Contacts of the helix formed by residues 179 - 195 (chain B) in PDB entry 7CE1
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 ASP 179 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ARG* 3.9 10.8 + - - +
178B PHE* 1.3 74.7 - - - +
180B ASN* 1.3 55.9 + - - +
181B GLU* 3.4 12.0 + - - +
182B ALA* 3.0 38.1 + - + +
183B TYR* 2.9 25.8 + - - +
338B VAL* 3.5 19.9 - - + +
339B SER 3.0 22.2 + - - +
340B ARG* 4.8 1.5 - - - +
341B PRO* 4.6 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ARG* 4.2 3.0 + - - +
177B ASP* 3.7 10.9 - - - +
178B PHE* 2.8 44.2 + - - +
179B ASP* 1.3 70.5 - - - +
181B GLU* 1.3 59.6 + - - +
183B TYR* 3.7 14.9 - - + +
184B ALA* 2.9 30.3 + - - +
210B PHE* 4.1 28.4 - - + +
213B HIS* 4.2 15.9 + - + +
214B ALA* 4.3 11.7 - - + +
264B ILE* 4.6 15.9 - - + +
310B GLU* 5.0 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ARG* 4.9 4.9 - - - +
179B ASP* 3.2 9.3 + - - +
180B ASN* 1.3 78.7 - - - +
182B ALA* 1.3 62.9 + - - +
184B ALA 3.6 0.2 + - - -
185B TYR* 3.3 19.8 + - - +
213B HIS* 3.4 30.6 + - + +
216B LYS* 5.9 1.6 - - + -
217B GLY* 3.6 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 3.0 35.8 + - + +
181B GLU* 1.3 73.8 - - - +
183B TYR* 1.3 64.6 + - - +
185B TYR* 3.4 5.8 + - - +
186B GLU* 3.1 35.4 + - - +
340B ARG* 5.9 0.2 - - - -
341B PRO* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PHE* 3.9 22.7 - + + -
179B ASP 2.9 16.1 + - - +
180B ASN* 3.8 9.0 - - - +
181B GLU 3.4 0.2 - - - -
182B ALA* 1.3 77.0 - - - +
184B ALA* 1.3 59.9 + - - +
186B GLU* 3.2 5.9 + - + +
187B ALA* 2.8 33.6 + - + +
262B VAL* 4.4 7.5 - - + +
263B SER 2.9 20.8 + - - -
264B ILE* 3.7 30.7 - - + -
290B VAL* 3.5 18.6 + - + +
291B SER* 3.2 8.5 + - - -
292B LYS* 3.1 18.2 + - + -
308B VAL* 3.2 38.8 - - + -
341B PRO* 4.3 9.3 - - + +
343B TRP* 5.6 4.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASN 2.9 18.9 + - - +
181B GLU 4.0 1.6 - - - +
183B TYR* 1.3 82.8 - - + +
185B TYR* 1.3 62.0 + - - +
187B ALA* 3.3 16.3 + - - +
188B VAL* 3.4 18.7 - - - +
201B ILE* 5.9 0.4 - - + -
214B ALA* 3.2 30.3 - - + +
217B GLY* 3.8 4.9 - - - -
218B PHE* 3.4 18.3 - - + +
262B VAL* 5.8 1.6 - - + -
264B ILE* 5.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLU 3.3 14.5 + - - +
182B ALA* 3.7 6.5 - - - +
183B TYR 3.3 0.4 - - - -
184B ALA* 1.3 77.2 - - - +
186B GLU* 1.3 62.4 + - + +
188B VAL* 3.7 5.4 + - - +
189B GLU* 3.5 17.3 + - - +
217B GLY* 3.5 18.3 + - - +
220B ARG* 6.2 0.7 - - + -
221B GLY* 4.5 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ALA* 3.1 23.9 + - - +
183B TYR* 3.7 5.3 - - + +
185B TYR* 1.3 74.6 - - + +
187B ALA* 1.3 64.5 + - - +
188B VAL 3.3 0.7 - - - -
189B GLU* 3.4 22.4 + - - +
190B ARG* 3.5 8.1 + - - +
341B PRO* 3.7 27.4 - - - +
343B TRP* 3.0 50.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 2.8 20.2 + - + +
184B ALA* 3.3 13.0 + - - +
186B GLU* 1.3 79.4 - - - +
188B VAL* 1.3 61.2 + - + +
190B ARG* 3.6 2.3 + - - +
191B LEU* 3.4 25.6 + - - +
262B VAL* 3.8 23.6 - - + -
290B VAL* 3.5 33.7 - - + +
343B TRP* 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ALA 3.4 15.7 + - - +
185B TYR 3.9 7.2 - - - +
186B GLU 3.3 0.2 - - - -
187B ALA* 1.3 75.6 - - - +
189B GLU* 1.3 63.9 + - - +
191B LEU* 3.6 8.3 + - + +
192B ALA* 3.2 20.6 + - - +
199B ILE* 5.2 13.0 - - + -
218B PHE* 3.9 41.7 - - + +
221B GLY* 3.6 28.5 - - - +
222B ILE* 3.9 8.3 - - + +
225B PHE* 3.8 13.0 - - + +
227B VAL* 5.6 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR 3.5 10.8 + - - +
186B GLU* 3.4 21.8 + - - +
187B ALA 3.3 0.8 - - - -
188B VAL* 1.3 78.6 - - - +
190B ARG* 1.3 61.4 + - + +
192B ALA* 3.1 11.0 - - - +
193B GLN* 3.1 21.3 + - + +
225B PHE* 5.3 4.0 - - - +
343B TRP* 5.3 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU 3.5 10.8 + - - +
187B ALA 3.6 6.2 + - - +
188B VAL 3.4 0.4 - - - -
189B GLU* 1.3 78.2 - - + +
191B LEU* 1.3 61.7 + - + +
192B ALA 3.1 1.3 - - - -
193B GLN* 3.0 18.1 + - + +
194B CYS* 2.6 41.8 + - - -
290B VAL* 4.8 7.0 - - + -
306B HIS* 2.8 52.2 + - + +
343B TRP* 4.1 38.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ALA 3.4 15.0 + - - +
188B VAL* 4.0 5.4 - - - +
189B GLU 3.4 0.4 - - - -
190B ARG* 1.3 78.8 - - + +
192B ALA* 1.3 61.1 + - - +
194B CYS* 3.3 8.0 + - + +
195B GLY 2.9 20.4 + - - -
196B ARG* 3.1 22.3 + - + +
199B ILE* 4.0 25.8 - - + -
260B GLY* 3.9 8.5 - - - -
261B ILE 3.7 23.3 - - - +
262B VAL* 4.0 22.4 - - + -
288B ASP* 3.3 36.3 - - + +
289B ILE 4.7 1.1 - - - +
290B VAL* 4.8 7.0 - - + +
306B HIS* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL 3.2 12.6 + - - +
189B GLU* 3.1 16.5 + - - +
191B LEU* 1.3 77.0 - - - +
193B GLN* 1.3 55.6 + - - +
195B GLY* 3.0 20.5 + - - -
196B ARG 5.1 3.4 - - - -
225B PHE* 4.5 17.0 - - + +
227B VAL* 5.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU* 3.1 8.5 + - + +
190B ARG* 3.0 29.1 + - + +
192B ALA* 1.3 76.7 - - - +
194B CYS* 1.3 58.0 + - - +
195B GLY* 3.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ARG* 2.6 26.7 + - - +
191B LEU* 3.7 9.6 - - - +
192B ALA 3.2 0.2 - - - -
193B GLN* 1.3 75.1 - - - +
195B GLY* 1.3 52.5 + - - +
196B ARG* 2.5 51.0 + - + -
288B ASP* 3.0 35.7 - - + +
306B HIS* 4.0 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LEU 2.9 4.6 + - - -
192B ALA* 3.0 13.7 + - - -
193B GLN 4.4 0.4 - - - -
194B CYS* 1.3 78.7 - - - +
196B ARG* 1.3 69.1 + - - +
197B LYS* 3.5 5.2 + - - +
----------------------------------------------------------
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