Contacts of the strand formed by residues 205 - 210 (chain R) in PDB entry 5G04
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 205 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200R VAL 3.9 0.3 - - - +
201R ALA* 3.6 2.6 - - - -
202R LEU* 2.8 40.2 + - - +
203R ASP 3.4 0.6 - - - -
204R ASN* 1.3 79.5 + - - +
206R VAL* 1.3 57.7 + - - +
207R TYR* 4.0 17.3 - - - -
218R GLN* 3.0 25.4 + - - -
220R LEU 3.4 9.6 - - - -
221R GLN* 3.4 21.7 + - - +
229R ILE* 3.6 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199R ALA* 4.5 4.7 - - + -
200R VAL 3.6 6.5 - - - +
201R ALA* 4.5 2.0 - - - -
205R SER* 1.3 72.9 - - - +
207R TYR* 1.3 65.4 + - - +
208R LEU* 4.0 13.9 - - + -
218R GLN* 3.7 4.5 - - - +
219R LEU* 3.0 31.2 + - + -
220R LEU* 3.4 29.2 + - + -
229R ILE* 3.7 22.8 - - + +
232R VAL* 4.1 22.0 - - + -
241R LEU* 3.7 26.5 - - + -
243R VAL* 4.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 207 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198R LEU 3.5 0.9 - - - +
199R ALA* 3.5 3.6 - - - -
200R VAL* 2.9 38.1 + - + +
202R LEU* 3.5 31.6 - - + -
205R SER* 4.0 18.3 - - - -
206R VAL* 1.3 75.8 - - - +
208R LEU* 1.3 61.8 + - - +
209R TRP 4.2 0.2 - - - -
216R ILE* 3.7 21.3 - - + -
217R LEU 3.4 8.5 - - - -
218R GLN* 3.7 35.0 + - + -
830S ALA* 3.7 20.2 - - + -
831S LEU* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197R VAL* 3.9 11.2 - - + -
198R LEU 3.2 3.6 - - - -
199R ALA* 3.8 27.8 - - + -
206R VAL* 4.0 11.9 - - + -
207R TYR* 1.3 75.6 - - - +
209R TRP* 1.3 61.2 + - - +
210R SER 4.1 0.2 - - - -
215R ASP 3.6 1.6 - - - +
216R ILE* 3.4 5.1 - - - -
217R LEU* 2.7 58.6 + - + +
219R LEU* 3.9 26.7 - - + -
234R TRP* 3.8 15.0 - - + -
241R LEU* 4.2 5.4 - - + -
255R VAL* 3.8 33.7 - - + -
831S LEU* 4.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 209 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174R ARG* 3.5 35.7 - - - -
176R LEU* 3.6 26.3 - - + +
192R TRP* 4.7 0.9 - + - -
197R VAL* 3.5 5.2 - - - +
198R LEU* 2.8 66.2 + - + +
208R LEU* 1.3 72.4 - - - +
210R SER* 1.3 68.8 + - - +
211R ALA* 3.5 30.5 + - + -
214R GLY* 3.6 18.2 + - - -
215R ASP 3.5 7.2 - - - -
216R ILE* 3.6 25.4 - - + -
469R LEU* 3.8 26.2 - - + -
831S LEU* 3.7 29.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196R ASN 4.2 6.1 + - - -
197R VAL* 4.7 9.8 - - - +
208R LEU 4.1 0.4 - - - -
209R TRP* 1.3 74.7 - - - +
211R ALA* 1.3 59.9 + - - +
212R SER* 3.7 7.4 + - - -
213R SER* 3.1 29.8 + - - -
214R GLY* 2.9 30.3 + - - -
215R ASP* 3.1 14.4 + - - -
----------------------------------------------------------
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