Contacts of the helix formed by residues 209 - 228 (chain A) in PDB entry 1ZHH
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 GLY 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A SER 3.3 2.3 + - - -
208A GLU* 1.3 77.6 - - - +
210A TYR* 1.3 65.4 + - - -
211A ILE 3.4 2.2 - - - -
212A SER* 3.3 6.8 + - - -
213A ASP* 3.1 32.9 + - - +
236A TYR* 4.8 0.8 - - - -
151B ASN* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 5.7 11.9 - + + -
162A THR* 3.7 31.4 + - - +
180A HIS* 4.0 24.0 - + - -
209A GLY* 1.3 71.6 - - - -
211A ILE* 1.3 74.4 + - + +
213A ASP* 3.1 9.5 + - - +
214A VAL* 3.0 46.8 + - + +
3256B NHE 4.4 16.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A HIS* 3.5 37.0 - - + +
206A PHE* 3.7 46.4 - - + -
209A GLY 3.4 0.4 - - - -
210A TYR* 1.3 84.5 - - + +
212A SER* 1.3 58.9 + - - +
214A VAL* 5.3 1.3 - - - -
215A ARG* 2.9 58.0 + - + +
264A CYS* 4.5 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 3.5 22.9 - - - +
206A PHE* 3.0 25.9 + - - +
207A SER 2.6 27.6 + - - -
209A GLY 3.3 7.0 + - - -
210A TYR 3.3 0.4 - - - -
211A ILE* 1.3 78.1 - - - +
213A ASP* 1.3 60.0 + - - +
216A GLY* 2.9 29.3 + - - +
217A ASP 3.2 3.3 + - - -
236A TYR* 3.7 13.0 - - - -
264A CYS* 4.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLY* 3.1 24.0 + - - +
210A TYR* 3.1 9.3 + - - +
212A SER* 1.3 78.7 - - - +
214A VAL* 1.3 60.1 + - - +
217A ASP* 3.2 41.8 + - - +
218A THR 3.4 0.9 + - - -
236A TYR* 4.7 6.1 + - - -
149B PHE* 3.3 13.4 - - + -
150B SER* 4.9 8.5 + - - +
151B ASN* 4.6 14.6 + - - +
152B ASN* 5.3 0.9 + - - -
3256B NHE 3.4 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 5.7 1.3 - - - +
180A HIS* 3.6 13.7 - - + -
181A ALA* 3.4 38.0 - - + +
184A SER* 3.7 4.7 + - - -
210A TYR* 3.0 47.6 + - + +
211A ILE 4.6 0.9 - - - +
213A ASP* 1.3 74.9 - - - +
215A ARG* 1.3 60.8 + - - +
218A THR* 3.0 23.9 + - - +
149B PHE* 4.9 1.3 - - + -
3256B NHE 3.7 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A HIS* 3.1 46.5 + - + +
184A SER* 3.1 20.7 + - - +
206A PHE* 5.8 0.4 - - - -
211A ILE* 2.9 29.8 + - + +
214A VAL* 1.3 78.6 - - - +
216A GLY* 1.3 62.6 + - - +
219A PHE* 3.5 4.3 + - - +
262A TYR* 2.8 24.2 + - - +
264A CYS* 2.9 38.7 + - + -
265A SER* 4.0 11.5 - - - +
266A THR 5.3 0.2 - - - +
289A TRP* 3.4 49.2 + - + +
310A ARG* 3.8 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 4.9 1.3 - - - -
205A TYR* 4.1 9.2 - - - -
212A SER 2.9 15.0 + - - -
215A ARG* 1.3 77.2 - - - +
217A ASP* 1.3 61.0 + - - -
218A THR 3.2 1.1 - - - -
219A PHE* 3.1 5.2 + - - +
220A ILE* 3.0 30.5 + - - +
262A TYR* 4.1 4.6 - - - -
264A CYS* 3.4 19.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 2.5 35.0 + - - -
212A SER 3.2 4.1 + - - +
213A ASP* 3.2 32.5 + - - +
216A GLY* 1.3 71.6 - - - +
218A THR* 1.3 59.3 + - - +
220A ILE* 3.8 9.8 - - - +
221A HIS* 3.1 29.3 + - - +
236A TYR* 4.5 5.0 + - - -
148B SER 3.9 17.0 - - - +
149B PHE* 3.9 10.6 - - + -
150B SER* 4.9 6.4 + - - -
171B ARG* 4.1 18.7 + - - -
185B PHE* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA* 4.1 16.7 - - + +
184A SER* 4.4 5.8 - - - -
185A ARG* 3.9 39.0 + - + +
213A ASP 3.4 2.6 + - - -
214A VAL* 3.0 31.8 + - - +
216A GLY 3.2 0.2 - - - -
217A ASP* 1.3 76.4 - - - +
219A PHE* 1.3 64.2 + - - +
221A HIS* 3.6 5.8 + - - +
222A GLN* 3.2 23.8 + - + +
149B PHE* 4.0 17.2 - - - -
3256B NHE 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A SER* 3.9 6.7 - - - +
188A ALA* 3.5 40.2 - - + -
191A PHE* 3.8 15.3 - + - -
201A TYR* 3.9 19.1 - + - -
215A ARG 3.5 13.8 + - - +
216A GLY 3.1 10.0 + - - +
218A THR* 1.3 77.4 - - - +
220A ILE* 1.3 71.1 + - + +
222A GLN* 3.3 2.1 + - - +
223A VAL* 3.1 42.4 + - + +
260A PHE* 3.7 18.8 - + - -
262A TYR* 3.3 56.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TYR* 3.5 24.0 - - + +
203A VAL* 3.8 27.6 - - + -
205A TYR* 3.5 29.2 - - + +
216A GLY 3.0 17.5 + - - +
217A ASP* 3.8 9.9 - - - +
219A PHE* 1.3 76.2 - - + +
221A HIS* 1.3 65.8 + - - +
224A ASN* 3.1 43.2 + - - +
231A LEU* 4.1 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASP 3.1 19.8 + - - +
218A THR* 3.8 6.4 + - - +
220A ILE* 1.3 78.5 - - - +
222A GLN* 1.3 58.4 + - - +
224A ASN* 3.9 3.6 - - - +
225A ARG* 3.1 65.4 + - + +
145B ASN* 4.8 11.9 + - - -
148B SER* 3.5 35.0 + - - +
149B PHE* 6.2 1.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ARG* 3.0 43.6 + - - +
188A ALA* 3.6 19.8 - - + +
189A THR* 3.2 28.9 + - - +
218A THR* 3.2 15.2 + - + +
219A PHE 3.9 2.7 - - - +
220A ILE 3.3 0.4 - - - -
221A HIS* 1.3 83.4 + - - +
223A VAL* 1.3 58.8 + - - +
225A ARG* 3.3 15.6 + - - +
226A ASP* 2.9 50.6 + - + +
227A ASN* 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ALA* 3.8 26.0 - - + +
191A PHE* 4.9 0.4 - - + -
201A TYR* 3.4 33.0 - - + +
219A PHE* 3.1 43.7 + - + +
220A ILE 3.6 0.2 - - - +
222A GLN* 1.3 76.3 - - - +
224A ASN* 1.3 64.0 + - - +
227A ASN* 3.1 31.2 + - - +
228A ASN 3.1 6.6 + - - -
229A PHE* 3.3 32.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A TYR* 2.9 27.2 + - - -
220A ILE* 3.1 27.1 + - - +
221A HIS* 3.9 4.7 - - - +
223A VAL* 1.3 79.8 - - - +
225A ARG* 1.3 58.4 + - - +
228A ASN* 3.2 25.5 + - - +
229A PHE 3.1 25.7 + - - +
231A LEU* 4.7 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ARG* 5.9 2.6 - - - +
221A HIS* 3.1 51.9 + - + +
222A GLN* 3.3 16.8 + - - +
224A ASN* 1.3 78.6 - - - +
226A ASP* 1.3 87.2 + - - +
228A ASN* 4.7 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LYS* 4.2 13.7 + - - -
222A GLN* 2.9 42.1 + - + +
225A ARG* 1.3 103.7 + - - +
227A ASN* 1.3 75.0 + - - +
228A ASN* 3.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ALA 4.6 1.9 - - - +
192A GLY* 3.3 41.3 + - - -
195A PHE 5.3 0.4 + - - +
197A LYS* 3.2 35.3 - - + +
198A HIS 3.4 0.2 + - - -
222A GLN* 4.8 1.0 - - - +
223A VAL* 3.1 24.6 + - - +
226A ASP* 1.3 94.4 + - - +
228A ASN* 1.3 74.6 + - - +
229A PHE* 3.2 20.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LYS* 4.2 19.9 - - + +
198A HIS* 3.2 45.9 + - + +
223A VAL 3.1 3.2 + - - -
224A ASN 3.2 18.9 + - - +
225A ARG 4.9 4.5 + - - +
226A ASP 5.0 1.4 + - - -
227A ASN* 1.3 82.0 + - - +
229A PHE* 1.3 67.2 + - - +
230A GLU* 3.6 3.5 + - - +
----------------------------------------------------------
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