Contacts of the helix formed by residues 199 - 212 (chain A) in PDB entry 2ZZ0
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 199 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ALA* 1.3 80.4 - - - +
200A TYR* 1.3 67.5 + - - +
201A VAL* 3.5 11.2 + - - +
202A ALA* 3.0 24.6 + - - +
203A LEU* 3.1 12.5 + - - +
225A LEU* 3.6 5.2 - - - +
290A ALA 3.1 19.1 + - - -
291A ILE 5.2 8.3 - - - -
292A GLY* 5.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 4.5 1.8 - - - -
199A SER* 1.3 75.0 - - - +
201A VAL* 1.3 96.7 + - + +
203A LEU* 3.8 1.1 - - - +
204A GLU* 2.8 42.6 + - - +
225A LEU* 3.5 16.4 - - + +
228A PHE* 4.3 21.9 - + + -
341A GLU 4.3 6.7 + - - -
342A LEU* 4.6 7.5 - - + +
373A THR 6.1 0.2 - - - -
374A VAL* 3.6 29.8 - - + -
900A FAD 3.3 53.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A SER* 4.3 12.6 - - - -
199A SER* 3.1 9.2 + - - +
200A TYR* 1.3 99.0 - - + +
202A ALA* 1.3 63.3 + - - +
204A GLU* 3.7 5.9 - - - +
205A CYS* 2.9 37.8 + - - -
288A MET* 4.6 1.1 - - + -
290A ALA* 4.4 13.5 - - + -
293A ARG* 5.6 5.2 - - - -
900A FAD 3.8 42.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 3.6 14.9 - - + +
197A GLY 3.1 29.8 - - - +
198A ALA* 3.7 0.9 - - - -
199A SER* 3.0 25.0 + - - +
201A VAL* 1.3 80.2 - - - +
203A LEU* 1.3 59.2 + - + +
205A CYS* 4.0 0.4 - - - -
206A ALA* 2.9 31.1 + - - +
218A VAL* 5.7 0.4 - - - -
290A ALA* 3.8 19.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
198A ALA* 4.2 15.0 - - + +
199A SER 3.1 9.9 + - - +
200A TYR 4.1 2.0 - - - +
202A ALA* 1.3 77.0 - - - +
204A GLU* 1.3 54.2 + - - +
206A ALA* 4.3 2.5 - - - -
207A GLY* 2.7 34.0 + - - -
218A VAL* 4.5 14.1 - - + -
224A LEU* 4.6 12.3 - - + -
225A LEU* 3.3 45.5 - - + +
233A ALA 6.0 0.2 - - - +
236A ILE* 5.6 3.8 - - + -
237A GLY* 6.1 1.8 - - - +
240A MET* 3.5 25.7 - - + +
247A PHE* 4.4 17.3 - - + -
376A THR* 3.8 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 2.6 56.7 + - + +
71A HIS* 6.0 0.3 + - - +
200A TYR* 2.8 41.4 + - - +
201A VAL* 3.7 6.1 - - - +
203A LEU* 1.3 71.6 - - - +
205A CYS* 1.3 59.6 + - - +
207A GLY* 3.3 2.1 + - - -
208A PHE* 2.9 31.9 + - + -
373A THR 4.2 0.3 - - - +
374A VAL* 3.6 12.7 - - + -
375A PHE* 2.8 45.6 + - - +
376A THR* 4.1 4.2 - - - +
900A FAD 4.6 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 5.4 2.7 - - - -
183A LEU* 4.0 6.3 - - + -
184A PHE* 4.4 11.9 - - - -
195A VAL* 5.2 1.6 - - + -
201A VAL* 2.9 28.9 + - - +
202A ALA 4.1 2.0 - - - +
204A GLU* 1.3 74.4 - - - +
206A ALA* 1.3 68.9 + - - +
207A GLY 3.0 1.3 - - - -
208A PHE* 3.2 30.4 + - + -
209A LEU* 3.0 31.6 + - + +
288A MET* 3.9 37.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 4.2 9.7 - - + +
202A ALA 2.9 19.7 + - - +
203A LEU* 3.6 5.8 - - - +
205A CYS* 1.3 75.6 - - - +
207A GLY* 1.3 64.3 - - - +
209A LEU* 3.9 0.8 - - - +
210A ALA* 2.9 26.5 + - - +
216A VAL* 3.7 20.8 - - + +
218A VAL* 3.5 29.6 - - + -
240A MET* 4.4 6.1 - - + -
245A ILE* 4.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 5.0 0.6 - - - +
203A LEU 2.7 17.5 + - - -
204A GLU 3.5 2.2 - - - -
205A CYS 3.0 0.6 - - - -
206A ALA* 1.3 80.0 - - - +
208A PHE* 1.3 57.6 + - - -
210A ALA* 3.4 2.9 - - - +
211A GLY* 2.9 23.4 + - - -
240A MET* 3.8 5.6 - - - +
245A ILE* 4.5 2.0 - - - -
377A PRO* 3.7 32.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 4.3 22.0 - - + -
70A MET* 3.0 60.1 - - + +
71A HIS* 3.9 15.5 + - + +
74A ALA* 3.9 10.6 - - + +
101A MET* 5.4 2.9 - - + -
183A LEU* 3.8 12.6 - - + -
184A PHE* 3.9 8.7 - + - -
204A GLU* 2.9 32.1 + - + +
205A CYS* 3.2 38.6 - - - -
207A GLY* 1.3 69.8 - - - +
209A LEU* 1.3 96.0 + - + +
211A GLY* 3.2 1.6 + - - -
212A ILE* 2.9 27.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
98A TRP* 3.7 28.9 - - + -
183A LEU* 4.3 17.5 - - + -
190A PRO* 4.0 8.5 - - + -
193A THR* 4.3 28.3 - - + +
195A VAL* 5.0 6.5 - - + -
205A CYS* 3.0 22.4 + - + +
206A ALA 3.9 2.2 - - - +
208A PHE* 1.3 88.9 - - + +
210A ALA* 1.3 62.4 + - - +
212A ILE* 2.8 25.6 - - + +
214A LEU* 3.3 33.6 + - + +
216A VAL* 3.9 9.6 - - + -
288A MET* 5.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ALA 2.9 13.5 + - - +
207A GLY 3.4 0.9 - - - +
209A LEU* 1.3 76.1 - - - +
211A GLY* 1.3 58.7 + - - +
213A GLY* 2.9 21.8 + - - -
214A LEU 3.7 15.2 + - - +
216A VAL* 3.5 8.8 - - + +
243A HIS 5.1 2.2 - - - +
244A GLY* 5.4 1.1 - - - -
245A ILE* 2.9 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 3.8 25.8 - - - +
77A GLY* 5.3 0.3 - - - -
207A GLY 2.9 12.3 + - - -
208A PHE 3.2 5.3 + - - -
210A ALA* 1.3 75.3 - - - +
212A ILE* 1.3 59.2 + - - +
213A GLY* 3.5 0.7 + - - -
88B TRP* 3.6 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 4.6 2.9 - - + +
73A ALA* 3.6 36.8 - - + +
74A ALA 4.1 2.2 - - - +
96A HIS* 3.1 65.5 + - + +
98A TRP* 5.1 7.4 - - + -
101A MET* 4.1 8.5 - - + -
208A PHE* 2.9 13.5 + - + +
209A LEU* 2.8 31.6 + - + +
211A GLY* 1.3 76.3 - - - +
213A GLY* 1.3 58.0 + - - +
214A LEU* 3.8 18.7 - - + +
88B TRP* 4.1 9.0 - - + -
----------------------------------------------------------
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