Contacts of the helix formed by residues 208 - 221 (chain N) in PDB entry 1CZA
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 ASN 208 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N THR* 5.8 1.1 - - + +
153N THR* 4.1 0.4 - - - -
154N PHE 3.9 4.7 - - - -
155N SER* 3.7 2.6 - - - +
156N PHE 3.6 21.6 + - - +
160N GLN* 5.3 3.0 + - - -
207N VAL* 1.3 79.3 - - - +
209N ASP* 1.3 63.3 + - - +
210N THR* 2.7 30.6 + - - +
211N VAL* 3.2 14.1 + - + +
212N GLY 3.1 17.2 + - - -
235N ASN* 3.0 5.2 + - - -
258N ASN* 3.6 21.8 - - + +
918N GLC 2.9 42.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 209 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153N THR* 3.6 15.8 - - + +
155N SER* 3.2 14.8 - - - -
208N ASN* 1.3 68.6 - - - +
210N THR* 1.3 67.0 + - - +
212N GLY 4.3 0.2 - - - +
213N THR* 2.9 28.8 + - - -
229N ILE* 3.7 12.1 - - + +
449N SER* 3.6 4.6 + - - +
918N GLC 2.6 47.2 + - - -
919N G6P 2.7 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208N ASN* 2.7 24.3 + - - +
209N ASP* 1.3 78.5 + - - +
211N VAL* 1.3 66.3 + - - +
213N THR* 3.3 5.0 + - - -
214N MET 3.0 24.1 + - - -
227N GLY* 3.4 10.5 - - - +
229N ILE* 3.7 15.9 - - + -
235N ASN* 3.5 47.9 + - + +
236N ALA* 3.6 2.0 - - - +
237N CYS* 3.3 31.5 - - - +
258N ASN* 4.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N THR* 3.6 29.2 - - + -
68N VAL* 3.9 31.4 - - + -
207N VAL* 4.0 14.6 - - + -
208N ASN* 3.2 21.0 + - + +
210N THR* 1.3 87.7 + - - +
212N GLY* 1.3 65.1 + - - +
214N MET* 3.4 3.1 + - + +
215N MET* 3.0 34.9 + - + +
237N CYS* 3.6 8.7 - - + -
256N CYS* 3.7 16.6 - - - -
258N ASN* 5.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 212 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207N VAL* 4.5 8.4 - - - +
208N ASN 3.1 12.9 + - - -
209N ASP 3.3 2.6 + - - -
211N VAL* 1.3 75.7 - - - +
213N THR* 1.3 57.0 + - - +
215N MET* 3.3 1.2 + - - -
216N THR* 2.8 35.1 + - - -
449N SER* 3.8 23.8 - - - -
452N GLY* 3.4 5.2 - - - -
453N ALA 4.3 9.0 - - - -
456N VAL* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 213 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209N ASP 2.9 18.3 + - - -
210N THR* 3.4 7.4 - - - -
212N GLY* 1.3 76.3 - - - +
214N MET* 1.3 57.1 + - - +
216N THR* 3.3 5.9 + - - -
217N CYS* 2.9 33.8 + - - +
228N LEU 4.1 4.5 - - - +
229N ILE* 3.5 13.4 - - - +
411N GLY 3.5 31.6 - - - +
412N VAL* 3.7 17.0 - - - +
413N ASP* 3.9 8.2 + - - +
445N SER* 3.9 11.5 + - - -
449N SER* 3.7 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 214 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68N VAL* 4.7 2.9 - - + -
71N ILE* 4.2 10.6 - - + +
210N THR 3.0 11.4 + - - +
211N VAL* 3.4 3.6 + - + +
213N THR* 1.3 76.5 - - - +
215N MET* 1.3 78.0 + - + +
217N CYS* 4.8 0.2 - - - -
218N GLY* 2.8 32.9 + - - -
224N CYS* 3.5 23.1 - - - -
225N GLU 3.9 17.3 - - - +
226N VAL* 3.9 5.6 - - - +
227N GLY* 3.6 19.7 - - - -
237N CYS* 4.0 5.6 - - - -
238N TYR* 4.8 0.2 - - - -
239N MET* 3.6 29.4 - - - +
256N CYS* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 215 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68N VAL* 3.7 17.3 - - + -
70N SER 3.3 27.1 - - - +
71N ILE* 3.7 11.0 - - - -
72N PRO* 3.5 31.4 - - + +
211N VAL* 3.0 23.1 + - + +
214N MET* 1.3 80.9 - - + +
216N THR* 1.3 59.7 - - - +
219N TYR* 3.0 27.0 + - - +
452N GLY* 3.5 22.8 - - - +
455N MET* 4.4 7.6 - - + -
456N VAL* 3.7 33.4 - - + +
459N VAL* 6.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 216 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212N GLY 2.8 20.9 + - - -
213N THR 3.6 4.5 - - - -
215N MET* 1.3 73.5 - - - +
217N CYS* 1.3 63.2 + - - +
219N TYR* 3.5 15.1 - - - +
220N ASP* 3.9 10.7 + - - +
445N SER* 3.6 24.0 - - - +
446N GLU 5.4 0.4 - - - +
447N SER* 4.4 9.0 - - - +
448N GLY 3.0 18.7 + - - +
449N SER 3.9 0.2 + - - -
451N LYS* 3.8 26.9 - - + +
452N GLY* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 217 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213N THR 2.9 17.5 + - - +
216N THR* 1.3 78.9 - - - +
218N GLY* 1.3 49.4 + - - +
220N ASP* 3.0 9.8 + - - +
221N ASP* 2.8 34.1 + - - +
224N CYS* 4.0 11.9 - - + -
411N GLY* 3.5 32.1 - - - -
443N LEU* 3.6 29.2 - - + +
444N LEU 4.3 2.2 - - - -
445N SER* 3.8 26.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 218 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71N ILE* 3.9 19.6 - - - +
72N PRO* 3.9 12.4 - - - +
214N MET 2.8 21.8 + - - -
215N MET 3.7 1.6 - - - -
217N CYS* 1.3 69.5 - - - +
219N TYR* 1.3 66.5 + - - +
221N ASP 3.3 23.8 + - - +
222N GLN* 4.1 1.9 + - - +
224N CYS* 3.7 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 219 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72N PRO* 3.7 18.3 - - + +
74N GLY* 5.0 9.8 - - - -
76N GLU* 4.3 11.7 - - + -
97N VAL* 4.9 3.2 - - + +
98N ASN* 3.7 22.3 + - - -
104N ASN* 3.7 29.1 - - + +
105N VAL* 3.8 17.2 - - + +
215N MET 3.0 12.7 + - - +
216N THR* 3.5 13.5 - - - +
217N CYS 3.2 0.2 - - - -
218N GLY* 1.3 79.6 - - - +
220N ASP* 1.3 65.5 + - - +
451N LYS* 3.7 19.5 - - - -
455N MET* 3.4 37.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 220 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104N ASN* 5.8 1.4 + - - -
216N THR* 4.3 9.6 - - - +
217N CYS* 3.0 8.8 + - - +
219N TYR* 1.3 93.8 - - - +
221N ASP* 1.3 60.1 + - - +
222N GLN 4.2 1.2 + - - -
441N ARG* 5.4 1.0 + - - +
443N LEU* 4.5 14.0 - - + +
451N LYS* 4.1 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 221 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71N ILE* 3.9 0.2 - - - +
217N CYS 2.8 10.9 + - - +
218N GLY* 3.3 17.8 - - - -
219N TYR 3.6 0.4 - - - -
220N ASP* 1.3 79.5 - - - +
222N GLN* 1.3 62.3 + - - +
223N HIS* 2.8 42.6 + - - +
224N CYS* 3.1 10.9 + - - +
407N ARG* 4.7 3.7 + - - -
409N THR* 2.7 29.6 + - + +
441N ARG* 2.8 35.3 + - - +
443N LEU* 4.0 8.1 - - + -
----------------------------------------------------------
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