Contacts of the helix formed by residues 193 - 208 (chain A) in PDB entry 2B7O
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 SER 193 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER 4.3 1.2 + - - -
190A GLY* 3.4 21.1 + - - -
191A LEU 3.4 0.4 - - - -
192A ALA* 1.3 73.3 - - - +
194A LEU* 1.3 64.1 + - - +
195A HIS* 3.6 10.7 + - - +
196A LEU* 3.1 18.5 + - - +
197A VAL* 3.0 22.2 + - - +
235A ASP* 6.0 6.1 - - - -
238A LEU* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU 6.1 0.2 - - - +
111A VAL* 4.3 27.0 - - + +
192A ALA 3.3 7.2 + - - +
193A SER* 1.3 71.4 + - - +
195A HIS* 1.3 69.4 + - + +
197A VAL* 3.4 8.3 + - + +
198A HIS* 3.0 25.6 + - - +
225A LEU* 3.9 27.2 - - + +
228A MSE 4.7 10.5 - - + -
238A LEU* 3.5 34.2 - - + +
239A GLN* 4.2 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A SER* 3.2 10.0 - - - +
194A LEU* 1.3 83.1 - - + +
196A LEU* 1.3 62.1 + - - +
198A HIS* 3.5 1.7 + - - +
199A ASP* 3.2 29.9 + - - +
225A LEU* 3.5 52.7 + - + +
226A ARG* 6.2 0.6 - - - +
228A MSE 4.6 8.8 - - + +
229A SER* 4.3 14.9 - - - -
233A VAL 5.0 6.3 + - - -
234A ALA* 6.1 0.2 - - - -
235A ASP* 5.5 8.7 + - - -
238A LEU* 5.2 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLY 3.2 25.1 - - - +
191A LEU* 4.2 3.6 - - + -
193A SER* 3.1 18.5 + - - +
195A HIS* 1.3 75.6 - - - +
197A VAL* 1.3 67.1 + - - +
199A ASP* 3.1 28.5 + - + +
200A TRP* 3.5 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 3.6 17.7 - - + +
108A GLN* 3.5 39.9 - - + +
111A VAL* 3.9 11.2 - - + -
191A LEU 3.3 22.7 - - - +
192A ALA 3.8 9.2 - - - +
193A SER 3.0 13.6 + - - +
194A LEU* 3.6 11.9 - - + +
196A LEU* 1.3 76.6 - - - +
198A HIS* 1.3 61.1 + - - +
200A TRP* 3.1 37.7 + - + +
201A ASN* 3.5 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A VAL* 4.4 7.2 - - + +
112A VAL* 4.6 1.6 - - + -
194A LEU 3.0 9.2 + - - +
195A HIS 4.4 1.1 - - - +
197A VAL* 1.3 73.9 - - - +
199A ASP* 1.3 61.8 + - - +
200A TRP 3.2 0.2 - - - -
201A ASN* 2.9 53.7 + - + +
202A ARG* 2.9 24.7 + - + +
218A ALA* 2.9 32.7 + - + -
221A ILE* 3.5 36.0 - - + +
222A ASP* 3.8 24.7 - - + -
225A LEU* 3.6 21.5 - - + -
454A PHE* 4.8 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A HIS* 3.2 18.3 + - - +
196A LEU* 3.1 22.6 + - + +
198A HIS* 1.3 76.5 - - - +
200A TRP* 1.3 56.0 + - + +
202A ARG* 2.8 39.1 + - - +
203A GLU* 3.1 40.4 + - - +
206A ARG* 4.4 1.0 + - - -
222A ASP* 5.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 4.3 20.9 - - + -
108A GLN* 3.6 32.9 + - + +
191A LEU* 3.6 40.8 - - + -
196A LEU* 3.6 37.8 - - + +
197A VAL* 3.1 48.9 + - + +
198A HIS 3.2 0.4 - - - -
199A ASP* 1.3 77.5 - - + +
201A ASN* 1.3 58.2 + - - +
203A GLU* 3.4 18.1 + - - +
204A PHE* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLN* 2.6 59.0 + - - +
111A VAL* 3.5 9.1 - - - +
112A VAL* 3.4 15.0 - - - +
197A VAL 3.5 4.0 + - - -
198A HIS* 2.9 43.4 + - + +
200A TRP* 1.3 77.8 - - - +
202A ARG* 1.3 55.3 + - - +
204A PHE* 3.3 14.0 - - - +
205A VAL* 3.1 25.3 + - - +
218A ALA* 5.4 0.7 - - - -
450A LEU* 3.8 7.1 - - - +
454A PHE* 4.6 9.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A HIS* 2.9 26.8 + - - +
199A ASP* 2.8 35.9 + - - +
200A TRP 3.2 0.4 - - - -
201A ASN* 1.3 72.9 - - - +
203A GLU* 1.3 65.2 + - - +
205A VAL* 3.1 9.6 + - - +
206A ARG* 3.0 62.3 + - - +
218A ALA* 4.6 10.5 - - + +
219A THR* 5.7 2.9 - - - +
222A ASP* 3.4 37.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 3.1 26.9 + - - +
200A TRP* 3.4 18.7 + - - +
202A ARG* 1.3 75.8 - - - +
204A PHE* 1.3 62.0 + - - +
206A ARG* 3.2 27.8 + - - +
207A THR* 3.1 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A TRP 2.9 13.8 + - - +
201A ASN 3.3 15.5 - - - +
203A GLU* 1.3 74.7 - - - +
205A VAL* 1.3 63.4 + - + +
207A THR* 4.1 4.7 + - - -
208A SER* 3.0 49.4 + - - -
211A GLY* 6.1 0.2 - - - -
214A TYR* 4.0 26.0 - + - -
447A GLN* 3.7 42.4 - - + -
450A LEU* 3.5 28.5 - - + -
451A GLU* 4.1 20.2 - - + -
454A PHE* 3.6 29.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASN 3.1 15.1 + - - +
202A ARG* 3.1 11.7 + - - +
204A PHE* 1.3 83.9 - - + +
206A ARG* 1.3 71.3 + - + +
208A SER 3.8 2.4 - - - +
211A GLY* 3.4 35.6 - - - +
214A TYR* 4.0 24.2 - - + -
215A GLU* 4.0 22.0 - - + -
218A ALA* 3.9 23.6 - - + -
454A PHE* 4.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 4.4 1.2 + - - +
202A ARG* 3.0 53.4 + - - +
203A GLU* 3.2 41.3 + - - +
205A VAL* 1.3 82.4 - - + +
207A THR* 1.3 64.7 + - + +
208A SER 3.9 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLU* 3.1 23.8 + - + +
204A PHE* 4.1 4.3 + - - -
206A ARG* 1.3 81.2 - - + +
208A SER* 1.3 63.6 + - - +
209A PRO* 3.9 4.9 - - - +
447A GLN* 4.9 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A PHE* 3.0 40.5 + - - -
205A VAL 3.8 3.0 + - - +
206A ARG 4.3 2.6 - - - +
207A THR* 1.3 79.9 + - - +
209A PRO* 1.4 80.1 + - - +
210A ALA 4.0 0.9 - - - -
211A GLY* 3.1 27.6 + - - -
214A TYR* 5.2 1.7 - - - -
447A GLN* 3.8 17.5 - - - -
451A GLU* 5.6 1.6 + - - -
----------------------------------------------------------
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