Contacts of the helix formed by residues 214 - 227 (chain B) in PDB entry 1ZQ1
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 ASP 214 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ALA* 3.6 2.0 - - - -
205B GLN* 3.0 21.6 + - - +
206B ARG* 2.9 27.6 + - - +
213B SER* 1.3 73.9 + - - +
215B ALA* 1.3 63.6 + - - +
216B ALA 3.4 1.6 - - - -
217B MSE 3.8 3.9 + - - +
218B ASN* 2.4 47.0 + - - -
237B MSE 3.4 9.4 - - - +
238B HIS* 3.2 26.7 + - + +
243B ASP* 5.5 0.4 - - - -
262B ARG* 3.8 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ILE* 3.8 22.2 - - + +
203B GLY 5.1 1.1 - - - -
204B ALA* 3.6 18.6 - - + +
208B SER* 3.5 23.3 - - - -
213B SER* 3.1 17.0 + - - +
214B ASP* 1.3 77.3 - - - +
216B ALA* 1.3 54.9 + - - +
218B ASN* 3.5 4.0 - - - +
219B LEU* 2.7 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ILE* 5.0 0.6 + - - +
127B LEU* 3.6 17.2 - - + +
213B SER* 4.9 5.2 + - - +
214B ASP 3.4 0.8 - - - -
215B ALA* 1.3 77.1 - - - +
217B MSE 1.3 66.9 + - - +
219B LEU* 2.8 5.2 + - - +
220B ILE* 2.8 29.9 + - + +
51D ARG* 3.3 48.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B SER 5.6 0.4 + - - -
214B ASP* 3.8 4.0 + - - +
215B ALA 3.6 0.2 - - - -
216B ALA* 1.3 78.7 - - - +
218B ASN* 1.3 57.1 + - - +
220B ILE* 3.5 12.1 + - + +
221B CYS* 2.9 32.1 + - - -
238B HIS* 3.8 29.8 - - + -
243B ASP* 3.1 42.6 - - + +
244B THR 4.0 8.5 - - - +
245B TYR 5.0 1.1 - - - -
246B CYS* 4.4 8.1 - - - -
278B PRO* 3.2 22.9 - - + -
49D ARG* 2.8 37.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 3.7 19.7 - - + +
203B GLY 3.5 6.2 + - - +
214B ASP* 2.4 48.7 + - - +
215B ALA 3.5 3.1 - - - +
217B MSE 1.3 72.5 - - - +
219B LEU* 1.3 56.5 + - - +
221B CYS* 3.2 2.3 + - - +
222B SER* 2.7 37.2 + - - -
236B VAL* 4.4 1.9 - - - +
237B MSE 2.8 36.4 - - - +
238B HIS* 3.1 16.6 + - - -
246B CYS* 3.2 18.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 4.0 21.5 - - + -
103B ILE* 3.3 39.5 - - + -
123B LEU* 4.8 8.3 - - + -
127B LEU* 3.2 27.8 - - + -
130B ILE* 3.9 22.0 - - + -
173B VAL* 4.4 12.1 - - + -
202B VAL* 4.2 4.4 - - + +
215B ALA 2.7 16.6 + - - +
216B ALA 2.8 7.6 + - - +
218B ASN* 1.3 71.4 - - - +
220B ILE* 1.3 52.5 + - - +
222B SER* 2.7 24.6 + - - -
223B VAL* 2.8 26.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 4.3 6.1 - - + -
129B GLU* 3.6 51.4 - - + +
130B ILE* 3.8 16.4 - - + +
133B VAL* 5.3 1.8 - - + +
216B ALA* 2.8 34.5 + - + +
217B MSE 3.6 10.5 - - - +
219B LEU* 1.3 72.6 - - - +
221B CYS* 1.3 59.9 + - - +
223B VAL* 3.6 2.4 + - - +
224B ARG* 2.9 38.2 + - + +
278B PRO* 4.0 33.7 - - + +
49D ARG* 6.3 0.2 - - - +
51D ARG* 4.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B MSE 2.9 26.1 + - - +
218B ASN 3.7 2.9 - - - +
220B ILE* 1.3 76.8 - - - +
222B SER* 1.3 63.1 + - - +
224B ARG* 3.4 6.8 + - - +
225B MSE 3.1 17.7 + - - +
236B VAL* 3.8 1.6 - - + -
246B CYS* 3.4 30.1 - - + -
276B ILE* 3.1 40.7 - - + +
277B TRP 4.2 0.9 - - - -
278B PRO* 3.8 33.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B VAL* 4.0 11.6 - - - +
200B VAL* 3.1 25.6 - - - +
202B VAL* 3.1 34.7 - - - +
218B ASN 2.7 10.1 + - - -
219B LEU* 2.7 14.6 + - - -
221B CYS* 1.3 75.5 - - - +
223B VAL* 1.3 57.7 + - - -
225B MSE 3.0 5.9 + - - +
226B ALA* 2.9 26.0 + - - +
236B VAL* 3.6 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 4.5 9.0 - - + -
96B ILE* 4.9 2.9 - - + -
130B ILE* 3.5 34.8 - - + +
133B VAL* 4.1 15.5 - - + -
134B ALA* 4.1 25.6 - - + +
136B VAL* 4.5 13.0 - - + -
173B VAL* 4.2 9.9 - - + -
219B LEU* 2.8 27.1 + - + +
220B ILE 4.1 1.8 - - - +
222B SER* 1.3 72.7 - - - +
224B ARG* 1.3 62.0 + - - +
226B ALA* 3.1 20.4 + - - +
227B THR* 3.3 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLU* 5.1 3.0 + - - +
132B GLU* 6.3 0.2 - - - +
133B VAL* 3.7 42.2 - - + +
220B ILE* 2.9 28.6 + - + +
221B CYS* 3.6 10.1 - - - +
222B SER 3.1 0.6 - - - -
223B VAL* 1.3 79.3 - - - +
225B MSE 1.3 63.4 + - + +
227B THR* 3.2 17.9 + - - -
228B SER* 3.5 5.4 + - - -
276B ILE* 5.3 5.6 - - + -
277B TRP 4.7 3.1 - - - +
278B PRO 3.2 27.1 + - - -
279B ASN 3.7 7.5 + - - -
280B GLY* 3.4 30.5 + - - +
282B ILE* 5.2 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B PRO* 3.4 8.9 - - - +
200B VAL* 4.0 5.4 - - + -
221B CYS 3.1 5.7 + - - +
222B SER 3.0 8.7 + - - +
224B ARG* 1.3 72.1 - - - +
226B ALA* 1.3 59.5 + - - +
227B THR 2.9 2.2 - - - -
228B SER* 2.3 59.5 + - - +
230B VAL* 4.3 10.5 - - + -
234B MSE 3.6 40.1 - - + +
236B VAL* 3.8 12.1 - - + -
248B ALA* 3.8 12.6 - - + -
273B ILE* 5.0 5.2 - - + -
274B ALA* 5.1 5.6 - - + -
276B ILE* 3.3 50.3 - - + -
282B ILE* 3.6 14.1 - - + -
284B PHE* 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 3.8 20.2 - - + -
170B TYR 3.8 0.6 - - - +
171B GLY* 3.6 17.4 + - - -
172B VAL 4.4 1.1 - - - +
173B VAL* 3.7 28.0 - - + -
198B PRO* 3.0 31.3 - - - +
200B VAL* 4.2 4.9 - - - +
222B SER 2.9 5.8 + - - -
223B VAL 3.1 11.2 + - - +
225B MSE 1.3 76.6 - - - +
227B THR* 1.3 56.4 + - - +
292B ARG* 3.4 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PRO* 4.5 8.6 - - + +
94B VAL* 4.7 1.6 - - - +
133B VAL* 4.4 14.7 - - + +
134B ALA* 4.4 11.8 - - - +
170B TYR* 3.6 34.8 + - + -
223B VAL 3.3 10.8 + - - -
224B ARG* 3.2 14.1 + - - -
225B MSE 2.9 0.4 - - - -
226B ALA* 1.3 77.2 - - - +
228B SER* 1.3 65.1 + - - +
292B ARG* 3.9 1.1 - - - -
----------------------------------------------------------
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