Contacts of the helix formed by residues 201 - 213 (chain D) in PDB entry 2ZSU
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 PHE 201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D TYR* 3.8 27.4 - + - -
11D PRO* 3.7 28.0 - - + -
164D ASP* 3.9 25.8 - - + -
196D GLY* 3.9 4.5 - - - -
197D SER* 2.8 48.1 + - - +
200D LEU* 1.3 84.9 - - + +
202D THR* 1.3 65.4 + - - +
203D ASP 3.3 2.7 - - - -
204D GLU* 3.0 50.6 + - + +
205D PHE* 3.0 5.7 + - - +
233D TRP* 4.1 6.1 - + - -
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Residues in contact with THR 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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197D SER 3.8 1.0 + - - -
198D VAL 2.8 24.5 + - - +
199D TYR* 3.3 15.4 + - - -
200D LEU 3.6 1.4 + - - -
201D PHE* 1.3 73.5 - - - +
203D ASP* 1.3 62.7 + - - +
205D PHE* 3.1 8.8 + - + +
206D LEU* 2.9 47.7 + - + +
275D TYR* 4.3 12.1 + - + -
276D ILE* 3.7 30.1 - - + -
279D MET* 5.1 3.1 - - + -
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Residues in contact with ASP 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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201D PHE 3.3 0.8 - - - -
202D THR* 1.3 78.9 - - - +
204D GLU* 1.3 62.5 + - - +
206D LEU* 3.9 14.9 - - - +
207D THR* 2.9 33.0 + - - +
279D MET* 4.7 8.8 - - - +
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Residues in contact with GLU 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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164D ASP* 4.5 22.3 - - - +
173D PHE* 4.6 13.0 - - + -
194D GLN* 5.4 0.5 + - - +
195D ALA* 3.2 25.9 - - + +
196D GLY* 3.9 2.6 + - - -
201D PHE* 3.0 50.1 + - + +
203D ASP* 1.3 77.9 - - - +
205D PHE* 1.3 66.7 + - - +
207D THR* 3.9 4.6 - - - -
208D ALA* 3.1 24.6 + - - +
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Residues in contact with PHE 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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195D ALA* 3.8 23.6 - - + +
197D SER 5.6 1.6 - - - +
198D VAL* 5.8 3.8 - - + -
201D PHE 3.0 7.5 + - - +
202D THR* 3.4 11.4 - - - +
204D GLU* 1.3 85.3 - - - +
206D LEU* 1.3 65.5 + - + +
208D ALA* 3.4 3.3 + - - +
209D TYR* 3.0 28.4 + - + +
221D TYR* 3.4 29.8 - + + -
234D ALA* 3.6 28.5 - - + -
235D PHE 4.1 2.5 - - - -
236D LEU* 3.4 25.8 - - + -
272D MET* 4.0 14.4 - - + -
276D ILE* 4.0 24.9 - - + -
280D LEU* 4.2 16.6 - - + -
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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 THR* 2.9 30.1 + - + +
203D ASP* 3.9 10.1 - - - +
205D PHE* 1.3 84.0 - - + +
207D THR* 1.3 61.3 + - - +
209D TYR* 3.4 4.8 + - - +
210D ARG* 3.0 53.5 + - - +
276D ILE* 4.0 15.0 - - + +
279D MET* 3.8 38.1 - - + -
280D LEU* 3.6 39.0 - - + +
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Residues in contact with THR 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 ASP* 2.9 23.5 + - - +
204D GLU* 3.9 5.4 - - - -
206D LEU* 1.3 76.4 - - - +
208D ALA* 1.3 64.3 + - - +
210D ARG* 3.3 16.0 + - - +
211D LYS* 3.1 50.8 + - + +
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Residues in contact with ALA 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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173D PHE* 4.0 17.0 - - + -
178D TYR* 3.6 25.1 - - + +
195D ALA* 5.7 0.2 - - + -
204D GLU 3.1 16.2 + - - +
205D PHE* 3.8 0.9 - - - +
207D THR* 1.3 75.7 - - - +
209D TYR* 1.3 67.2 + - - +
211D LYS* 3.1 6.0 + - - +
212D MET* 2.9 27.4 + - - +
236D LEU* 3.6 22.0 - - + -
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Residues in contact with TYR 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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205D PHE* 3.0 20.0 + + + +
206D LEU* 3.5 6.5 - - - +
208D ALA* 1.3 76.1 - - - +
210D ARG* 1.3 63.4 + - + +
212D MET* 3.2 5.6 + - - +
213D ARG* 2.9 72.6 + - + +
219D VAL* 3.8 32.6 + - + -
221D TYR* 4.0 25.2 - + + -
236D LEU* 3.8 23.0 - - + +
280D LEU* 3.8 55.0 - - + +
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Residues in contact with ARG 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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206D LEU* 3.0 46.5 + - - +
207D THR* 3.6 13.9 + - - +
208D ALA 3.2 0.2 - - - -
209D TYR* 1.3 83.0 - - + +
211D LYS* 1.3 61.3 + - + +
213D ARG* 3.4 14.9 + - - +
214D LYS* 3.3 21.2 - - + +
279D MET* 2.7 33.3 + - - +
280D LEU 3.1 21.6 + - - +
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Residues in contact with LYS 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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173D PHE 3.7 25.6 + - - +
174D SER* 4.4 6.5 - - - +
175D GLU* 4.0 24.6 - - + +
178D TYR* 4.0 13.7 - - + -
207D THR* 3.1 42.0 + - + +
208D ALA* 3.7 6.1 - - - +
210D ARG* 1.3 75.6 - - + +
212D MET* 1.3 62.7 + - - +
214D LYS* 3.2 36.3 + - - +
215D VAL* 3.6 12.6 - - - +
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Residues in contact with MET 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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178D TYR* 3.5 37.5 - - + -
191D TYR* 4.0 15.9 - - + -
193D THR* 4.8 0.2 - - - -
208D ALA 2.9 15.0 + - - +
209D TYR 3.6 3.8 - - - +
211D LYS* 1.3 76.4 - - - +
213D ARG* 1.3 56.8 + - - +
214D LYS 3.0 0.2 - - - -
215D VAL* 3.0 16.9 + - - +
216D PHE* 3.0 24.7 + - + -
219D VAL* 3.3 16.4 - - + +
236D LEU* 3.7 33.2 - - + -
237D VAL 3.4 42.6 - - - +
238D GLY* 3.6 9.9 - - - +
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Residues in contact with ARG 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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209D TYR* 2.9 63.3 + - + +
210D ARG* 3.6 9.4 - - - +
211D LYS 3.2 0.4 - - - -
212D MET* 1.3 75.7 - - - +
214D LYS* 1.3 60.2 + - + +
216D PHE 4.5 6.6 - - - +
219D VAL* 3.7 31.2 + - + +
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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