Contacts of the helix formed by residues 194 - 206 (chain U) in PDB entry 3A9Q
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 GLY 194 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190N ARG* 3.3 35.5 - - - +
192U GLY 3.8 0.4 + - - -
193U LYS* 1.3 71.2 - - - +
195U HIS* 1.3 66.2 + - - -
196U GLY 3.2 1.2 + - - -
197U VAL* 3.3 6.6 + - - +
198U TRP* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 195 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190N ARG 3.6 4.2 + - - -
191N VAL* 3.7 23.7 + - + +
195N HIS* 3.7 43.7 + + - +
196N GLY* 3.8 22.7 + - - -
199N HIS* 2.8 31.3 + - + +
195T HIS* 3.6 22.4 + + + +
193U LYS 3.7 2.6 + - - -
194U GLY* 1.3 70.5 - - - -
196U GLY* 1.3 63.6 + - - +
198U TRP* 3.2 13.7 + + - +
199U HIS* 2.9 19.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 196 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195T HIS* 3.8 17.1 + - - -
191U VAL* 3.5 42.2 + - - +
192U GLY 3.7 2.4 + - - -
193U LYS 4.2 2.0 + - - -
194U GLY 3.2 0.6 - - - -
195U HIS* 1.3 77.7 - - - +
197U VAL* 1.3 55.9 + - - +
199U HIS* 3.1 3.5 + - - +
200U PHE 2.9 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190N ARG* 3.8 21.3 - - - +
77U LEU* 4.2 10.5 - - + -
80U LEU* 6.0 0.4 - - + -
127U GLY* 6.5 0.2 - - - -
128U ASP* 5.0 0.4 - - - +
129U ALA* 3.7 27.1 - - + -
130U LEU* 5.7 2.7 - - + +
188U LEU* 4.0 18.2 - - + +
191U VAL* 4.2 4.3 - - + -
192U GLY 3.2 19.2 + - - +
193U LYS* 3.8 17.0 - - + -
194U GLY 3.3 10.4 + - - +
196U GLY* 1.3 74.4 - - - +
198U TRP* 1.3 58.1 + - - +
200U PHE* 3.3 6.0 + - + +
201U ASP* 2.8 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 198 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187N GLN* 2.8 47.1 + - + +
190N ARG* 4.0 13.7 - - - +
191N VAL* 3.5 25.8 - - + -
199N HIS* 3.5 39.3 - + + -
200N PHE* 3.9 19.3 - + - -
203N MET* 3.8 30.5 - - + -
76U ALA 5.0 1.3 - - - -
77U LEU* 4.5 7.0 - - + -
194U GLY 3.1 13.2 + - - +
195U HIS* 3.6 13.0 - + - +
197U VAL* 1.3 78.3 - - - +
199U HIS* 1.3 62.8 + - - +
201U ASP* 3.2 9.9 + - + +
202U GLN* 3.0 55.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 199 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199N HIS* 3.4 33.4 + + + -
195T HIS* 2.9 25.8 + - + +
198T TRP* 3.6 20.0 - + + -
199T HIS* 3.5 43.0 + + - -
202T GLN* 5.7 1.4 - - - +
195U HIS 2.9 12.6 + - - +
196U GLY 3.1 8.0 + - - +
198U TRP* 1.3 81.0 - - + +
200U PHE* 1.3 65.7 + - - +
202U GLN* 3.1 9.8 + - + +
203U MET* 3.0 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 200 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198T TRP* 3.7 17.3 - + + -
80U LEU* 4.3 7.4 - - + -
133U MET* 4.5 2.0 - - + -
184U TYR* 3.6 36.8 - + + -
187U GLN* 3.8 33.7 - - + -
188U LEU* 3.5 36.3 - - + -
191U VAL* 4.3 6.7 - - + -
196U GLY 2.9 12.6 + - - +
197U VAL 3.6 6.7 - - - +
199U HIS* 1.3 74.7 - - - +
201U ASP* 1.3 68.1 + - - +
203U MET* 3.1 29.5 + - + +
204U LEU* 2.9 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 201 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76U ALA 5.0 0.3 - - - +
77U LEU* 3.3 29.8 - - + +
78U ARG* 3.1 9.4 + - - +
79U GLY* 2.8 19.9 + - - -
80U LEU* 2.7 39.1 + - + +
197U VAL* 2.8 15.3 + - + +
198U TRP* 3.4 11.3 - - + +
200U PHE* 1.3 82.7 - - - +
202U GLN* 1.3 63.9 + - - +
204U LEU* 3.3 4.0 + - - +
205U LEU* 2.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 202 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199N HIS* 5.6 1.6 - - - +
203N MET* 3.3 21.7 - - - +
78U ARG* 3.0 26.6 + - - +
198U TRP* 3.0 52.1 + - + +
199U HIS* 3.1 13.7 + - + +
201U ASP* 1.3 77.1 - - - +
203U MET* 1.3 65.9 + - - +
205U LEU* 3.2 11.8 + - - +
206U HIS* 3.1 50.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 203 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78T ARG* 3.7 10.3 - - - +
198T TRP* 3.8 10.3 - - + -
202T GLN* 3.4 30.5 - - - +
206T HIS* 6.0 0.2 - - + -
184U TYR* 4.9 2.2 - - + -
187U GLN* 3.7 15.3 - - - +
199U HIS* 3.0 14.0 + - + +
200U PHE* 3.3 44.6 - - + +
202U GLN* 1.3 74.6 - - - +
204U LEU* 1.3 65.1 + - + +
206U HIS* 3.1 6.5 + - - +
207U GLU* 2.8 56.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79U GLY* 3.8 21.2 - - - +
80U LEU* 3.9 25.4 - - + -
82U LYS* 4.4 7.3 + - - +
83U PHE* 3.9 22.9 - - + -
133U MET* 4.3 6.7 - - + -
180U ARG* 5.3 1.3 - - - +
184U TYR* 3.4 37.5 - - + +
200U PHE* 2.9 26.9 + - + +
201U ASP* 3.6 8.3 - - - +
203U MET* 1.3 80.6 - - + +
205U LEU* 1.3 62.5 + - - +
206U HIS 3.2 0.7 + - - -
207U GLU* 3.2 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78U ARG* 3.8 53.8 - - + +
79U GLY* 3.6 10.9 - - - +
82U LYS* 3.6 34.0 + - + +
201U ASP 2.8 20.5 + - - +
202U GLN* 3.2 21.3 + - - +
204U LEU* 1.3 72.9 - - - +
206U HIS* 1.3 84.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 206 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82U LYS* 5.7 0.2 - - - -
202U GLN* 3.1 38.6 + - + +
203U MET* 3.1 6.8 + - - +
205U LEU* 1.3 102.5 + - + +
207U GLU* 1.3 64.6 + - - +
----------------------------------------------------------
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