Contacts of the helix formed by residues 180 - 196 (chain B) in PDB entry 5FW2
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 180 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ASP* 3.9 13.7 + - - +
178B ASN 3.6 0.2 - - - -
179B SER* 1.3 92.6 + - - +
181B VAL* 1.3 53.8 + - - +
182B ASP* 3.2 7.2 - - - -
183B LYS* 3.1 26.1 + - + +
184B LEU* 2.7 54.9 + - + +
299B ALA* 5.1 0.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASN* 3.8 27.6 - - - +
179B SER 3.5 2.4 - - - -
180B ASP* 1.3 75.5 - - - +
182B ASP* 1.3 54.3 + - - +
184B LEU* 4.3 2.0 - - - +
185B PHE* 2.7 33.8 + - + +
208B ALA* 4.5 6.5 - - + -
209B LYS* 3.6 33.8 - - + +
212B LEU* 5.3 0.4 - - + -
213B SER* 6.3 0.9 - - - -
296B LEU* 3.7 12.0 - - + +
299B ALA* 4.0 18.6 - - + +
300B ILE* 3.1 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B SER 3.6 4.9 - - - +
180B ASP 3.7 0.2 - - - -
181B VAL* 1.3 75.9 - - - +
183B LYS* 1.3 83.3 + - - +
185B PHE* 4.0 3.8 - - - +
186B ILE* 3.0 40.6 + - + +
208B ALA* 5.3 5.2 - - + +
209B LYS* 3.1 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASP* 3.1 27.1 + - + +
182B ASP* 1.3 95.2 + - - +
184B LEU* 1.3 57.1 + - + +
186B ILE* 3.4 11.2 + - + +
187B GLN* 2.7 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASP* 2.7 36.2 + - + +
181B VAL* 4.5 0.4 - - - +
183B LYS* 1.3 71.1 - - + +
185B PHE* 1.3 60.7 + - - +
187B GLN* 3.1 19.8 + - - +
188B LEU* 2.9 27.7 + - - +
292B ALA* 5.0 2.0 - - - +
295B ASN* 3.4 45.8 - - + +
296B LEU* 3.6 21.6 - - + +
299B ALA* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B VAL 2.7 21.8 + - - +
182B ASP 4.0 2.2 - - - +
184B LEU* 1.3 72.5 - - - +
186B ILE* 1.3 70.4 + - + +
188B LEU* 3.0 4.9 + - + +
189B VAL* 3.0 45.8 + - + +
203B ALA* 5.4 7.2 - - - -
206B VAL* 5.0 14.8 - - + -
208B ALA* 3.6 29.2 - - + -
212B LEU* 4.7 4.7 - - + -
225B LEU* 3.8 31.6 - - + -
229B LEU* 5.2 7.2 - - + -
238B PHE* 4.1 8.1 - + - -
242B ILE* 3.5 26.0 - - + -
296B LEU* 3.6 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ASP* 3.0 27.7 + - + +
183B LYS* 3.7 10.3 - - + +
185B PHE* 1.3 82.3 - - + +
187B GLN* 1.3 58.4 + - - +
189B VAL* 3.6 7.2 + - - +
190B GLN* 2.8 41.1 + - - +
203B ALA* 4.3 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LYS 2.7 21.5 + - - +
184B LEU* 3.3 24.4 - - - +
185B PHE 3.1 0.2 - - - -
186B ILE* 1.3 72.7 - - - +
188B LEU* 1.3 60.5 + - - +
190B GLN* 3.0 13.3 + - + +
191B THR* 2.9 42.7 + - + +
292B ALA* 4.7 6.5 - - + +
295B ASN* 4.5 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU 2.9 13.0 + - - +
185B PHE* 3.5 9.4 - - - +
187B GLN* 1.3 75.5 - - - +
189B VAL* 1.3 65.8 + - + +
190B GLN 3.0 0.5 + - - -
191B THR* 3.1 1.9 + - - -
192B TYR* 2.9 21.9 + - + +
238B PHE* 4.4 14.4 - - + -
241B LEU* 4.6 14.6 - - + +
242B ILE* 4.4 18.8 - - + -
245B SER* 5.4 0.9 - - - -
289B LEU* 4.0 26.5 - - + +
292B ALA* 3.5 32.9 - - + +
293B ALA* 4.3 19.1 - - + -
296B LEU* 4.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 3.0 35.9 + - + +
186B ILE* 3.8 6.3 - - - +
188B LEU* 1.3 75.0 - - - +
190B GLN* 1.3 61.5 + - - +
192B TYR* 3.9 1.5 - - - +
193B ASN* 3.1 47.8 + - - +
201B ILE* 3.7 28.9 - - + +
203B ALA* 4.3 16.8 - - + +
238B PHE* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 2.8 31.0 + - - +
187B GLN* 3.1 18.4 - - + +
188B LEU 2.9 0.4 - - - -
189B VAL* 1.3 76.9 - - - +
191B THR* 1.3 66.0 + - + +
193B ASN* 3.1 8.0 + - - +
194B GLN* 3.0 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLN* 2.9 26.0 + - + +
188B LEU 3.2 6.4 + - - -
190B GLN* 1.3 74.8 - - + +
192B TYR* 1.3 66.6 + - - +
194B GLN* 2.8 22.0 + - - +
195B LEU* 2.9 14.0 + - - +
288B ASP* 4.0 27.1 + - + +
289B LEU* 3.7 13.9 - - - +
292B ALA* 4.1 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 2.9 13.6 + - + +
189B VAL* 3.9 5.8 - - - +
191B THR* 1.3 81.2 + - - +
193B ASN* 1.3 72.3 + - - +
195B LEU* 3.0 3.4 + - - -
196B PHE* 2.8 70.0 + + + +
199B ASN 4.5 5.4 - - - -
200B PRO 5.0 0.2 - - - -
201B ILE* 3.4 28.7 - - + -
232B GLU* 4.2 14.5 + - - -
237B LEU* 3.9 15.7 - - + +
238B PHE* 4.1 28.7 + + + +
241B LEU* 4.4 1.8 - - + -
289B LEU* 3.4 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 3.1 23.5 + - - +
190B GLN* 3.1 5.0 + - - +
192B TYR* 1.3 85.5 - - - +
194B GLN* 1.3 64.2 + - - +
196B PHE 3.1 21.6 - - - +
197B GLU* 3.7 7.4 - - - +
200B PRO* 3.2 17.4 - - + +
201B ILE* 2.4 52.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLN* 3.0 32.9 + - + +
191B THR* 2.8 17.5 + - - +
193B ASN* 1.3 82.1 + - - +
195B LEU* 1.3 55.9 + - - +
197B GLU* 2.9 26.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
191B THR 2.9 11.5 + - - +
192B TYR* 3.7 6.7 - - - +
194B GLN* 1.3 79.4 - - - +
196B PHE* 1.3 70.2 + - + +
197B GLU* 3.6 9.1 + - - +
285B GLN* 3.4 45.3 - - + +
286B TYR* 3.3 44.9 - - + -
289B LEU* 4.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B TYR* 2.8 50.8 + + + +
193B ASN* 3.1 14.1 - - - +
195B LEU* 1.3 85.5 - - + +
197B GLU* 1.3 59.3 + - - +
198B GLU* 3.5 2.0 - - - +
199B ASN* 2.5 48.4 - - - +
200B PRO* 4.0 0.7 - - - +
237B LEU* 3.2 36.1 - - + -
256B PHE* 5.5 0.7 - + - -
286B TYR* 3.8 25.4 - + - -
289B LEU* 4.4 4.0 - - + -
----------------------------------------------------------
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