Contacts of the helix formed by residues 184 - 196 (chain F) in PDB entry 5A0Q
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 LEU 184 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F THR* 3.8 2.8 - - - +
43F HIS* 3.0 48.2 - - + +
45F VAL* 3.7 10.3 - - + -
183F ASN* 1.3 76.8 + - - +
185F ASN* 1.3 66.5 + - - +
187F LEU* 3.7 8.3 - - - -
188F VAL* 3.1 31.6 + - + +
214F ILE* 2.6 60.6 - - + -
219F LEU* 4.7 5.4 - - + -
224F TYR* 4.8 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 185 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F ASN* 3.4 11.3 + - - +
184F LEU* 1.3 83.6 - - - +
186F GLU* 1.4 58.2 + - - +
188F VAL* 3.3 5.0 + - - +
189F LYS* 3.0 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 186 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F CYS* 3.3 37.6 - - + -
183F ASN* 3.0 5.2 + - - +
185F ASN* 1.4 74.7 - - - +
187F LEU* 1.4 64.9 + - - +
189F LYS* 3.3 34.1 + - + +
190F HIS* 3.1 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F LEU* 3.6 26.2 - - + +
39F LYS 4.3 1.8 - - - +
40F SER* 3.5 24.2 - - - +
43F HIS 3.6 7.9 - - - +
45F VAL* 3.4 30.5 - - + -
179F PHE* 3.1 37.5 - - + +
182F CYS* 3.2 16.4 + - + +
183F ASN 3.1 9.0 + - - +
184F LEU* 3.6 19.1 - - + +
185F ASN 3.3 0.2 - - - -
186F GLU* 1.4 75.1 - - - +
188F VAL* 1.4 52.9 + - - +
190F HIS* 3.2 8.1 + - - +
191F GLY* 2.8 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F VAL* 3.7 25.8 - - + -
47F VAL* 5.5 1.1 - - + +
184F LEU* 3.1 19.7 + - + +
185F ASN* 3.6 4.7 - - - +
187F LEU* 1.4 70.8 - - - +
189F LYS* 1.4 65.8 + - + +
190F HIS 3.2 0.2 - - - -
191F GLY* 3.6 4.0 - - - +
192F LEU* 3.0 30.2 + - + +
212F ILE* 3.2 35.2 - - + -
214F ILE* 3.8 18.4 - - + -
224F TYR* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F ASN* 3.0 24.2 + - + +
186F GLU* 3.3 39.3 - - - +
187F LEU 3.3 0.4 - - - -
188F VAL* 1.4 75.9 - - + +
190F HIS* 1.3 63.3 + - - +
192F LEU* 3.8 13.6 - - + +
193F ARG* 3.7 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 190 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171F TYR* 3.0 28.8 + - - +
175F HIS* 6.3 1.8 - + - -
179F PHE* 3.5 31.6 - + + -
182F CYS* 6.1 1.1 - - + -
186F GLU* 3.1 45.5 + - + +
187F LEU 3.4 7.9 - - - +
189F LYS* 1.3 79.2 - - + +
191F GLY* 1.3 61.4 + - - +
192F LEU 3.3 1.6 - - - -
193F ARG* 3.3 29.0 + - - -
194F ALA* 3.1 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 191 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F VAL* 4.9 2.4 - - - +
38F LEU* 4.3 11.4 - - - -
47F VAL* 4.2 25.9 - - - +
187F LEU 2.8 17.3 + - - -
188F VAL 3.0 5.1 + - - -
190F HIS* 1.3 74.0 - - - +
192F LEU* 1.3 57.8 + - - +
194F ALA* 3.5 7.4 + - - +
195F LEU* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F VAL* 4.4 3.8 - - + -
188F VAL* 3.0 23.8 + - + +
189F LYS* 3.8 13.9 - - + +
191F GLY* 1.3 76.8 - - - +
193F ARG* 1.4 56.4 + - - +
195F LEU* 3.4 7.1 + - - +
196F ARG* 3.2 33.1 + - - +
210F VAL* 3.6 43.5 - - + +
212F ILE* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171F TYR* 3.6 25.2 - - + +
189F LYS* 3.7 11.8 + - - +
190F HIS* 3.3 31.4 + - - +
191F GLY 3.3 0.4 - - - -
192F LEU* 1.4 75.2 - - - +
194F ALA* 1.4 61.9 + - - +
196F ARG* 3.6 21.1 + - - +
197F GLU* 3.5 23.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
36F VAL* 4.3 20.4 - - + -
38F LEU* 6.4 0.2 - - + -
168F ALA* 3.9 16.9 - - + +
171F TYR* 3.5 34.1 - - + -
172F LEU* 5.3 2.7 - - + -
179F PHE* 6.0 0.4 - - + -
190F HIS 3.1 7.5 + - - +
191F GLY* 3.5 11.0 - - - +
193F ARG* 1.4 73.4 - - - +
195F LEU* 1.3 64.9 + - - +
196F ARG 3.3 0.7 - - - -
197F GLU* 3.3 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F ALA* 4.5 13.5 - - + +
35F THR* 5.4 0.2 - - - -
36F VAL* 4.4 19.9 - - + +
47F VAL* 4.3 9.9 - - + -
48F ALA* 4.9 0.9 - - - -
49F LEU* 3.5 54.6 - - + +
191F GLY 3.0 18.3 + - - +
192F LEU* 3.6 7.9 - - - +
193F ARG 3.4 0.2 - - - -
194F ALA* 1.3 75.6 - - - +
196F ARG* 1.3 62.5 + - - +
197F GLU 3.3 4.9 + - - -
210F VAL* 3.0 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 196 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F ARG* 5.8 0.2 + - - -
192F LEU* 3.2 20.7 + - - +
193F ARG* 3.8 22.3 - - - +
194F ALA 3.3 1.0 - - - -
195F LEU* 1.3 76.1 - - - +
197F GLU* 1.3 67.7 + - - +
----------------------------------------------------------
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