.9 - - - -
200J PHE* 1.3 80.3 - - - +
202J GLU* 1.3 61.4 + - - +
204J LEU* 4.2 2.6 - - - +
205J GLY* 3.0 22.3 + - - -
38K LEU 4.9 2.1 - - - +
39K ASP* 5.6 0.9 - - - -
41K TRP* 5.1 7.0 - - - -
42K ALA* 5.2 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198J GLN 3.1 17.5 + - - +
199J LEU* 3.7 25.9 - - - +
200J PHE 3.2 0.2 - - - -
201J SER* 1.3 76.6 - - - +
203J TYR* 1.3 65.7 + - - +
205J GLY* 4.0 0.9 - - - -
206J ALA* 3.3 20.6 + - - +
7L GLN* 2.7 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166J PHE* 3.8 29.4 - + + -
199J LEU* 3.0 39.0 + - + +
200J PHE 3.8 3.4 - - - +
202J GLU* 1.3 87.5 - - - +
204J LEU* 1.3 65.3 + - - +
206J ALA* 3.2 20.2 - - - +
207J PHE* 3.2 13.7 - - - -
7L GLN* 3.7 20.9 - - + -
8L ASN 3.6 10.1 + - - -
9L PHE* 3.5 30.7 - + + -
10L GLN* 3.0 45.9 + - - +
12L LEU* 3.5 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166J PHE* 4.2 14.5 - - + -
169J MET* 4.3 9.0 - - + -
185J ILE* 5.7 0.7 - - + -
189J ILE* 5.2 4.3 - - + -
200J PHE* 2.9 37.0 + - + +
201J SER* 4.2 3.1 - - - +
203J TYR* 1.3 78.3 - - - +
205J GLY* 1.3 55.8 + - - +
207J PHE* 3.0 25.3 + - - +
229J LEU* 4.0 27.4 - - + -
38K LEU* 3.6 38.8 - - + +
41K TRP* 3.5 46.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201J SER 3.0 18.4 + - - -
202J GLU 4.0 1.8 - - - -
203J TYR 3.3 0.2 - - - -
204J LEU* 1.3 75.7 - - - +
206J ALA* 1.3 59.6 + - - +
207J PHE 3.1 1.3 - - - -
208J ARG* 3.2 39.3 + - - +
38K LEU 3.8 21.0 + - - -
39K ASP* 4.0 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202J GLU 3.3 12.0 + - - +
203J TYR* 3.2 17.6 + - - +
204J LEU 3.1 0.2 - - - -
205J GLY* 1.3 75.9 - - - +
207J PHE* 1.3 57.6 + - + +
208J ARG* 3.4 5.7 + - - +
209J ASP 5.1 1.0 + - - -
2L ASN* 4.5 6.5 - - - +
3L ASP* 3.4 22.4 - - - +
4L TYR* 3.2 42.9 + - + +
7L GLN* 4.7 7.0 - - - +
9L PHE* 4.8 2.7 - - + -
----------------------------------------------------------
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