Contacts of the helix formed by residues 204 - 212 (chain A) in PDB entry 2WQO
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 CYS 204 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TYR 4.2 4.5 - - - -
182A TYR* 3.5 36.1 + - + -
200A TRP* 2.9 45.6 + - - -
201A SER 3.6 5.2 - - - +
203A GLY* 1.3 72.3 - - - +
205A LEU* 1.4 61.2 + - - +
207A TYR* 3.5 2.0 - - - +
208A GLU* 2.9 29.6 + - - +
215A PRO* 3.9 27.0 - - + +
216A PHE* 4.9 0.7 - - - -
252A LEU* 3.7 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.9 22.2 - - + -
98A ILE* 5.2 1.0 - - - +
116A VAL* 4.1 7.6 - - + -
120A LEU* 3.9 28.9 - - + -
142A LEU* 4.0 15.7 - - + -
143A LYS* 4.0 15.7 - - - -
144A PRO* 4.2 6.7 - - + -
147A VAL* 3.9 17.7 - - + -
182A TYR* 3.4 19.4 + - + +
201A SER 3.1 12.2 + - - +
202A LEU* 3.6 8.3 - - + +
204A CYS* 1.4 73.8 - - - +
206A LEU* 1.3 74.2 + - + +
208A GLU* 3.2 3.5 + - - +
209A LEU* 2.9 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 4.0 13.9 - - + +
116A VAL* 3.9 17.7 - - + -
117A MET* 3.7 54.5 - - + +
202A LEU* 2.9 35.8 + - + +
203A GLY 3.9 2.2 - - - +
205A LEU* 1.3 76.1 - - + +
207A TYR* 1.3 64.1 + - - +
209A LEU* 3.3 7.2 + - + +
210A CYS* 3.1 26.5 + - - -
248A ILE* 3.8 19.5 - - + -
251A MET* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLY 2.8 19.2 + - - +
204A CYS* 3.5 6.1 - - - +
205A LEU 3.1 0.2 - - - -
206A LEU* 1.3 77.9 - - - +
208A GLU* 1.3 57.5 + - - +
210A CYS* 3.0 4.9 + - - +
211A ALA* 2.8 43.0 + - + +
213A MET* 3.4 20.1 - - + +
214A PRO 4.0 2.0 - - - -
215A PRO* 3.5 40.9 + - + +
233A PHE* 3.9 14.2 - + - +
234A ARG* 2.7 45.3 + - - +
235A ARG 4.1 2.3 + - - -
236A ILE* 3.7 22.7 - - + -
248A ILE* 4.0 12.7 - - + +
252A LEU* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 4.1 28.3 - - + +
144A PRO* 4.3 5.1 - - - +
182A TYR* 2.7 35.2 + - - +
204A CYS 2.9 16.1 + - - +
205A LEU 3.8 3.1 - - - +
207A TYR* 1.3 77.2 - - - +
209A LEU* 1.3 60.2 + - - +
212A LEU* 2.8 32.4 + - - +
213A MET* 3.2 30.6 - - - +
214A PRO* 3.9 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.9 27.1 - - + -
97A VAL* 4.9 0.2 - - + -
98A ILE* 3.7 23.0 - - + +
108A LEU* 3.3 48.3 + - + +
112A PHE* 4.1 4.0 - - + -
113A VAL* 4.4 15.9 - - + -
116A VAL* 3.7 43.1 - - + -
205A LEU* 2.9 17.3 + - + +
206A LEU* 3.5 15.3 - - + +
207A TYR 3.2 0.2 - - - -
208A GLU* 1.3 77.2 - - - +
210A CYS* 1.3 62.1 + - - +
212A LEU* 3.8 6.9 - - - +
240A TYR* 4.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 3.3 26.0 - - - -
113A VAL* 3.7 29.4 - - - -
206A LEU 3.1 15.7 + - - +
207A TYR 3.0 7.8 + - - +
209A LEU* 1.3 79.3 - - - +
211A ALA* 1.3 59.3 + - - +
212A LEU* 3.6 0.3 + - - +
236A ILE* 3.9 21.5 - - + -
237A PRO* 3.7 2.5 - - - +
240A TYR* 3.5 26.7 + - + -
244A LEU* 4.0 11.9 - - - -
248A ILE* 4.0 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TYR* 4.0 9.5 + - - -
207A TYR* 2.8 44.7 + - + +
210A CYS* 1.3 73.1 - - - +
212A LEU* 1.3 68.0 + - - +
213A MET* 3.0 26.4 + - + +
235A ARG 5.6 0.7 - - - +
236A ILE* 4.9 1.3 - - - -
237A PRO* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 3.9 32.8 - - + +
101A GLY* 3.6 32.3 - - - +
102A THR* 3.7 22.2 + - + +
105A ARG* 5.7 0.4 - - - -
106A GLN 3.9 8.5 - - - +
107A TYR* 3.8 26.9 - - + -
108A LEU* 4.8 9.6 - - + +
208A GLU* 2.8 19.5 + - - +
209A LEU 3.8 17.3 - - - +
210A CYS 4.3 0.2 - - - +
211A ALA* 1.3 80.7 - - - +
213A MET* 1.3 63.0 + - + +
----------------------------------------------------------
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