Contacts of the helix formed by residues 195 - 204 (chain A) in PDB entry 1SXQ
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 ARG 195 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 3.0 21.2 + - - -
190A PHE 4.8 2.2 + - - -
191A ARG* 3.2 13.6 - - + +
193A GLY 3.1 0.6 - - - -
194A GLN* 1.3 78.5 - - + +
196A GLU* 1.3 64.7 + - - +
197A SER 3.4 2.9 - - - -
198A LYS* 3.2 18.9 + - + +
199A MET* 3.0 37.1 + - + +
256A ILE* 3.4 31.2 + - + -
257A GLY* 3.2 26.5 - - - +
258A ASP* 2.8 36.7 + - - +
261A TYR* 3.5 9.9 - - - -
400A UDP 2.8 45.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 3.4 22.9 - - + -
193A GLY* 3.3 21.6 + - - +
194A GLN 3.7 0.2 - - - -
195A ARG* 1.3 76.5 - - - +
197A SER* 1.3 63.7 + - - +
199A MET* 3.3 9.6 + - - +
200A VAL* 2.9 33.0 + - + +
220A GLN 4.4 0.9 - - - +
221A PHE* 3.6 23.2 - - + +
222A LYS 3.5 7.4 + - - -
223A ASN* 3.1 48.7 + - - +
226A TYR* 4.2 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ARG 3.4 1.0 - - - -
196A GLU* 1.3 77.7 - - - +
198A LYS* 1.3 62.6 + - - +
200A VAL* 3.5 1.4 + - - +
201A GLU* 2.9 30.5 + - - +
226A TYR* 3.5 47.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ARG* 3.2 20.5 + - + +
197A SER* 1.3 79.1 - - - +
199A MET* 1.3 66.5 + - - +
201A GLU* 3.3 4.7 + - + -
202A PHE* 3.1 40.9 + - + +
256A ILE* 4.1 15.9 - - + +
257A GLY 4.4 15.5 - - - +
262A ASN* 5.7 1.8 - - - +
283A ASP* 2.6 34.8 + - - +
285A GLU* 2.8 36.7 + - - +
301A ASN 5.4 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 3.7 20.9 - - + +
189A SER 3.4 26.0 - - - +
190A PHE* 4.5 13.0 - - - +
191A ARG* 5.3 2.2 - - - -
195A ARG* 3.0 37.7 + - + +
196A GLU* 3.3 5.1 + - - +
198A LYS* 1.3 78.3 - - - +
200A VAL* 1.3 57.2 + - - +
203A LEU* 2.9 43.3 + - + +
204A PHE* 3.4 3.4 - - - -
212A PHE* 3.8 16.8 - - + -
221A PHE* 3.7 34.5 - - + -
256A ILE* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLU* 2.9 24.2 + - + +
197A SER 3.9 3.1 - - - +
199A MET* 1.3 73.3 - - - +
201A GLU* 1.3 66.4 + - - +
204A PHE* 3.3 29.3 + - + -
221A PHE* 4.0 21.1 - - + -
226A TYR* 3.8 28.0 - - + +
227A PRO 3.8 22.7 - - - +
228A TRP* 4.2 10.1 - - + -
303A ARG* 2.8 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A SER* 2.9 21.0 + - - +
198A LYS* 3.6 9.2 - - + +
199A MET 3.3 0.2 - - - -
200A VAL* 1.3 76.9 - - - +
202A PHE* 1.3 76.7 + - + +
301A ASN 5.5 0.4 - - - +
302A ASN* 3.2 14.5 - - - +
303A ARG* 2.9 76.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LYS* 3.1 29.2 + - + +
201A GLU* 1.3 86.0 - - + +
203A LEU* 1.3 65.1 + - - +
204A PHE 3.8 0.2 - - - -
206A THR* 3.7 10.4 - - - +
210A ILE* 3.9 2.1 - - - +
254A LEU* 3.6 22.0 - - + -
256A ILE* 3.7 14.6 - - + -
283A ASP* 3.7 39.0 - - + -
300A VAL* 3.8 19.3 - - + -
301A ASN 3.9 15.5 - - - -
302A ASN* 3.4 34.1 - - - -
303A ARG* 4.0 1.6 - - - +
306A LEU* 3.1 37.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL* 4.3 11.2 - - + -
186A TYR* 3.9 29.8 - - + -
199A MET* 2.9 24.4 + - + +
202A PHE* 1.3 85.7 - - - +
204A PHE* 1.3 66.5 + - + +
205A ASP 4.4 0.2 + - - -
206A THR* 4.0 4.7 + - - +
210A ILE* 3.7 32.4 - - + +
212A PHE* 3.8 32.1 - - + -
232A PRO* 3.5 29.4 - - + +
254A LEU* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A MET* 3.4 20.0 - - + -
200A VAL* 3.3 18.0 + - + +
203A LEU* 1.3 83.2 - - + +
205A ASP* 1.3 67.8 + - - +
206A THR* 3.1 7.0 + - - +
212A PHE* 5.1 1.8 - + - -
218A GLU* 5.4 0.4 - - + -
221A PHE* 3.6 39.3 - + - -
228A TRP* 3.4 52.7 - + + -
230A LYS 3.6 4.5 - - - +
231A ALA* 3.5 28.7 - - + -
232A PRO* 3.7 16.8 - - + -
234A PHE* 4.0 10.3 - + - -
303A ARG* 3.1 23.1 + - - +
----------------------------------------------------------
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