Contacts of the helix formed by residues 198 - 216 (chain D) 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 HIS 198 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ASP* 3.0 33.5 + - - -
10D TYR* 4.3 9.9 - + + -
15D LEU* 3.5 4.2 - - - +
17D VAL* 5.3 0.4 - - - -
151D TRP* 3.0 37.4 + + + -
196D ILE* 3.6 8.3 - - - +
197D HIS* 1.3 81.2 - - + +
199D PRO* 1.3 89.6 - - + +
200D GLU* 2.8 36.0 + - + +
201D GLN* 3.0 33.1 + - + +
202D ALA* 3.0 12.0 + - - +
255D ILE* 5.3 1.6 - - - -
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Residues in contact with PRO 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D TYR* 3.3 43.7 - - + +
15D LEU* 3.8 4.7 - - + -
198D HIS* 1.3 98.5 - - + +
200D GLU* 1.3 60.1 + - + +
202D ALA* 3.6 5.4 + - - +
203D LYS 3.5 13.5 + - - -
251D ILE* 4.1 0.2 - - - +
252D PRO* 3.5 40.9 - - + +
255D ILE* 4.0 26.9 - - + -
256D GLU* 4.8 4.0 - - + +
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Residues in contact with GLU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D TRP* 3.6 24.2 - - + -
198D HIS* 2.8 19.7 + - + +
199D PRO* 1.3 73.0 - - + +
201D GLN* 1.3 63.9 + - - +
202D ALA 3.1 2.0 - - - -
203D LYS* 3.3 24.8 + - - +
204D VAL* 2.9 30.8 + - - +
252D PRO* 3.3 23.4 - - - +
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Residues in contact with GLN 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D THR* 3.2 29.2 - - + +
151D TRP* 3.7 26.1 - - + +
152D GLY 3.5 5.7 + - - -
153D ALA 4.8 0.6 + - - -
154D VAL* 3.4 25.7 - - + +
196D ILE* 3.4 5.5 - - + +
197D HIS* 2.8 53.5 + - - -
198D HIS* 3.0 23.9 + - + +
200D GLU* 1.3 80.8 - - - +
202D ALA* 1.3 58.6 + - - +
204D VAL* 3.3 3.9 + - - +
205D VAL* 3.1 22.7 + - - +
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Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 4.4 4.7 - - + -
19D LEU* 4.1 3.4 - - + +
196D ILE* 4.0 21.5 - - + +
198D HIS 3.0 8.6 + - - +
199D PRO 3.6 4.5 - - - +
200D GLU 3.1 0.2 - - - -
201D GLN* 1.3 75.9 - - - +
203D LYS* 1.3 56.9 + - - +
204D VAL 3.1 0.3 + - - -
205D VAL* 3.2 1.9 + - - +
206D ALA* 2.7 38.7 + - - +
230D LEU* 4.8 3.4 - - + -
251D ILE* 3.6 6.5 - - + -
255D ILE* 3.3 33.7 - - + -
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Residues in contact with LYS 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D PRO 3.5 2.4 + - - -
200D GLU* 3.3 20.9 + - - +
202D ALA* 1.3 78.0 - - - +
204D VAL* 1.3 55.0 + - + +
206D ALA* 4.1 6.3 - - - -
207D LYS* 2.7 42.8 + - + +
248D LEU* 3.5 23.5 - - + +
249D ASP* 2.7 38.3 + - - +
251D ILE* 3.8 5.7 - - - +
252D PRO* 3.5 33.7 - - + +
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D VAL* 5.3 2.5 - - + -
148D GLU 4.5 7.4 - - - +
149D THR* 2.9 24.2 - - - +
150D PRO* 4.3 8.7 - - + -
151D TRP* 3.5 26.0 - - + -
200D GLU* 2.9 24.5 + - - +
201D GLN 3.4 2.7 - - - +
202D ALA 3.1 0.2 - - - -
203D LYS* 1.3 76.5 - - + +
205D VAL* 1.3 55.6 + - - +
207D LYS* 3.0 8.4 + - - +
208D PHE* 2.8 36.5 + - + +
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Residues in contact with VAL 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.3 3.6 - - + -
147D VAL* 3.8 31.6 - - + +
149D THR* 4.6 4.7 - - - +
154D VAL* 3.6 40.2 - - + -
156D ILE* 5.2 1.8 - - + -
192D THR* 4.0 16.2 - - + +
196D ILE* 4.2 6.1 - - + -
201D GLN 3.1 14.0 + - - +
202D ALA 3.8 4.7 - - - +
204D VAL* 1.3 78.5 - - - +
206D ALA* 1.3 63.8 + - - +
208D PHE* 3.8 0.7 - - - +
209D ILE* 3.1 42.3 + - + +
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.7 17.4 - - + +
21D ILE* 4.3 8.8 - - - +
202D ALA 2.7 22.2 + - - +
203D LYS 3.7 0.4 - - - +
205D VAL* 1.3 74.3 - - - +
207D LYS* 1.3 63.5 + - - +
209D ILE* 3.8 2.3 - - - +
210D GLY* 3.1 18.5 + - - -
228D GLN* 4.0 9.2 - - - +
248D LEU* 3.3 8.9 - - + +
251D ILE* 3.2 31.4 - - + -
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Residues in contact with LYS 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LYS* 2.7 28.4 + - + +
204D VAL* 3.5 5.4 - - - +
206D ALA* 1.3 70.4 - - - +
208D PHE* 1.3 69.6 + - - +
210D GLY* 2.7 14.3 + - - -
211D ASP* 2.8 35.5 + - - +
248D LEU* 3.2 29.1 - - + +
460D GLN* 3.7 28.7 - - - +
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Residues in contact with PHE 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LEU 3.3 26.9 - - - -
111D LEU* 3.8 11.7 - - + -
112D ASN* 5.3 3.4 - - - -
146D LYS 4.6 4.9 - - - -
147D VAL* 3.4 40.2 - - + -
148D GLU 5.6 0.4 - - - -
204D VAL* 2.8 21.7 + - + +
205D VAL 3.8 2.7 - - - +
207D LYS* 1.3 72.9 - - - +
209D ILE* 1.3 65.8 + - - +
211D ASP* 2.7 25.1 + - + +
212D ALA* 2.8 13.3 + - + +
458D LEU* 3.2 35.4 - - + -
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Residues in contact with ILE 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 5.0 0.4 - - + -
21D ILE* 3.9 25.6 - - + -
111D LEU* 4.4 18.4 - - + -
147D VAL* 4.4 9.4 - - + -
156D ILE* 4.9 3.8 - - + -
190D ILE* 3.3 47.6 - - + +
192D THR* 4.6 8.5 - - - +
205D VAL* 3.1 33.2 + - + +
206D ALA* 3.8 4.0 - - - +
208D PHE* 1.3 76.9 - - - +
210D GLY* 1.3 63.8 + - - +
212D ALA* 3.0 10.5 + - - +
213D LEU* 2.9 29.9 + - + +
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Residues in contact with GLY 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE* 5.9 1.3 - - - -
23D ARG* 4.8 5.9 + - - -
206D ALA 3.1 8.2 + - - -
207D LYS* 2.7 16.4 + - - -
209D ILE* 1.3 76.8 - - - +
211D ASP* 1.3 60.6 + - - -
213D LEU* 3.5 10.7 + - - +
214D ARG* 3.2 19.6 + - - +
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Residues in contact with ASP 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D LYS* 2.8 50.7 + - - +
208D PHE* 2.7 19.0 + - + +
210D GLY* 1.3 70.6 - - - +
212D ALA* 1.3 54.6 + - - +
214D ARG* 2.8 6.8 + - - +
215D ALA 2.7 31.7 + - - -
458D LEU* 4.9 6.1 - - + -
459D PRO* 3.4 40.1 - - + +
460D GLN* 5.2 6.2 + - - +
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Residues in contact with ALA 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ILE* 4.8 3.8 - - + +
110D LEU* 3.1 49.3 - - + +
111D LEU* 3.8 20.4 - - + -
208D PHE* 2.8 13.5 + - + +
209D ILE 3.0 8.9 + - - +
211D ASP* 1.3 76.3 - - - +
213D LEU* 1.3 61.4 + - - +
215D ALA* 3.4 11.1 - - - +
216D THR* 3.5 5.0 - - - +
458D LEU* 4.5 8.3 - - + +
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Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE* 4.6 10.3 - - + -
23D ARG* 3.9 40.8 - - + +
107D ILE* 3.2 46.0 - - + -
188D ILE* 4.5 6.1 - - + -
190D ILE* 3.9 13.5 - - + -
209D ILE* 2.9 30.9 + - + +
210D GLY* 3.7 9.0 - - - +
212D ALA* 1.3 72.9 - - - +
214D ARG* 1.3 61.5 + - - +
216D THR* 2.6 28.8 + - - -
217D LYS 4.1 0.2 + - - -
219D VAL* 3.1 18.2 - - + +
226D ILE* 5.9 0.4 - - + -
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Residues in contact with ARG 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ARG* 5.3 3.8 - - - +
210D GLY 3.2 11.1 + - - +
211D ASP* 2.8 9.7 + - - +
213D LEU* 1.3 76.2 - - - +
215D ALA* 1.3 55.7 + - - +
217D LYS* 2.7 34.1 + - - +
219D VAL* 5.3 3.6 - - - -
459D PRO* 4.0 16.4 - - + -
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Residues in contact with ALA 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D LEU* 4.1 2.9 - - + -
211D ASP 2.7 11.0 + - - +
212D ALA 3.4 13.9 - - - +
214D ARG* 1.3 76.4 - - - +
216D THR* 1.3 55.8 + - - +
217D LYS* 3.0 9.4 + - - +
456D PRO* 3.0 26.9 - - + +
457D GLU* 3.7 35.5 + - - +
458D LEU* 4.0 15.3 - - + -
459D PRO* 4.5 2.6 - - - +
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Residues in contact with THR 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D VAL* 4.5 9.8 - - + +
106D GLN* 3.2 33.5 + - + +
107D ILE* 3.5 31.6 - - + -
110D LEU* 4.2 4.7 - - + -
212D ALA 3.5 13.0 - - - +
213D LEU 2.6 19.3 + - - +
215D ALA* 1.3 76.0 - - - +
217D LYS* 1.3 55.8 + - - +
218D LYS* 2.6 27.6 + - - +
219D VAL* 3.2 14.7 - - - +
456D PRO* 4.2 0.9 - - - -
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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) + - + + + + + -
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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