Contacts of the helix formed by residues 196 - 207 (chain F) 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 ALA 196 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 4.6 16.6 - - + +
15D PHE* 3.9 29.2 - - + -
20D GLU* 3.4 13.9 - - - +
192F TRP* 3.0 15.3 + - - +
195F TYR* 1.3 80.9 - - + +
197F PRO* 1.3 65.2 - - - +
198F GLN 3.4 2.5 - - - -
199F LEU* 5.0 2.9 - - + -
200F PHE* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 197 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLU* 3.3 11.2 - - - +
51D SER* 5.5 11.4 - - - -
53D PHE* 6.1 0.9 - - + -
193F TYR* 3.4 41.9 - - + +
194F ARG 3.9 7.6 - - - +
195F TYR 3.4 6.7 - - - +
196F ALA* 1.3 89.2 - - - +
198F GLN* 1.3 63.0 + - + +
200F PHE* 4.2 0.2 - - - +
201F SER* 3.2 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 198 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLU* 3.4 24.7 + - - +
197F PRO* 1.3 81.7 - - + +
199F LEU* 1.3 63.8 + - + +
201F SER* 4.0 2.9 - - - -
202F GLU* 3.3 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLN* 3.6 30.7 - - + +
12D LEU* 4.8 9.0 - - + -
15D PHE* 4.4 19.1 - - + -
20D GLU* 3.5 20.3 + - + +
196F ALA* 3.8 4.2 + - + +
197F PRO 3.5 0.2 - - - -
198F GLN* 1.3 76.1 - - + +
200F PHE* 1.3 57.2 + - - +
202F GLU* 3.1 17.3 + - - +
203F TYR* 2.8 76.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 200 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TRP* 4.2 19.5 - + + -
12D LEU* 4.5 9.7 - - + +
166F PHE* 4.5 18.2 - + - -
189F ILE* 3.7 35.2 - - + -
192F TRP* 3.6 42.8 - + + +
193F TYR* 4.4 15.5 - + + -
196F ALA 3.2 20.0 + - - +
197F PRO 4.2 1.8 - - - +
199F LEU* 1.3 77.3 - - - +
201F SER* 1.3 63.2 + - - +
203F TYR* 3.2 4.6 + - - +
204F LEU* 2.9 62.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 201 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU 4.8 2.7 - - - +
39C ASP* 5.2 3.6 - - - +
41C TRP* 5.3 4.4 - - - +
42C ALA* 4.7 10.4 + - - +
193F TYR* 4.0 17.3 - - - -
197F PRO 3.2 18.1 + - - -
198F GLN* 4.0 3.1 - - - -
200F PHE* 1.3 83.5 - - - +
202F GLU* 1.3 60.3 + - - +
204F LEU* 5.0 2.2 - - - -
205F GLY* 3.4 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D GLN* 2.8 37.2 + - - +
198F GLN 3.3 13.8 + - - +
199F LEU* 3.1 27.5 + - - +
201F SER* 1.3 76.1 - - - +
203F TYR* 1.3 61.8 + - + +
205F GLY* 3.2 2.5 + - - -
206F ALA* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D GLN* 4.0 13.2 - - - +
8D ASN 4.1 4.3 + - - -
9D PHE* 3.7 33.7 - + + -
10D GLN* 2.8 58.0 + - - +
12D LEU* 3.8 23.3 - - + -
166F PHE* 3.7 37.9 - + + -
199F LEU* 2.8 46.3 + - + +
200F PHE 3.8 2.0 - - - +
202F GLU* 1.3 72.9 - - + +
204F LEU* 1.3 64.5 + - - +
206F ALA* 3.3 10.3 - - - +
207F PHE* 3.2 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 3.3 37.8 - - + +
41C TRP* 3.6 34.5 - - + +
166F PHE* 3.9 10.6 - - + -
169F MET* 3.9 24.2 - - + -
185F ILE* 6.1 1.1 - - + -
189F ILE* 4.6 8.7 - - + -
200F PHE* 2.9 51.7 + - + +
201F SER* 4.9 2.2 - - - +
203F TYR* 1.3 72.9 - - - +
205F GLY* 1.3 58.2 + - - +
207F PHE* 2.9 24.6 + - - +
229F LEU* 4.4 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU 3.6 1.5 + - - -
39C ASP* 3.6 26.1 - - - +
201F SER 3.4 15.7 + - - -
202F GLU 3.2 8.6 + - - -
204F LEU* 1.3 78.8 - - - +
206F ALA* 1.3 61.3 + - - +
207F PHE 3.2 0.4 - - - -
208F ARG* 3.2 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ASN 3.7 16.5 + - - -
3D ASP* 3.7 19.7 - - + +
4D TYR* 3.5 40.0 + - - +
7D GLN* 3.9 9.2 - - - +
9D PHE* 4.8 2.2 - - + -
202F GLU 3.0 10.8 + - - +
203F TYR* 3.3 15.0 - - - +
205F GLY* 1.3 78.8 - - - +
207F PHE* 1.3 62.5 + - + +
208F ARG* 3.2 2.1 + - - +
209F ASP 4.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 4.2 7.6 - - + -
4D TYR* 4.4 16.4 - + + -
9D PHE* 4.4 12.3 - + - -
166F PHE* 4.0 15.0 - + - -
169F MET* 3.4 48.0 - - + -
170F LYS* 3.9 30.1 - - + -
173F VAL* 4.3 4.7 - - + -
203F TYR 3.2 21.3 - - - -
204F LEU 2.9 11.1 + - - +
206F ALA* 1.3 77.2 - - + +
208F ARG* 1.3 52.1 + - - +
209F ASP 2.6 17.7 + - - -
210F VAL* 2.9 36.5 + - + -
211F LEU* 3.1 25.3 + - + +
----------------------------------------------------------
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