Contacts of the helix formed by residues 187 - 198 (chain B) in PDB entry 6FEQ
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 187 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLY 3.7 2.3 + - - -
186B VAL* 1.3 78.7 - - - +
188B GLY* 1.3 59.9 + - - +
189B GLY* 3.8 8.4 + - - -
190B GLU* 3.0 36.2 + - - +
191B ARG* 3.1 10.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
186B VAL 3.9 0.4 + - - -
187B SER* 1.3 72.9 - - - +
189B GLY* 1.3 59.7 + - - +
190B GLU 3.2 1.1 + - - -
191B ARG* 4.0 18.2 - - - +
192B LYS* 3.7 14.0 + - - +
216B LEU* 3.4 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER* 3.2 7.5 + - - -
188B GLY* 1.3 76.9 - - - +
190B GLU* 1.3 60.7 + - - +
192B LYS* 4.4 2.9 - - - +
193B ARG* 3.4 24.5 + - - +
216B LEU* 3.9 5.0 - - - +
220B THR* 3.7 28.0 - - - +
224B VAL* 4.4 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLY 5.4 0.7 - - - +
170B LEU* 3.9 16.7 - - + +
173B VAL* 3.4 19.7 - - - +
186B VAL* 3.3 29.6 - - + +
187B SER* 3.0 14.2 + - - +
189B GLY* 1.3 80.1 - - - +
191B ARG* 1.3 62.7 + - - +
192B LYS 3.2 0.2 - - - -
193B ARG* 3.2 37.1 + - - +
194B THR* 2.8 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASP* 2.8 46.8 + - + +
130B VAL* 4.4 5.1 - - + +
132B GLY* 6.2 0.2 - - - -
178B VAL* 4.0 25.8 + - + +
179B GLY* 3.4 31.8 + - - -
180B THR* 4.3 6.5 + - - +
186B VAL* 3.9 16.6 + - + +
187B SER 3.1 12.2 + - - +
188B GLY* 4.1 16.0 - - - +
189B GLY 3.8 0.2 - - - -
190B GLU* 1.3 76.5 - - - +
192B LYS* 1.3 57.9 + - - +
194B THR* 3.1 10.6 + - - -
195B SER* 3.0 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 3.6 18.7 - - + +
125B VAL 3.2 24.7 + - - -
126B GLN 3.6 13.6 + - - +
127B ASP 6.4 0.4 - - - -
128B ASP* 5.7 1.8 - - - +
188B GLY 3.7 13.5 + - - +
189B GLY 4.5 5.4 - - - +
191B ARG* 1.3 77.7 - - - +
193B ARG* 1.3 63.1 + - - +
195B SER* 3.4 6.5 + - - +
196B ILE* 3.2 45.0 + - + +
209B LEU* 4.8 1.2 - - - +
210B ASP 4.3 5.5 + - - +
211B GLU 4.4 0.4 + - - -
212B PRO* 3.7 44.2 - - - +
216B LEU* 4.7 13.2 - - + -
224B VAL* 4.7 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 3.3 41.1 + - + +
169B GLY 4.4 8.7 + - - -
170B LEU* 3.8 23.9 - - + +
189B GLY 3.4 15.0 + - - +
190B GLU* 3.2 43.9 + - - +
192B LYS* 1.3 78.7 - - - +
194B THR* 1.3 60.8 + - - +
196B ILE* 3.9 7.6 + - + +
197B GLY 3.7 4.3 + - - -
223B ALA* 3.5 37.0 + - - +
224B VAL* 5.2 11.2 - - + +
227B LEU* 5.0 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 4.2 16.8 - - + -
136B VAL* 3.5 43.0 - - + +
139B ASN* 4.6 17.3 - - + +
140B LEU* 4.3 5.3 - - + +
168B LEU* 5.1 1.1 - - - +
170B LEU* 4.1 7.7 - - - +
178B VAL* 5.2 4.1 - - + +
186B VAL* 5.7 1.4 - - - +
190B GLU 2.8 18.2 + - - -
191B ARG* 3.1 12.6 + - - -
193B ARG* 1.3 78.7 - - - +
195B SER* 1.3 62.8 + - - +
197B GLY* 3.2 11.6 + - - -
198B MET* 3.3 14.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 4.1 19.0 - - - +
125B VAL* 5.2 3.1 + - - +
127B ASP 5.6 0.3 + - - -
128B ASP* 5.3 8.3 - - - -
129B VAL* 4.6 12.3 + - - +
130B VAL* 3.8 20.9 - - - +
191B ARG 3.0 15.0 + - - -
192B LYS* 3.4 9.4 + - - -
194B THR* 1.3 74.0 - - - +
196B ILE* 1.3 66.0 + - - +
198B MET* 3.2 23.1 + - - +
199B GLU* 3.9 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 4.3 15.0 - - + -
168B LEU* 5.4 1.3 - - + -
192B LYS* 3.2 35.9 + - + +
193B ARG* 4.3 7.0 - - + +
194B THR 3.3 0.2 - - - -
195B SER* 1.3 75.8 - - - +
197B GLY* 1.3 63.0 + - - +
199B GLU* 3.2 14.9 + - - +
200B LEU* 3.4 15.2 + - + +
207B LEU* 4.7 10.8 - - + +
209B LEU* 3.8 33.2 - - + -
224B VAL* 4.6 15.5 - - + -
227B LEU* 6.0 4.0 - - + -
228B LEU* 5.0 6.1 - - + -
231B MET* 4.1 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.8 8.9 - - - +
164B VAL* 4.1 5.1 - - - +
168B LEU* 3.8 21.6 - - - +
193B ARG 3.7 4.9 + - - -
194B THR 3.2 8.4 + - - -
196B ILE* 1.3 80.5 - - - +
198B MET* 1.3 59.2 + - - +
200B LEU* 3.1 23.7 + - - +
201B ILE* 3.3 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 5.4 9.9 - - + +
130B VAL* 3.7 35.9 - - - -
131B MET 6.1 0.2 - - - +
139B ASN* 5.0 15.9 - - + +
140B LEU* 3.8 18.4 - - + -
142B PHE* 5.6 6.3 - - + -
143B SER* 2.9 35.7 + - - +
147B ARG* 3.1 9.4 + - - -
194B THR* 3.3 14.0 + - + +
195B SER* 3.2 14.7 + - - +
197B GLY* 1.3 76.7 - - - +
199B GLU* 1.3 65.4 + - + +
201B ILE* 3.4 3.9 - - - +
454B LEU* 5.9 2.7 - - + -
458B GLU* 5.3 5.8 - - - +
463B TYR* 4.3 15.7 + - + +
----------------------------------------------------------
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