Contacts of the helix formed by residues 191 - 209 (chain A) in PDB entry 1FR8
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 ARG 191 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GDU 3.2 76.4 + - - +
188A PHE* 3.2 24.3 - - + -
189A ARG 3.3 9.1 + - - -
190A ASN* 1.3 96.2 + - - +
192A GLN* 1.3 65.2 + - - +
193A GLU* 3.2 4.0 - - - +
194A HIS* 3.2 32.2 + - + -
195A LEU 3.0 17.7 + - - -
253A VAL* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 4.1 18.6 - - - +
188A PHE* 3.6 14.2 - - + -
190A ASN* 3.7 3.8 - - - +
191A ARG* 1.3 76.8 - - - +
193A GLU* 1.3 64.0 + - - +
195A LEU* 3.3 20.6 + - - +
196A LYS* 3.1 36.0 + - - +
391A TYR* 3.7 23.9 + - - -
393A LYS* 5.1 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PRO* 5.6 5.9 - - - +
153A VAL* 5.6 3.6 + - - +
191A ARG* 3.2 1.0 - - - +
192A GLN* 1.3 80.4 - - + +
194A HIS* 1.3 66.8 + - + +
196A LYS* 3.1 48.3 + - - +
197A TYR* 3.4 26.7 + - - -
347A HIS* 4.9 14.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GDU 5.0 0.4 - - - -
191A ARG* 3.2 41.9 + - + +
193A GLU* 1.3 78.4 - - + +
195A LEU* 1.3 58.2 + - - +
197A TYR 3.2 2.9 + - - -
198A TRP* 2.9 28.1 + - - +
253A VAL* 4.0 17.9 - - + +
254A ASP* 4.6 13.8 - - + +
345A ILE* 3.0 58.1 - - + +
347A HIS* 4.1 20.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 4.5 8.7 - - + -
188A PHE* 4.4 8.7 - - + -
191A ARG 3.0 12.9 + - - +
192A GLN* 3.4 26.5 - - - +
193A GLU 3.2 0.2 - - - -
194A HIS* 1.3 76.7 - - - +
196A LYS* 1.3 52.8 + - - +
198A TRP* 3.2 3.8 + - + -
199A LEU* 2.8 54.7 + - + +
217A VAL* 4.2 20.9 - - + -
253A VAL* 4.0 22.1 - - + +
391A TYR* 3.5 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL* 3.8 32.1 + - + +
154A ASP* 4.8 2.6 - - - +
155A LEU* 3.7 54.0 - - + +
158A VAL* 4.7 0.2 - - - +
192A GLN* 3.1 31.7 + - - +
193A GLU* 3.1 37.5 + - - +
195A LEU* 1.3 74.7 - - - +
197A TYR* 1.3 62.9 + - + +
199A LEU* 3.5 2.3 + - - +
200A TYR* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU 4.5 2.7 - - - -
149A PHE* 2.8 52.3 + + + -
151A ILE* 3.5 23.1 - - + -
152A PRO* 3.4 28.0 - - + +
153A VAL* 4.1 12.3 - - + +
193A GLU* 3.4 25.5 + - - -
194A HIS 3.2 6.9 + - - +
196A LYS* 1.3 77.0 - - - +
198A TRP* 1.3 67.0 + - - +
200A TYR* 3.2 6.0 + + - +
201A TYR* 3.0 34.9 + + + -
256A ILE* 4.6 0.2 - - - -
345A ILE* 3.8 26.2 - - + -
347A HIS* 3.6 25.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 3.9 26.9 - - + -
186A ILE* 3.8 28.2 - - + +
194A HIS 2.9 14.3 + - - +
195A LEU* 3.4 13.7 - - + +
197A TYR* 1.3 78.1 - - - +
199A LEU* 1.3 74.3 + - + +
202A LEU* 2.9 64.3 + - + +
203A HIS* 5.4 1.6 - + - -
206A LEU* 4.6 3.6 - - + -
215A ILE* 3.9 27.6 - - + -
251A SER* 3.4 20.8 + - - -
252A ASP 3.9 0.9 - - - -
253A VAL* 2.9 30.7 - - + +
255A LEU 3.4 19.2 + - - -
256A ILE* 3.7 10.3 - - + -
264A TYR* 4.9 3.8 + + - -
345A ILE* 4.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 3.6 27.8 - - + -
158A VAL* 3.9 7.2 - - + +
195A LEU* 2.8 43.9 + - + +
196A LYS 3.9 2.9 - - - +
198A TRP* 1.3 87.8 - - + +
200A TYR* 1.3 68.6 + - - +
203A HIS* 3.2 43.2 + - + +
215A ILE* 4.4 1.8 - - + -
390A LEU* 3.6 28.5 - - + +
391A TYR* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 4.0 23.2 - - + +
153A VAL* 4.0 23.8 - - + -
157A LEU* 5.0 10.1 - - + -
158A VAL* 3.9 29.2 - - + +
161A GLN* 4.3 21.7 + - - -
162A ASN* 4.8 0.8 + - - -
196A LYS 3.0 18.2 + - - +
197A TYR* 3.2 8.5 + + - +
199A LEU* 1.3 76.8 - - - +
201A TYR* 1.3 88.8 + + - +
204A PRO* 3.1 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET* 6.5 0.2 - - - -
146A LEU 3.6 8.9 + - - -
147A ILE* 3.5 29.1 - - + -
148A GLU* 2.7 47.4 + - - +
149A PHE* 4.0 16.6 - + - -
151A ILE* 4.8 2.3 - - - +
197A TYR* 3.0 31.2 + + - +
200A TYR* 1.3 105.9 - + - +
202A LEU* 1.3 62.1 + - + +
204A PRO* 3.0 16.8 - - - +
205A ILE* 3.2 21.8 + - + +
256A ILE* 3.6 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TRP* 2.9 63.1 + - + +
201A TYR* 1.3 72.7 - - - +
203A HIS* 1.3 66.8 + - - +
205A ILE* 3.1 9.2 + - + +
206A LEU* 2.8 38.6 + - + +
255A LEU 4.5 0.2 - - - +
256A ILE* 3.7 26.7 - - + -
257A PRO* 3.7 23.1 - - + -
264A TYR* 3.8 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 4.8 0.4 - - + -
162A ASN* 3.9 14.4 - - - +
165A VAL* 3.7 28.1 - - + +
169A GLY 4.1 2.0 - - - -
198A TRP* 5.4 1.6 - + - -
199A LEU* 3.2 39.2 + - + +
202A LEU* 1.3 75.6 - - - +
204A PRO* 1.3 74.1 - - + +
206A LEU* 4.3 2.0 - - + +
207A GLN* 2.9 28.4 + - - +
213A TYR* 2.9 29.0 + + - -
215A ILE* 3.8 19.2 - - + +
390A LEU* 2.7 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLN* 6.4 0.7 - - - +
162A ASN* 3.6 16.6 - - - +
200A TYR 3.1 22.2 - - - +
201A TYR* 3.0 15.0 - - - +
203A HIS* 1.3 97.4 - - + +
205A ILE* 1.3 63.2 + - + +
207A GLN* 3.2 11.9 + - - +
208A ARG* 3.0 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET* 3.6 24.5 - - + -
147A ILE* 5.6 1.6 - - + -
201A TYR* 3.2 26.9 + - + +
202A LEU* 3.1 14.5 + - + +
204A PRO* 1.3 81.2 - - + +
206A LEU* 1.3 58.6 + - + +
208A ARG* 3.1 28.5 + - - +
209A GLN* 2.9 55.0 + - - +
256A ILE* 5.0 0.4 - - + -
257A PRO* 3.8 30.1 - - + +
260A ASP* 4.0 12.1 - - + -
264A TYR* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 4.4 11.2 - - + -
198A TRP* 4.6 2.0 - - + -
202A LEU* 2.8 45.1 + - + +
203A HIS* 4.3 1.1 - - - +
205A ILE* 1.3 70.4 - - + +
207A GLN* 1.3 60.7 + - - +
209A GLN* 3.1 20.9 + - - +
210A GLN 3.2 7.1 + - - -
211A LEU* 3.3 24.4 + - + +
213A TYR* 3.3 43.3 - - + +
215A ILE* 4.1 13.2 - - + -
264A TYR* 3.7 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 4.0 9.7 - - - +
162A ASN* 2.9 34.3 + - - +
164A LYS* 4.1 18.1 + - + +
165A VAL* 3.9 18.2 - - - +
171A TYR* 3.4 48.2 + - + +
203A HIS 2.9 18.9 + - - +
204A PRO* 3.2 7.0 + - - +
206A LEU* 1.3 72.2 - - - +
208A ARG* 1.3 63.2 + - + +
210A GLN* 2.9 18.7 + - - +
213A TYR* 3.4 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A SER* 2.5 31.5 + - - -
140A LEU* 3.4 39.1 - - + +
141A LEU* 3.5 8.5 - - + +
142A VAL* 3.9 16.0 - - - +
145A MET* 3.0 37.0 - - - +
204A PRO* 3.0 38.5 + - + +
205A ILE* 3.1 21.4 + - - +
207A GLN* 1.3 80.0 - - + +
209A GLN* 1.3 53.0 + - - +
210A GLN* 3.0 2.5 + - - +
260A ASP* 3.1 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A SER* 4.3 8.1 - - - -
141A LEU* 4.4 4.5 - - + -
180A HIS* 5.6 1.6 - - - -
205A ILE* 2.9 35.4 + - + +
206A LEU* 3.1 10.0 + - - +
208A ARG* 1.3 75.3 - - - +
210A GLN* 1.3 74.2 + - - +
211A LEU* 3.4 23.9 + - + +
257A PRO* 6.1 0.2 - - - +
260A ASP* 3.0 32.9 + - + +
262A ASN 3.4 19.4 + - - -
263A THR* 3.4 15.3 - - + +
264A TYR* 2.8 30.0 + - - +
----------------------------------------------------------
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