Contacts of the helix formed by residues 185 - 198 (chain B) in PDB entry 3QFR
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 ASN 185 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B MET 4.4 0.4 + - - -
142B THR* 3.1 10.2 + - - -
175B GLY* 2.9 40.0 - - - +
176B LEU 3.1 15.6 + - - +
177B GLY* 3.8 0.8 + - - -
183B HIS 3.0 0.6 + - - -
184B PHE* 1.3 88.8 - - + +
186B ALA* 1.3 65.2 + - - +
187B MET 3.1 3.7 + - - -
188B GLY 3.2 2.1 + - - +
189B LYS* 2.9 23.6 + - + +
208B LEU* 3.9 24.0 - - + +
209B GLY 3.2 23.9 + - - +
751B FMN 2.9 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 3.4 1.8 + - - -
146B GLY* 3.5 36.6 - - - +
183B HIS* 3.2 16.3 + - + -
184B PHE 3.1 5.0 + - - -
185B ASN* 1.3 76.3 - - - +
187B MET* 1.3 56.8 + - - +
189B LYS* 3.8 6.5 - - - +
190B TYR* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B MET* 3.4 42.6 - - + -
141B ALA 3.8 16.2 - - - +
142B THR* 3.3 17.8 + - + +
146B GLY 4.5 2.0 + - - +
147B ASP 4.4 1.3 - - - +
148B PRO* 3.5 36.1 - - + -
149B THR 5.2 0.2 - - - +
152B ALA* 4.1 2.9 - - + -
155B PHE* 4.1 9.9 - - + -
156B TYR* 4.0 26.2 - - + -
185B ASN 3.1 1.0 - - - -
186B ALA* 1.3 76.5 - - - +
188B GLY* 1.3 66.3 + - - +
190B TYR* 3.0 4.9 + - - +
191B VAL* 2.8 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B MET* 4.5 7.4 + - - +
142B THR* 4.0 2.8 + - - -
173B VAL* 3.8 12.8 - - - +
175B GLY* 4.2 23.8 - - - -
185B ASN* 3.2 7.8 + - - +
187B MET* 1.3 79.4 - - - +
189B LYS* 1.3 62.9 + - - +
191B VAL* 3.4 0.8 + - - -
192B ASP* 3.1 27.2 + - - +
206B LEU* 4.2 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PHE* 3.1 43.4 + - - +
185B ASN* 2.9 14.6 + - - +
186B ALA* 3.9 6.5 - - - +
188B GLY* 1.3 74.6 - - - +
190B TYR* 1.3 57.1 + - - +
192B ASP* 4.2 1.7 - - - +
193B LYS* 3.1 31.2 + - - +
206B LEU* 3.9 22.6 - - + +
208B LEU* 3.9 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TYR* 3.4 41.3 - + + -
159B LEU* 4.0 19.1 - - + -
160B GLN* 3.2 33.8 - - + +
186B ALA 2.9 21.0 + - - +
187B MET* 3.0 5.6 + - - +
189B LYS* 1.3 75.8 - - - +
191B VAL* 1.3 66.6 + - + +
193B LYS* 4.6 17.5 - - + -
194B ARG* 2.8 70.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 3.9 23.6 - - + -
140B MET* 4.2 10.1 - - + -
155B PHE* 3.4 29.6 - - + -
159B LEU* 3.8 13.5 - - + -
173B VAL* 4.1 6.5 - - + -
187B MET* 2.8 41.6 + - + +
188B GLY 4.1 2.2 - - - +
190B TYR* 1.3 72.7 - - + +
192B ASP* 1.3 57.7 + - - +
195B LEU* 3.0 56.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PHE* 3.8 15.6 - - - -
173B VAL* 3.9 20.4 + - + +
188B GLY 3.1 17.5 + - - +
189B LYS 4.2 3.2 - - - +
191B VAL* 1.3 78.3 - - - +
193B LYS* 1.3 66.4 + - - +
196B GLU* 3.7 10.6 + - - +
202B ARG* 2.6 53.2 + - - +
204B PHE 5.0 0.5 - - - +
206B LEU* 3.9 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LYS 3.1 20.4 + - - +
190B TYR* 4.0 21.8 - - - +
192B ASP* 1.3 79.9 + - - +
194B ARG* 1.3 65.7 + - - +
196B GLU* 3.3 14.9 + - - +
197B GLN* 3.3 46.3 + - + +
202B ARG* 4.7 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU* 2.9 39.1 + - + +
160B GLN* 4.7 6.1 + - - -
162B THR 3.3 24.7 + - - -
163B ASP* 3.4 18.8 + - - -
190B TYR* 2.8 53.7 + - + +
191B VAL 4.1 2.2 - - - +
193B LYS* 1.3 79.4 - - - +
195B LEU* 1.3 60.2 + - - +
197B GLN* 2.9 41.9 + - - +
198B LEU* 3.3 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 4.2 16.6 - - + -
138B PHE* 3.7 20.0 - - + -
155B PHE* 5.1 0.4 - - + -
159B LEU* 4.3 16.4 - - + -
166B LEU* 3.7 25.4 - - + -
169B VAL* 6.1 2.0 - - + -
171B PHE* 3.8 36.1 - - + -
191B VAL* 3.0 47.7 + - + +
193B LYS 3.3 0.2 - - - -
194B ARG* 1.3 76.1 - - - +
196B GLU* 1.3 62.2 + - - +
198B LEU* 3.1 15.2 + - - +
200B ALA* 3.2 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PHE* 4.1 5.1 - - + -
192B ASP 3.7 8.9 + - - +
193B LYS* 3.3 10.8 + - - +
195B LEU* 1.3 78.4 - - - +
197B GLN* 1.3 61.5 + - + +
198B LEU 3.2 0.2 - - - -
199B GLY* 3.3 12.1 + - - -
200B ALA 4.0 15.2 - - - +
202B ARG* 2.8 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASP* 5.4 2.1 - - - +
193B LYS* 3.3 48.9 + - + +
194B ARG* 2.9 42.9 + - - +
195B LEU 3.1 1.0 - - - -
196B GLU* 1.3 74.3 - - + +
198B LEU* 1.3 63.1 + - - +
199B GLY 3.1 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TRP* 4.4 10.8 - - + -
159B LEU* 4.2 21.5 - - + -
162B THR* 4.6 6.1 - - + +
163B ASP* 4.1 19.1 - - - +
164B VAL* 3.8 17.3 - - + +
165B ASP* 3.2 9.3 - - - +
166B LEU* 2.6 62.0 + - + -
194B ARG* 3.3 44.2 - - - +
195B LEU* 3.1 9.1 + - - +
197B GLN* 1.3 77.7 - - - +
199B GLY* 1.3 56.6 + - - +
200B ALA 3.4 0.4 - - - -
----------------------------------------------------------
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