Contacts of the helix formed by residues 204 - 223 (chain A) in PDB entry 1PTG
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 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A VAL 3.8 1.8 + - - -
203A SER* 1.3 70.3 - - - +
205A ASP* 1.3 74.0 + - - +
207A LYS* 3.0 8.0 + - - +
208A VAL* 2.8 47.6 + - + +
235A LEU* 5.3 1.1 - - - -
248A TYR* 3.5 42.1 + + + -
251A TYR* 3.2 41.2 + + + +
252A ILE* 3.5 26.9 + - + +
255A GLU* 4.1 13.4 + - - +
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Residues in contact with ASP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A SER* 3.0 8.3 + - - +
204A TYR* 1.3 90.4 - - - +
206A GLU* 1.3 63.8 + - - +
208A VAL* 3.4 4.2 + - - +
209A LYS* 3.1 21.7 + - - +
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LYS* 3.4 22.8 + - + +
202A VAL* 3.5 27.8 - - + +
203A SER* 3.0 19.7 + - - +
205A ASP* 1.3 78.8 - - - +
207A LYS* 1.3 56.9 + - - +
209A LYS* 3.4 10.6 + - + +
210A SER* 2.9 42.1 + - - +
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Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLN* 3.2 21.6 + - - +
198A ASP 4.7 0.2 - - - -
199A LYS* 3.1 29.3 + - + +
202A VAL* 3.4 8.0 - - + +
203A SER 2.8 13.0 + - - +
204A TYR* 3.3 9.6 - - - +
206A GLU* 1.3 76.7 - - - +
208A VAL* 1.3 63.8 + - - +
210A SER* 3.1 14.8 + - - -
211A ILE* 3.2 22.8 + - + +
232A PHE* 2.9 28.7 + - - +
233A THR 3.9 5.4 - - - -
234A SER 3.0 29.9 + - - -
235A LEU* 3.8 21.3 - - + -
252A ILE* 3.9 13.5 - - + -
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 2.8 56.2 + - + +
205A ASP* 3.8 4.3 - - - +
207A LYS* 1.3 74.1 - - + +
209A LYS* 1.3 62.1 + - - +
211A ILE* 3.5 11.3 + - - +
212A LYS* 3.3 51.4 + - + +
252A ILE* 4.9 6.7 - - + -
255A GLU* 4.0 19.5 - - + +
256A ILE* 4.6 3.1 - - + -
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Residues in contact with LYS 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 ASP 3.1 15.4 + - - +
206A GLU* 3.6 9.4 - - + +
208A VAL* 1.3 80.2 - - - +
210A SER* 1.3 60.3 + - - +
212A LYS* 3.4 5.4 + - - -
213A ASP* 2.6 60.5 + - - +
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Residues in contact with SER 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A THR* 4.6 3.1 - - - -
197A GLN* 4.0 24.5 - - - -
199A LYS* 3.3 32.0 + - - +
206A GLU* 2.9 20.0 + - - +
207A LYS* 3.1 6.5 + - - -
209A LYS* 1.3 75.3 + - - +
211A ILE* 1.3 60.3 + - - +
213A ASP* 4.0 4.8 - - - +
214A THR* 2.8 35.9 + - - -
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Residues in contact with ILE 211 (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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197A GLN* 3.7 16.6 - - - +
207A LYS* 3.2 27.8 + - + +
208A VAL* 3.6 8.5 - - - +
210A SER* 1.3 75.6 - - - +
212A LYS* 1.3 52.9 + - - +
214A THR 3.2 2.1 + - - -
215A MET* 2.7 52.1 + - + +
231A ASN* 3.3 25.8 + - - +
232A PHE 4.3 2.2 - - - +
233A THR* 3.8 18.4 - - + -
252A ILE* 3.6 30.1 - - + -
256A ILE* 3.7 22.2 - - + -
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Residues in contact with LYS 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 VAL* 3.3 31.4 + - + +
209A LYS* 3.9 5.2 - - - +
211A ILE* 1.3 79.1 - - - +
213A ASP* 1.3 57.2 + - - +
215A MET* 3.1 8.5 + - - +
216A ASP* 2.7 41.5 + - - +
255A GLU* 3.0 32.8 + - - -
256A ILE* 4.2 12.1 - - + -
259A TYR* 4.0 46.3 - - + +
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Residues in contact with ASP 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LYS* 2.6 66.2 + - - +
210A SER* 4.0 5.6 - - - +
212A LYS* 1.3 76.8 - - - +
214A THR* 1.3 62.4 + - - +
216A ASP* 3.3 11.3 + - - +
217A GLU* 3.2 19.2 + - - +
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Residues in contact with THR 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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183A THR* 4.7 7.3 - - - +
195A THR* 4.2 24.9 - - + +
196A VAL 5.4 0.2 - - - -
197A GLN* 3.4 23.3 - - + +
210A SER 2.8 20.7 + - - -
213A ASP* 1.3 73.2 - - - +
215A MET* 1.3 63.5 + - - +
217A GLU* 3.2 15.6 + - - +
218A THR* 2.9 28.3 + - + +
229A TYR* 4.8 5.6 - - + -
230A ILE 4.9 5.4 - - - +
231A ASN* 3.3 22.0 - - + +
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Residues in contact with MET 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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211A ILE* 2.7 32.2 + - + +
212A LYS* 3.4 8.1 - - - +
214A THR* 1.3 78.2 - - - +
216A ASP* 1.3 62.4 + - - +
218A THR* 3.1 9.0 + - - +
219A MET* 3.1 36.7 + - + +
231A ASN* 3.6 9.1 - - - +
256A ILE* 3.5 25.6 - - + -
259A TYR* 4.0 18.4 - - + -
260A ILE* 3.7 28.0 - - + -
268A VAL* 3.8 32.1 - - + +
271A VAL* 4.4 12.6 - - + -
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Residues in contact with ASP 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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212A LYS* 2.7 22.4 + - - +
213A ASP* 3.6 9.6 - - - +
214A THR 3.2 0.2 - - - -
215A MET* 1.3 73.2 - - - +
217A GLU* 1.3 58.6 + - - +
218A THR 3.3 0.5 + - - -
219A MET* 3.3 14.6 + - - +
220A ASN* 2.7 39.1 + - - +
259A TYR* 2.6 30.7 + - - -
263A LYS* 3.7 11.2 + - - -
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Residues in contact with GLU 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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195A THR* 3.8 22.2 + - - +
213A ASP 3.2 9.1 + - - +
214A THR* 3.2 14.3 + - - +
216A ASP* 1.3 80.6 - - - +
218A THR* 1.3 57.2 + - - +
220A ASN* 3.9 6.9 - - - +
221A ASN* 3.0 28.0 + - + +
227A HIS* 4.5 4.2 + - - -
229A TYR* 3.3 29.9 + - + +
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Residues in contact with THR 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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214A THR* 2.9 22.9 - - + +
215A MET* 3.1 9.3 + - - +
217A GLU* 1.3 72.6 - - - +
219A MET* 1.3 59.7 + - - +
220A ASN 3.1 2.2 - - - -
221A ASN 3.5 0.3 - - - -
222A SER* 2.9 30.5 + - - -
229A TYR* 3.6 50.3 - - + -
231A ASN* 5.2 1.8 - - + +
267A ARG* 3.2 26.7 + - - +
268A VAL* 3.4 16.1 - - - +
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Residues in contact with MET 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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215A MET* 3.1 28.4 + - + +
216A ASP* 3.3 19.7 + - - +
218A THR* 1.3 77.6 + - - +
220A ASN* 1.3 62.5 - - - +
222A SER* 3.2 20.8 + - - -
259A TYR* 3.7 33.4 - - + +
260A ILE* 5.2 0.9 - - - -
263A LYS* 3.9 27.8 - - + +
265A PRO* 3.6 34.8 - - + -
266A ALA* 5.2 4.2 + - - +
267A ARG* 3.5 13.0 - - - +
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Residues in contact with ASN 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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216A ASP* 2.7 28.4 + - - +
217A GLU* 3.9 6.3 - - - +
218A THR 3.1 0.4 - - - -
219A MET* 1.3 80.0 - - - +
221A ASN* 1.3 57.6 + - - +
222A SER* 2.9 14.5 + - - -
223A GLU 4.7 0.5 + - - -
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Residues in contact with ASN 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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217A GLU* 3.0 17.0 + - + +
218A THR* 3.5 2.9 - - - +
220A ASN* 1.3 75.1 - - - +
222A SER* 1.3 63.1 + - - +
223A GLU 3.2 1.8 - - - -
224A ASP* 2.9 52.7 + - - +
227A HIS* 4.0 4.2 + - - -
229A TYR* 2.7 32.4 + - + +
267A ARG* 3.7 4.7 + - - -
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Residues in contact with SER 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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25A ARG* 3.5 17.2 + - - -
218A THR 2.9 9.3 + - - -
219A MET 3.2 20.0 + - - -
220A ASN 2.9 5.0 + - - -
221A ASN* 1.3 76.4 - - - +
223A GLU* 1.3 77.8 + - - +
224A ASP 3.2 3.2 + - - -
266A ALA* 4.7 7.7 - - - +
267A ARG* 3.2 40.5 + - - +
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 3.6 26.4 + - - +
220A ASN 4.7 0.6 + - - -
221A ASN 2.9 3.8 + - - -
222A SER* 1.3 92.0 + - - +
224A ASP* 1.3 58.2 + - - +
225A LEU* 3.4 20.4 + - - +
266A ALA* 4.6 8.0 - - - +
294A SER* 6.0 0.3 - - - -
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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