Contacts of the helix formed by residues 204 - 223 (chain A) in PDB entry 1ZP2
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 LYS 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ASP 5.0 3.1 - - - +
202A LEU 4.0 10.8 - - - +
203A ILE* 1.3 77.5 - - - +
205A SER* 1.3 54.6 + - - +
206A THR* 4.1 14.6 - - - +
207A ASP* 2.6 42.9 + - - +
208A ALA* 3.1 7.7 + - - -
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE 4.1 1.0 + - - -
204A LYS* 1.3 72.1 - - - +
206A THR* 1.3 67.4 + - - +
207A ASP 3.0 1.4 + - - -
208A ALA* 3.2 25.4 + - - +
209A PHE* 4.4 2.1 + - - +
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Residues in contact with THR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLN* 4.1 5.4 + - - -
204A LYS* 2.9 13.5 + - - +
205A SER* 1.3 81.0 + - - +
207A ASP* 1.3 66.1 + - - +
209A PHE* 5.3 1.3 + - - +
210A LYS* 5.2 3.6 + - - +
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Residues in contact with ASP 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A HIS* 3.2 26.0 + - - -
179A GLN* 3.1 26.0 + - + +
182A TYR* 4.7 2.0 - - + -
202A LEU 4.5 2.3 - - - +
203A ILE* 4.2 6.3 - - + -
204A LYS* 2.6 42.3 + - - +
206A THR* 1.3 79.0 - - - +
208A ALA* 1.3 65.5 + - - +
209A PHE 3.2 2.5 - - - -
210A LYS* 2.8 17.9 + - - +
211A VAL* 2.9 25.7 + - + -
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ILE* 4.2 12.7 - - + +
204A LYS 3.1 6.8 + - - +
205A SER* 3.2 26.2 + - - +
207A ASP* 1.3 73.7 - - - +
209A PHE* 1.3 62.0 + - - +
211A VAL* 3.3 3.4 + - - +
212A ILE* 3.0 35.6 + - + +
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Residues in contact with PHE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A SER 4.4 2.2 + - - +
206A THR 6.0 0.9 - - - +
207A ASP 2.9 2.8 + - - -
208A ALA* 1.3 77.0 - - - +
210A LYS* 1.3 66.6 + - + +
212A ILE* 3.2 15.5 + - + +
213A LEU* 2.6 50.7 + - + +
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Residues in contact with LYS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A MET* 3.3 30.6 + - - +
175A ALA* 4.7 1.8 - - + +
176A HIS* 5.8 2.0 - - + -
179A GLN* 3.0 39.0 - - + +
206A THR 5.2 3.6 + - - +
207A ASP 2.8 9.1 + - - +
209A PHE* 1.3 81.9 - - + +
211A VAL* 1.3 55.5 + - - +
213A LEU* 2.9 25.3 + - + +
214A CYS* 2.6 40.7 + - - +
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLN* 3.9 25.3 - - - +
182A TYR* 4.3 6.7 - - + -
183A ALA* 3.9 13.2 - - - +
186A LEU* 3.6 31.6 - - + -
203A ILE* 3.9 15.9 - - + -
207A ASP* 2.9 32.7 + - + +
208A ALA* 3.5 7.9 - - - +
210A LYS* 1.3 73.8 - - - +
212A ILE* 1.3 67.5 + - + +
214A CYS* 3.0 5.4 + - - +
215A VAL* 2.9 28.6 + - + +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ALA* 3.0 24.8 + - + +
209A PHE* 3.4 16.6 - - + +
211A VAL* 1.3 77.6 - - + +
213A LEU* 1.3 65.2 + - - +
215A VAL* 3.2 12.2 + - + +
216A GLN* 3.0 26.8 + - + +
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 4.6 7.0 - - + -
174A MET* 4.5 21.1 - - + +
175A ALA* 5.5 1.1 - - + -
209A PHE* 2.6 34.2 + - + +
210A LYS* 2.9 43.7 + - + +
212A ILE* 1.3 75.9 - - - +
214A CYS* 1.3 64.6 + - - +
216A GLN* 3.2 16.8 + - - +
217A ARG* 3.1 45.3 + - + +
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Residues in contact with CYS 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 3.9 14.1 - - - -
175A ALA* 3.6 27.6 - - - -
179A GLN 4.3 1.6 - - - -
180A LEU* 3.5 42.6 - - + -
183A ALA* 3.5 15.0 - - + -
210A LYS 2.6 15.5 + - - -
211A VAL 3.2 8.5 - - - +
213A LEU* 1.3 72.2 - - - +
215A VAL* 1.3 67.1 + - - +
217A ARG* 2.8 17.0 + - - +
218A ILE* 2.9 15.7 + - - +
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ALA* 3.4 25.5 - - + +
186A LEU* 5.1 6.1 - - + -
187A ILE* 4.0 23.3 - - + -
211A VAL* 2.9 24.9 + - + +
212A ILE* 3.5 10.8 - - + +
214A CYS* 1.3 70.6 - - - +
216A GLN* 1.3 64.0 + - - +
218A ILE* 3.8 1.1 - - - +
219A ILE* 3.1 46.1 + - + +
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Residues in contact with GLN 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.3 31.6 + - + +
15A PHE* 3.7 23.6 - - + +
16A LEU 5.4 1.8 + - - +
212A ILE* 3.0 16.4 + - + +
213A LEU* 3.3 16.2 - - - +
214A CYS 2.8 1.4 + - - -
215A VAL* 1.3 80.6 - - - +
217A ARG* 1.3 92.4 + - - +
219A ILE* 3.1 5.7 + - - +
220A SER* 2.9 20.5 + - - -
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Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 5.8 2.6 - - - +
16A LEU 5.4 10.3 + - - +
17A SER* 5.6 3.2 - - - +
27A CYS* 3.4 26.1 - - - -
28A LEU* 3.6 9.1 - - + +
169A SER* 4.9 7.6 - - - -
171A LEU* 3.7 34.5 - - + -
174A MET* 3.8 11.5 - - - +
213A LEU* 3.1 33.4 + - - +
214A CYS 2.8 10.1 + - - +
216A GLN* 1.3 108.8 + - - +
218A ILE* 1.3 62.5 + - - +
220A SER* 2.6 26.7 + - - -
221A ILE* 2.8 17.4 + - - +
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Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ILE* 3.7 30.1 - - + +
166A SER* 4.9 8.3 - - - -
171A LEU* 4.2 11.0 - - + -
180A LEU* 4.0 21.8 - - + -
183A ALA* 4.1 16.2 - - + -
184A ALA* 4.2 4.5 - - + +
187A ILE* 3.4 33.0 - - + -
214A CYS 2.9 16.0 + - - +
215A VAL 3.8 2.0 - - - +
217A ARG* 1.3 74.3 - - - +
219A ILE* 1.3 66.4 + - - +
221A ILE* 3.0 28.4 - - + +
222A TYR* 3.3 23.8 + - + -
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 3.3 27.6 - - + -
187A ILE* 4.5 11.0 - - + -
215A VAL* 3.1 34.1 - - + +
216A GLN* 3.1 8.8 + - - +
218A ILE* 1.3 74.7 - - - +
220A SER* 1.3 66.7 + - - +
221A ILE 3.1 0.2 + - - -
222A TYR* 3.2 7.7 + - - +
223A TYR* 3.1 35.8 + - + +
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Residues in contact with SER 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 3.5 43.9 - - - -
28A LEU* 3.1 16.6 - - - +
216A GLN 2.9 6.7 + - - -
217A ARG* 2.6 32.8 + - - -
219A ILE* 1.3 77.0 - - - +
221A ILE* 1.3 63.4 + - - +
223A TYR* 2.9 15.4 + - - +
224A PHE* 3.2 16.6 + - - +
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.4 28.9 - - + -
33A ILE* 5.8 3.5 - - + +
165A ASP* 3.9 13.0 - - + +
166A SER* 3.9 22.0 - - - -
168A ALA* 5.1 4.5 - - + -
169A SER* 3.6 26.0 - - - +
217A ARG 2.8 24.7 + - - +
218A ILE* 3.0 19.3 + - + +
220A SER* 1.3 77.7 + - - +
222A TYR* 1.3 80.7 + - + +
223A TYR 3.3 0.3 + - - -
224A PHE* 3.5 7.1 + - - +
225A GLU* 3.3 26.4 + - - +
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Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PHE* 6.6 0.2 - + - -
161A SER* 4.4 0.3 - - - -
162A ILE* 3.3 26.6 - - + +
165A ASP* 2.5 47.2 + - + +
187A ILE* 6.3 0.9 - - + -
218A ILE* 3.4 39.9 - - + -
219A ILE* 3.2 5.3 + - - +
221A ILE* 1.3 86.3 - - + +
223A TYR* 1.3 74.7 + + + +
224A PHE 3.4 0.9 - - - -
225A GLU* 3.7 24.3 - - - +
226A ASP* 2.7 32.8 + - - +
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Residues in contact with TYR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 5.2 12.2 - + + -
219A ILE* 3.1 29.1 + - + +
220A SER* 2.9 11.7 + - - +
222A TYR* 1.3 92.3 - + + +
224A PHE* 1.3 56.8 + - - +
225A GLU 3.5 0.4 - - - -
226A ASP* 4.0 27.2 + - + -
227A ILE* 4.2 23.5 - - + +
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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
------------------------------------------------------------
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