Contacts of the helix formed by residues 189 - 205 (chain A) in PDB entry 3R9X
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 PRO 189 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASP* 3.4 7.3 - - - +
188A LEU* 1.3 96.1 - - + +
190A LEU* 1.3 67.3 + - - +
191A ARG* 4.3 25.8 - - + +
192A LEU* 3.0 29.7 + - + +
193A LEU* 3.0 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU 3.9 1.4 + - - -
189A PRO* 1.3 72.0 - - - +
191A ARG* 1.3 57.7 + - - +
192A LEU 3.1 0.2 - - - -
193A LEU* 4.3 21.8 - - + -
194A ALA* 3.0 37.4 + - + +
221A ILE* 3.8 26.7 - - + -
231A LEU* 4.1 25.8 - - + -
233A ILE* 5.1 4.7 - - + -
267A LEU* 5.0 3.8 - - + -
271A LEU* 3.6 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PRO* 4.3 18.7 - - + +
190A LEU* 1.3 78.5 - - - +
192A LEU* 1.3 92.1 + - - +
195A ALA* 3.5 8.1 - - - +
217A LYS* 4.5 20.2 + - - +
218A ILE* 3.3 45.6 + - + +
221A ILE* 4.1 15.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 4.5 21.1 - - + -
188A LEU* 3.8 20.4 - - + -
189A PRO* 3.0 26.5 + - + +
191A ARG* 1.3 113.8 - - + +
193A LEU* 1.3 69.2 + - - +
195A ALA* 3.2 7.8 + - + +
196A GLU* 3.1 25.6 + - - +
217A LYS* 5.9 2.5 - - - +
297A PHE 4.5 17.0 - - - +
298A GLY* 5.1 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS 5.7 3.6 - - - +
28A VAL* 5.0 13.2 - - - +
186A THR* 6.2 3.6 - - + -
188A LEU* 3.6 24.2 - - + +
189A PRO 3.0 12.3 + - - +
190A LEU* 3.8 22.0 - - + +
192A LEU* 1.3 75.0 - - - +
194A ALA* 1.3 65.4 + - - +
196A GLU* 2.9 18.3 + - + +
197A ILE* 2.9 30.4 + - + +
267A LEU* 5.2 1.6 - - + -
270A ILE* 3.8 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU* 3.0 18.9 + - + +
191A ARG* 5.0 0.2 - - - -
193A LEU* 1.3 80.1 - - - +
195A ALA* 1.3 61.2 + - - +
197A ILE* 4.0 2.0 - - - +
198A VAL* 3.1 30.0 + - + +
218A ILE* 4.0 18.8 - - + -
221A ILE* 6.2 0.4 - - + -
233A ILE* 4.7 13.5 - - + -
267A LEU* 3.8 29.8 - - + +
277A LEU* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 5.9 1.6 - - + -
191A ARG 3.5 20.2 + - - +
192A LEU* 3.2 13.9 + - + +
193A LEU 3.2 1.6 - - - -
194A ALA* 1.3 78.0 - - - +
196A GLU* 1.3 64.9 + - - +
198A VAL 4.1 0.2 - - - -
199A ARG* 3.3 10.6 + - - +
216A VAL* 3.2 52.8 - - + +
218A ILE* 3.8 10.9 - - + +
297A PHE 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 3.4 27.6 - - + +
38A THR* 5.5 0.5 - - - -
39A ARG 5.0 1.4 + - - -
40A MET* 3.1 39.2 - - + +
188A LEU* 4.9 7.6 - - + -
192A LEU 3.1 14.6 + - - +
193A LEU* 2.9 9.8 + - + +
195A ALA* 1.3 80.2 - - - +
197A ILE* 1.3 57.9 + - + +
198A VAL 3.1 1.3 - - - -
199A ARG* 3.0 42.4 + - - +
200A GLU* 2.7 35.0 + - - +
299A TYR* 4.3 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 5.8 0.9 - - - +
30A ILE* 4.4 6.5 - - + -
193A LEU* 2.9 30.9 + - + +
194A ALA* 3.5 5.6 + - - +
196A GLU* 1.3 77.3 - - + +
198A VAL* 1.3 62.1 + - - +
200A GLU* 3.5 8.0 + - - +
201A LYS* 3.1 37.5 + - - +
263A ALA* 4.0 25.8 - - + +
266A GLU* 4.2 21.5 - - + +
267A LEU* 3.8 22.2 - - + -
270A ILE* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA* 3.1 18.2 + - + +
196A GLU 3.1 0.2 - - - -
197A ILE* 1.3 76.3 - - + +
199A ARG* 1.3 63.6 + - - +
201A LYS* 3.1 6.1 + - - +
202A ALA* 2.9 20.5 + - + +
216A VAL* 3.6 30.1 - - + -
218A ILE* 5.5 2.9 - - + -
237A ILE* 4.2 21.1 - - + -
259A ILE* 4.2 4.4 - - + +
263A ALA* 3.9 23.3 - - + -
267A LEU* 5.5 2.0 - - + -
277A LEU* 4.2 13.0 - - + -
279A LEU* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 3.3 6.9 - - - +
36A GLY 4.0 0.8 + - - -
37A THR 2.7 30.1 + - - -
39A ARG* 3.4 54.1 - - - +
195A ALA 3.3 12.6 + - - +
196A GLU* 3.0 43.8 + - - +
198A VAL* 1.3 78.8 - - - +
200A GLU* 1.3 64.7 + - - +
202A ALA* 3.1 6.8 + - - +
203A MET* 2.8 50.2 + - + +
211A PRO 5.6 0.6 + - - +
214A ILE* 3.7 15.3 - - + +
215A ALA* 4.4 3.6 - - - +
216A VAL* 3.7 12.3 - - + +
299A TYR* 3.7 13.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 2.9 30.7 + - - -
30A ILE* 3.6 27.5 - - + +
31A ILE* 3.1 43.5 + - - +
32A SER* 5.0 1.0 - - - -
37A THR* 5.4 0.4 - - + -
196A GLU 2.7 19.5 + - - +
197A ILE* 3.6 5.2 - - - +
199A ARG* 1.3 73.6 - - - +
201A LYS* 1.3 89.9 + - - +
203A MET* 3.1 15.0 + - - +
204A MET* 3.1 21.9 + - - +
266A GLU* 3.9 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 5.0 0.6 - - - +
197A ILE* 3.1 20.4 - - - +
198A VAL 3.1 4.8 + - - +
200A GLU* 1.3 96.2 + - - +
202A ALA* 1.3 67.4 + - - +
204A MET* 3.0 37.1 + - + +
205A LEU* 3.2 16.1 + - - +
259A ILE* 3.9 22.2 - - + +
262A ARG* 3.7 31.8 + - + +
263A ALA* 3.9 16.8 - - + +
266A GLU* 3.1 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A VAL* 2.9 13.8 + - + +
199A ARG* 3.6 11.4 - - - +
201A LYS* 1.3 75.3 - - - +
203A MET* 1.3 59.5 + - - +
205A LEU 3.6 0.3 + - - -
206A THR* 3.0 31.9 + - + +
214A ILE* 3.9 26.0 - - + +
237A ILE* 4.9 9.2 - - + -
248A ILE* 5.7 1.3 - - + -
259A ILE* 3.9 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER* 3.7 24.7 - - - +
34A LYS* 3.1 29.1 - - + -
36A GLY 4.0 9.6 - - - +
37A THR* 3.7 30.3 - - - +
199A ARG* 2.8 47.7 + - + +
200A GLU* 3.4 9.9 - - - +
201A LYS 3.0 0.4 - - - -
202A ALA* 1.3 76.5 - - - +
204A MET* 1.3 63.0 + - - +
206A THR* 3.2 15.7 + - - +
211A PRO* 3.7 41.9 - - + +
212A THR* 4.3 3.4 - - + -
214A ILE* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE 4.5 9.9 - - - +
32A SER* 4.7 4.3 - - - -
33A PRO* 4.6 18.8 - - + -
34A LYS* 4.5 9.0 + - - +
200A GLU* 3.1 26.4 + - - +
201A LYS* 3.0 33.5 + - + +
203A MET* 1.3 77.1 - - - +
205A LEU* 1.3 64.2 + - + +
206A THR 3.4 2.9 + - - +
262A ARG* 3.3 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LYS 3.2 10.4 + - - +
202A ALA 3.6 1.5 + - - +
203A MET 3.2 0.8 - - - -
204A MET* 1.3 82.9 - - + +
206A THR* 1.3 65.9 + - - +
207A ARG* 5.6 1.5 - - - -
255A ARG* 3.4 27.2 - - + +
258A GLU* 3.6 29.6 - - + -
259A ILE* 3.4 37.5 - - + +
262A ARG* 4.1 33.7 - - - +
1531C A 4.0 4.3 - - - -
----------------------------------------------------------
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