Contacts of the helix formed by residues 195 - 209 (chain D) in PDB entry 3ZXR
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 TYR 195 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138D ILE* 3.8 54.6 + - + -
140D ASP* 4.8 0.5 + - - -
157D ALA* 4.0 6.9 - - - +
158D ILE* 3.8 12.2 + - + +
159D SER* 3.0 45.1 + - - -
193D ASP* 3.1 2.4 + - - -
194D GLN* 1.3 93.1 - - + +
196D VAL* 1.3 58.8 + - - +
197D ASP 3.4 1.8 - - - -
198D LEU* 3.4 14.7 + - + +
199D ARG* 2.9 45.5 + - - +
218D HIS* 4.0 13.5 - + - -
224D GLY* 3.4 23.4 - - - -
258D LYS* 4.4 17.3 - - - -
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Residues in contact with VAL 196 (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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34C HIS* 4.0 12.1 - - + -
84C ARG* 3.4 52.5 - - + +
190D ALA* 4.3 13.0 - - + -
193D ASP* 3.4 37.9 - - + +
194D GLN 3.6 2.0 + - - -
195D TYR* 1.3 77.6 - - - +
197D ASP* 1.3 65.3 + - - +
199D ARG* 3.4 10.1 + - - +
200D ASP* 3.0 23.7 + - - +
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Residues in contact with ASP 197 (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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83C PHE 4.8 4.4 - - - +
84C ARG* 3.7 16.1 - - - +
85C ALA* 3.6 32.5 + - - +
86C ALA 5.0 0.3 + - - -
255C GLN* 5.3 5.0 + - - -
195D TYR 3.4 0.4 - - - -
196D VAL* 1.3 76.0 - - - +
198D LEU* 1.3 65.1 + - - +
200D ASP* 3.3 11.2 + - - +
201D LYS* 3.1 33.0 + - - +
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Residues in contact with LEU 198 (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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138D ILE* 3.8 25.8 - - + -
195D TYR* 3.4 18.2 + - + +
196D VAL 3.3 0.8 - - - -
197D ASP* 1.3 79.4 - - - +
199D ARG* 1.3 61.1 + - - +
201D LYS* 2.9 21.3 + - + +
202D MET* 3.0 25.0 + - + +
252D THR* 4.2 14.4 - - + +
253D ALA* 4.5 1.3 - - - -
256D ASN* 3.8 36.3 - - + +
258D LYS* 3.8 32.3 - - + -
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Residues in contact with ARG 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C HIS* 4.2 11.7 - - - -
36C THR* 5.4 3.8 + - - -
138D ILE* 4.3 17.3 - - + -
193D ASP* 2.7 42.8 + - - -
195D TYR* 2.9 29.8 + - - +
196D VAL* 3.9 11.4 - - - +
198D LEU* 1.3 76.0 - - - +
200D ASP* 1.3 52.6 + - - +
202D MET* 3.1 15.8 + - - +
203D LEU* 2.8 43.8 + - + +
216D GLY 4.5 3.4 + - - -
217D HIS* 3.5 23.8 - - - +
218D HIS* 3.4 26.5 - - - +
226D ALA* 3.6 25.9 - - + +
227D GLU 4.9 2.2 - - - -
228D ILE* 4.1 8.6 - - + +
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Residues in contact with ASP 200 (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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20C TYR* 3.4 12.5 + - + -
36C THR* 4.9 0.2 - - - -
84C ARG* 2.7 50.8 + - - +
86C ALA* 3.8 29.7 + - + +
88C THR* 4.3 0.2 + - - -
196D VAL 3.0 14.4 + - - +
197D ASP* 3.3 15.6 - - - +
199D ARG* 1.3 76.0 - - - +
201D LYS* 1.3 56.1 + - + +
203D LEU* 3.2 14.1 + - - +
204D THR* 2.8 33.6 + - - -
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Residues in contact with LYS 201 (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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197D ASP* 3.1 22.9 + - - +
198D LEU* 2.9 13.7 + - + +
200D ASP* 1.3 73.4 - - + +
202D MET* 1.3 60.3 + - - +
204D THR* 3.4 6.0 + - - -
205D ASN* 2.9 37.4 + - - +
252D THR* 3.9 13.2 - - + -
256D ASN* 3.1 34.1 + - - +
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Residues in contact with MET 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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136D PHE* 3.9 23.6 - - + -
138D ILE* 4.0 22.2 - - + -
198D LEU* 3.0 19.8 + - + +
199D ARG* 3.3 21.8 - - - +
201D LYS* 1.3 75.7 - - - +
203D LEU* 1.3 61.5 + - - +
205D ASN* 3.4 2.3 + - - +
206D LEU* 3.0 30.4 + - - +
228D ILE* 3.7 12.3 - - + -
248D ILE* 4.4 0.6 - - - +
249D ILE* 3.6 40.8 - - + +
252D THR* 3.7 24.0 - - + +
253D ALA* 4.0 18.8 - - + +
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Residues in contact with LEU 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 3.2 34.8 - - + +
36C THR* 4.4 12.8 - - + +
38C PRO* 5.8 2.9 - - + -
199D ARG* 2.8 25.5 + - + +
200D ASP* 3.5 17.5 - - - +
202D MET* 1.3 71.6 - - - +
204D THR* 1.3 58.7 + - - +
206D LEU* 3.3 6.9 + - - +
207D ILE* 2.9 34.0 + - + +
213D LEU* 3.8 18.2 - - + +
215D LYS* 4.3 8.5 - - - +
216D GLY* 4.4 13.9 - - - +
228D ILE* 3.7 33.2 - - + -
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Residues in contact with THR 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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19C GLU* 4.2 12.5 + - - +
20C TYR* 2.8 24.8 + - - -
86C ALA* 5.1 2.1 - - - +
200D ASP 2.8 18.7 + - - -
201D LYS* 3.7 6.7 - - - -
203D LEU* 1.3 70.1 - - - +
205D ASN* 1.3 63.0 + - - +
207D ILE* 3.2 8.0 + - + +
208D ASN* 2.8 47.7 + - - +
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Residues in contact with ASN 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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82D PRO* 4.5 18.0 - - + +
83D PHE* 3.7 14.6 - - - -
201D LYS* 2.9 25.3 + - - +
202D MET 3.8 0.7 - - - +
204D THR* 1.3 75.7 - - - +
206D LEU* 1.3 61.5 + - - +
208D ASN* 3.4 9.7 + - - +
209D SER* 3.0 28.6 + - - -
248D ILE* 3.7 19.1 - - + -
252D THR* 2.9 29.7 + - - +
255D GLN* 5.8 0.2 + - - -
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Residues in contact with LEU 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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202D MET 3.0 23.0 + - - +
203D LEU* 3.6 4.3 - - - +
205D ASN* 1.3 73.3 - - - +
207D ILE* 1.3 64.8 + - - +
209D SER 3.0 10.2 + - - -
211D PHE* 3.0 53.4 + - + +
213D LEU* 3.9 17.3 - - + -
228D ILE* 3.7 30.7 - - + -
230D TYR* 5.5 0.7 - - + -
245D TYR* 3.9 27.8 - - + +
248D ILE* 3.8 25.1 - - + -
249D ILE* 4.1 9.6 - - + -
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Residues in contact with ILE 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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19C GLU 5.6 1.3 - - - +
20C TYR* 3.8 28.5 - - + +
38C PRO* 4.4 15.5 - - + -
40C SER* 5.7 1.6 - - - +
203D LEU 2.9 20.5 + - - +
204D THR* 3.5 6.1 - - + +
206D LEU* 1.3 74.5 - - - +
208D ASN* 1.3 68.7 + - - +
210D GLY* 3.0 20.6 + - - -
211D PHE 3.9 11.4 + - - +
213D LEU* 3.5 20.2 - - + +
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Residues in contact with ASN 208 (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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80D ILE* 5.4 3.5 - - - +
82D PRO* 5.9 4.3 - - + -
204D THR* 2.8 37.9 + - - +
205D ASN* 3.9 10.5 + - - +
206D LEU 3.3 0.2 - - - -
207D ILE* 1.3 85.3 - - - +
209D SER* 1.3 56.8 + - - +
210D GLY 3.3 2.3 + - - -
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Residues in contact with SER 209 (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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79D ARG* 3.3 30.9 + - - +
80D ILE 4.3 8.7 + - - +
82D PRO* 4.0 16.6 - - - +
205D ASN 3.0 15.7 + - - -
206D LEU 3.0 6.1 + - - -
208D ASN* 1.3 75.8 - - - +
210D GLY* 1.3 60.8 + - - +
211D PHE* 3.3 13.2 + - - -
244D LEU* 4.5 6.7 - - - -
248D ILE* 3.3 25.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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