Contacts of the strand formed by residues 200 - 209 (chain G) in PDB entry 1R8Y
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 LYS 200 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G TYR* 4.1 28.5 + - + -
175G ARG* 5.5 5.5 - - - +
187G PRO 4.9 1.8 + - - -
188G PRO* 4.1 14.4 - - + +
189G GLY* 3.5 32.2 - - - +
190G LYS 5.4 0.4 - - - +
191G ASN* 6.5 1.1 - - - -
196G SER* 4.7 13.2 - - - +
198G LEU* 3.3 22.2 + - + +
199G THR* 1.3 77.7 - - - +
201G ASP* 1.3 61.1 + - - +
202G ILE* 3.4 29.1 - - + +
220G TYR* 3.6 26.2 + - + -
221G THR 3.8 3.6 - - - -
222G VAL* 4.4 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 201 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G PRO* 5.4 0.9 - - - -
199G THR 5.0 0.9 - - - +
200G LYS* 1.3 75.4 - - - +
202G ILE* 1.3 85.0 + - - +
203G THR* 5.6 0.5 + - - -
219G ASP 3.4 3.5 - - - +
220G TYR* 3.5 1.0 - - - -
221G THR* 2.7 59.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210F ASN* 4.0 8.5 + - - +
175G ARG* 5.9 1.3 - - - +
186G ALA 3.6 21.8 - - - +
187G PRO 4.9 0.4 - - - +
188G PRO* 3.7 30.0 - - + +
200G LYS* 3.4 30.3 - - + +
201G ASP* 1.3 89.0 + - - +
203G THR* 1.3 74.1 + - - +
204G THR* 4.2 5.5 + - - +
218G LEU* 4.3 18.2 - - + -
219G ASP 3.8 1.1 - - - -
220G TYR* 3.4 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209F VAL* 3.7 20.6 - - + -
210F ASN* 3.3 23.0 + - - +
201G ASP* 4.3 0.5 + - - -
202G ILE* 1.3 76.9 + - - +
204G THR* 1.3 61.0 + - - +
205G SER* 3.8 2.0 + - - +
217G THR 3.7 1.4 - - - +
218G LEU* 3.5 4.9 - - - -
219G ASP* 3.1 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 204 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F THR 3.4 2.1 - - - +
209F VAL* 3.4 1.1 - - - -
210F ASN* 2.7 41.2 + - - -
180G ILE* 4.5 2.7 - - + -
184G GLY 3.3 24.7 - - - +
185G CYS* 3.4 3.5 - - - +
186G ALA* 2.7 36.6 + - + +
202G ILE* 4.2 2.6 + - - +
203G THR* 1.3 70.6 - - - +
205G SER* 1.3 60.6 + - - +
206G VAL* 4.4 8.5 - - + -
216G VAL* 4.2 13.5 - - + -
217G THR 3.8 2.5 - - - -
218G LEU* 3.9 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 205 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F LEU* 4.0 14.8 - - - -
208F THR 3.2 3.6 - - - -
209F VAL* 3.9 25.7 - - - +
203G THR* 4.2 1.4 + - - +
204G THR* 1.3 75.0 - - - +
206G VAL* 1.3 63.2 + - - +
215G MET 3.8 0.7 - - - +
216G VAL* 3.5 3.0 - - - -
217G THR* 2.8 52.5 + - - -
219G ASP* 4.1 13.9 + - - -
239G ARG* 4.8 4.0 + - - -
5H TYR* 4.7 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F VAL 3.5 1.6 - - - +
207F LEU* 3.5 5.5 - - - +
208F THR* 2.7 50.1 + - + +
180G ILE* 5.2 1.6 - - + -
181G LEU* 3.8 28.3 - - + +
184G GLY* 4.5 16.6 - - - +
204G THR* 4.4 13.5 - - + -
205G SER* 1.3 75.9 - - - +
207G LEU* 1.3 63.5 + - - +
208G THR* 3.9 18.8 - - - +
213G ALA* 5.1 2.0 - - + -
215G MET 3.4 8.3 - - - +
216G VAL* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E TYR* 4.0 34.3 - - + +
205F SER* 4.2 15.7 - - - -
206F VAL 3.6 16.2 - - - +
207F LEU* 4.3 15.5 - - + +
205G SER 3.9 0.8 + - - -
206G VAL* 1.3 74.4 - - - +
208G THR* 1.3 62.0 + - - +
209G VAL* 3.9 12.8 - - + -
213G ALA* 3.9 0.5 - - - -
214G HIS* 2.9 45.8 + - + +
215G MET* 2.9 37.3 + - + +
5H TYR* 4.6 8.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 208 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F GLY* 5.3 3.4 - - - +
204F THR 3.7 1.6 - - - +
205F SER* 3.4 1.4 - - - -
206F VAL* 2.8 51.2 + - + +
206G VAL* 3.9 12.9 + - - +
207G LEU* 1.3 75.3 + - - +
209G VAL* 1.3 61.9 + - - +
210G ASN 3.9 0.2 + - - -
211G ASN* 3.7 36.5 + - - +
212G LYS 3.8 6.3 - - - +
213G ALA* 3.8 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F THR* 3.8 26.9 - - + -
204F THR 3.7 4.5 - - - +
205F SER* 4.1 16.4 - - - +
207G LEU* 3.9 10.4 + - + -
208G THR* 1.3 70.5 - - - +
210G ASN* 1.3 78.4 + - + +
211G ASN 3.1 2.0 - - - -
212G LYS* 2.8 28.4 + - - +
214G HIS* 4.1 28.9 - - + -
----------------------------------------------------------
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