Contacts of the helix formed by residues 185 - 202 (chain F) in PDB entry 3D29
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 185 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F CYS* 3.7 2.2 - - - -
43F ASN* 3.7 14.4 - - - +
184F LEU* 1.3 78.3 - - - +
186F ALA* 1.3 56.0 + - - +
187F ARG* 3.6 8.2 + - - +
188F GLU* 3.1 28.1 + - - +
189F ALA* 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F GLU* 3.8 7.6 - - + -
42F CYS* 3.5 20.8 - - - -
43F ASN* 4.2 3.2 - - - +
44F ASP* 4.1 2.0 + - - +
47F VAL* 4.0 1.7 - - + +
185F SER* 1.3 74.6 - - - +
187F ARG* 1.3 63.2 + - - +
189F ALA* 3.7 2.3 - - - +
190F VAL* 3.0 29.1 + - - +
214F TRP* 3.7 21.3 - - + -
216F SER* 3.6 29.8 - - - +
218F SER* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 187 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F GLU* 3.2 41.6 + - - +
185F SER* 3.2 8.2 + - - +
186F ALA* 1.3 80.8 - - - +
188F GLU* 1.3 63.0 + - + +
190F VAL* 3.4 6.6 + - - +
191F LYS* 3.4 31.5 + - - +
214F TRP* 4.0 11.2 - - - -
228F LEU* 3.4 36.9 - - + +
231F GLU* 5.0 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 188 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F HIS* 5.4 4.0 - - - +
184F LEU* 3.3 27.1 - - + +
185F SER* 3.1 17.8 + - - +
187F ARG* 1.3 78.0 - - + +
189F ALA* 1.3 66.0 + - - +
191F LYS* 3.2 31.3 + - - +
192F GLN* 2.9 42.4 + - - +
235F PHE* 5.6 3.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F ILE* 3.6 18.1 - - + +
42F CYS* 4.0 10.5 - - + -
47F VAL* 3.4 24.9 - - + +
184F LEU* 3.5 21.7 - - + +
185F SER 2.7 21.0 + - - +
186F ALA 3.7 0.4 - - - +
188F GLU* 1.3 72.0 - - - +
190F VAL* 1.3 57.8 + - - +
192F GLN* 4.4 0.7 - - - -
193F ALA* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F VAL* 4.0 18.2 - - + -
186F ALA 3.0 18.0 + - - +
187F ARG* 3.5 8.5 - - - +
189F ALA* 1.3 76.3 - - - +
191F LYS* 1.3 63.6 + - + +
193F ALA* 3.3 4.3 + - - +
194F ALA* 3.1 17.5 + - - +
212F ILE* 3.8 19.3 - - + +
214F TRP* 3.5 30.5 - - + -
224F VAL* 4.1 26.9 - - + -
228F LEU* 4.6 11.7 - - + +
232F ALA* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187F ARG* 3.4 18.7 + - - +
188F GLU* 3.2 30.3 + - - +
190F VAL* 1.3 77.4 - - + +
192F GLN* 1.3 64.3 + - - +
194F ALA* 3.1 6.1 + - - +
195F LYS 3.1 18.0 + - - -
228F LEU* 5.9 3.4 - - + -
231F GLU* 3.4 29.3 + - + +
232F ALA* 4.2 17.9 - - + -
235F PHE* 3.6 46.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F HIS* 5.6 1.5 - - - +
40F ILE* 4.3 1.3 - - + -
179F LEU* 3.2 50.5 - - + +
184F LEU* 4.5 5.1 - - + +
188F GLU* 2.9 33.3 + - - +
189F ALA* 3.9 6.1 - - - +
191F LYS* 1.3 77.6 - - - +
193F ALA* 1.3 57.5 + - - +
195F LYS* 2.8 38.8 + - - +
196F ILE* 2.8 36.2 + - + +
235F PHE* 4.0 15.2 - - - -
239F GLU* 5.1 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ILE* 3.8 6.5 - - + +
40F ILE* 3.7 17.5 - - + +
47F VAL* 4.0 16.8 - - + -
49F ALA* 4.0 17.5 - - + -
189F ALA 2.8 20.1 + - - +
190F VAL 3.4 5.4 - - - +
192F GLN* 1.3 73.9 - - - +
194F ALA* 1.3 66.1 + - - +
196F ILE* 3.3 2.4 + - - +
197F ILE* 3.1 29.2 + - - +
212F ILE* 4.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190F VAL 3.1 4.0 + - - +
191F LYS 3.1 9.3 + - - +
193F ALA* 1.3 79.5 - - - +
195F LYS* 1.3 60.1 + - - +
197F ILE* 3.6 1.6 + - - +
198F TYR* 3.0 30.7 + - - -
210F LEU* 3.5 31.2 - - + -
212F ILE* 4.0 3.0 - - + +
232F ALA* 3.5 35.7 - - + +
236F ALA* 3.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175F GLU* 3.8 15.8 + - - -
191F LYS 3.1 11.7 + - - +
192F GLN* 2.8 39.7 - - - +
193F ALA 3.1 0.2 - - - -
194F ALA* 1.3 75.5 - - - +
196F ILE* 1.3 85.8 + - - +
198F TYR* 2.9 5.5 + - - +
199F LEU* 2.8 48.0 + - + +
235F PHE* 4.2 8.3 - - + -
236F ALA* 3.7 15.6 - - + +
239F GLU* 3.0 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 196 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ILE* 3.9 14.1 - - + -
40F ILE* 4.7 5.6 - - + -
171F SER 5.9 0.2 - - - -
172F ALA* 3.6 33.2 - - + -
175F GLU* 3.1 35.7 - - + +
176F LEU* 3.7 15.9 - - + +
179F LEU* 4.6 11.0 - - + -
192F GLN 2.8 25.0 + - - +
193F ALA* 3.3 6.7 + - - +
195F LYS* 1.3 88.2 - - - +
197F ILE* 1.3 59.7 + - - +
199F LEU* 3.4 6.2 + - - +
201F ALA* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F THR* 4.2 16.9 - - + +
38F ILE* 3.9 28.7 - - + +
49F ALA* 3.8 21.8 - - + +
50F VAL* 4.1 7.2 - - - -
51F GLU* 4.3 14.4 - - + -
193F ALA 3.1 21.2 + - - +
194F ALA 3.8 4.9 - - - +
196F ILE* 1.3 73.9 - - - +
198F TYR* 1.3 66.4 + - - +
201F ALA* 3.3 5.3 + - + +
202F HIS* 3.0 21.3 + - - +
208F PHE* 3.7 27.1 - - + -
210F LEU* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 198 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F ALA 3.0 21.9 + - - +
195F LYS 2.9 8.4 + - - +
197F ILE* 1.3 80.0 - - + +
199F LEU* 1.3 63.4 + - + +
202F HIS* 3.2 16.6 + - - +
203F GLU* 4.2 4.0 + - - +
208F PHE* 3.7 36.6 - + - -
210F LEU* 4.2 21.6 + - + +
233F ILE* 3.4 31.1 - - + +
236F ALA* 3.5 22.2 - - + +
237F GLN* 2.9 37.4 + - + +
240F ILE* 3.8 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171F SER* 4.7 6.5 - - - -
175F GLU* 3.1 43.3 - - + +
195F LYS* 2.8 45.1 + - + +
196F ILE* 3.7 4.7 - - - +
198F TYR* 1.3 74.3 - - + +
201F ALA* 1.3 58.8 + - - +
202F HIS 2.9 9.8 + - - -
203F GLU* 3.1 24.0 + - - +
204F ASP* 4.7 0.9 - - - +
236F ALA 5.7 0.2 - - - +
239F GLU 4.8 4.3 - - - +
240F ILE* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F THR* 4.1 23.2 - - + +
51F GLU* 4.9 0.3 - - - +
167F LYS* 6.0 0.2 - - - +
168F GLY* 3.7 30.6 - - - +
171F SER* 3.8 17.0 - - - -
172F ALA* 4.3 7.0 - - + +
196F ILE 2.9 18.6 + - - +
197F ILE* 3.7 5.8 - - + +
199F LEU* 1.3 74.8 - - - +
202F HIS* 1.3 59.1 + - - +
203F GLU 3.1 2.8 + - - -
204F ASP* 3.6 14.7 + - - +
205F ASN* 5.4 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 202 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LYS 2.9 28.9 + - - -
51F GLU* 2.6 32.2 + - - +
53F LEU* 3.8 4.7 - - + -
197F ILE 3.0 11.5 + - - +
198F TYR 3.2 15.0 - - - +
199F LEU 2.9 1.8 + - - -
201F ALA* 1.3 76.5 - - - +
203F GLU* 1.3 64.1 + - - +
204F ASP 3.2 0.4 - - - -
205F ASN* 3.1 16.9 + - - -
206F LYS* 2.9 28.5 + - - -
207F ASP* 4.4 2.0 + - - -
208F PHE* 3.3 47.4 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F TYR 4.6 2.7 - - - +
199F LEU* 3.1 15.1 + - - +
202F HIS* 1.3 79.9 - - - +
204F ASP* 1.3 62.6 + - - +
205F ASN 2.8 11.6 + - - -
206F LYS* 3.1 62.9 + - - +
240F ILE* 3.8 25.8 - - - +
----------------------------------------------------------
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