Contacts of the helix formed by residues 203 - 224 (chain A) in PDB entry 2Y48
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 PRO 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A GLY* 1.4 85.1 - - - +
204A GLN* 1.3 55.3 + - - +
205A GLN* 2.8 22.0 + - + +
206A THR* 2.9 41.1 + - - +
207A GLN* 3.4 8.8 + - - +
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Residues in contact with GLN 204 (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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202A GLY 3.8 1.8 + - - +
203A PRO* 1.3 70.6 - - - +
205A GLN* 1.3 61.9 + - - +
207A GLN* 3.6 32.8 + - - +
208A LYS* 3.5 36.0 + - - +
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Residues in contact with GLN 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 PRO* 2.8 9.2 + - + +
204A GLN* 1.3 77.1 - - - +
206A THR* 1.3 64.5 + - - +
208A LYS* 3.3 20.0 + - - +
209A VAL* 3.3 24.7 + - + +
241A PRO* 6.0 4.0 - - - +
242A TYR* 6.2 0.8 - - - -
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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
----------------------------------------------------------
199A ILE* 4.6 21.1 + - + -
203A PRO* 2.9 32.1 + - - +
205A GLN* 1.3 76.7 - - - +
207A GLN* 1.3 53.7 + - - +
209A VAL* 2.8 33.4 + - + +
210A PHE* 2.8 17.5 + - - +
248A LEU* 5.1 13.3 - - + +
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Residues in contact with GLN 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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188A MET* 4.4 8.8 - - - +
199A ILE* 3.8 22.6 + - + +
200A ILE* 2.9 42.6 + - - +
202A GLY 3.2 18.0 + - - -
203A PRO 3.6 11.1 + - - +
204A GLN* 3.7 34.6 + - - +
205A GLN 3.2 0.2 - - - -
206A THR* 1.3 77.0 - - - +
208A LYS* 1.3 52.7 + - + +
210A PHE* 3.2 3.0 + - - +
211A LEU* 2.8 47.5 + - + +
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Residues in contact with LYS 208 (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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204A GLN* 3.5 23.4 + - - +
205A GLN* 3.3 18.7 + - - +
206A THR 3.1 0.6 - - - -
207A GLN* 1.3 76.2 - - + +
209A VAL* 1.3 61.5 + - + +
211A LEU* 3.8 12.1 - - + +
212A PHE* 2.8 30.7 + - - +
242A TYR* 5.2 1.5 - - - -
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Residues in contact with VAL 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 GLN* 3.3 33.0 - - + +
206A THR* 2.8 17.5 + - + +
208A LYS* 1.3 74.0 - - + +
210A PHE* 1.3 57.2 + - - +
212A PHE* 3.3 4.7 + - - +
213A ILE* 2.8 55.9 + - + +
241A PRO* 5.0 3.4 - - + +
242A TYR* 3.6 36.3 - - + +
245A ASP* 6.6 0.2 - - + -
248A LEU* 4.6 9.2 - - + -
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Residues in contact with PHE 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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188A MET* 3.5 43.7 - - + -
192A GLU* 3.7 33.7 - - + -
196A PHE* 3.6 24.5 - + - -
199A ILE* 3.9 30.1 - - + -
206A THR 2.8 10.8 + - - +
207A GLN 3.2 6.7 + - - +
209A VAL* 1.3 75.5 - - - +
211A LEU* 1.3 61.4 + - + +
213A ILE* 2.9 9.3 + - - +
214A ARG* 2.8 44.3 + - + +
248A LEU* 4.7 3.9 - - + +
252A VAL* 3.3 32.5 - - + -
255A TYR* 5.5 2.5 - + - -
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Residues in contact with LEU 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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185A HIS 4.3 8.5 - - - +
186A ASP* 3.8 24.0 - - - +
187A ARG* 3.2 34.3 - - - +
188A MET* 3.7 17.3 - - + +
207A GLN* 2.8 31.6 + - + +
208A LYS* 3.9 12.6 - - + +
210A PHE* 1.3 74.7 - - + +
212A PHE* 1.3 57.2 + - - +
214A ARG* 3.4 22.7 - - - +
215A ASN* 2.8 38.1 + - - +
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Residues in contact with PHE 212 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A VAL* 4.4 23.6 - - + -
208A LYS 2.8 22.0 + - - +
209A VAL 3.7 3.8 - - - +
210A PHE 3.1 0.2 - - - -
211A LEU* 1.3 71.8 - - - +
213A ILE* 1.3 64.4 + - - +
215A ASN* 3.7 4.7 - - - +
216A ARG* 2.8 60.1 + - + +
238A LEU* 4.6 6.3 - - + -
239A GLU* 5.9 4.3 - - + -
242A TYR* 3.5 55.9 - + + +
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Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A VAL* 2.8 50.7 + - + +
210A PHE* 3.6 3.4 - - - +
212A PHE* 1.3 74.8 - - - +
214A ARG* 1.3 59.3 + - - +
216A ARG* 3.8 3.0 - - - +
217A THR* 2.6 39.3 + - - +
238A LEU* 4.4 21.7 - - + +
242A TYR* 4.2 15.9 - - + +
245A ASP* 6.4 0.2 - - + -
248A LEU* 3.8 26.5 - - + -
249A VAL* 3.9 30.5 - - + -
252A VAL* 4.1 17.7 - - + -
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Residues in contact with ARG 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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178A ALA* 4.1 5.1 - - - +
183A LEU* 4.1 11.7 - - - +
184A PRO 3.2 19.6 + - - -
185A HIS* 4.0 3.2 - - - +
187A ARG 2.7 28.3 + - - -
188A MET* 4.1 0.2 - - - +
189A THR* 4.4 5.7 - - - +
192A GLU* 3.0 40.0 + - - +
210A PHE* 2.8 28.7 + - + +
211A LEU* 3.4 17.9 - - - +
213A ILE* 1.3 75.3 - - - +
215A ASN* 1.3 99.7 + - - +
217A THR* 3.2 2.4 + - - -
218A LEU* 3.1 40.8 + - + +
252A VAL* 3.8 16.4 - - + +
255A TYR* 5.7 0.2 - - + -
256A LEU* 4.1 16.4 - - + +
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Residues in contact with ASN 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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174A VAL* 3.7 33.2 - - + +
175A GLU* 5.0 1.0 - - - +
177A ALA* 3.8 4.7 - - - +
178A ALA* 3.6 13.2 - - - +
185A HIS* 2.9 37.8 + - - +
211A LEU 2.8 24.0 + - - +
212A PHE* 3.9 3.0 - - - +
214A ARG* 1.3 102.9 + - - +
216A ARG* 1.3 61.1 + - - +
218A LEU* 3.4 8.8 - - - +
219A GLN* 3.1 22.3 + - - +
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Residues in contact with ARG 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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174A VAL* 4.1 10.5 - - + +
212A PHE* 2.8 47.7 + - + +
213A ILE* 3.9 3.6 - - - +
215A ASN* 1.3 70.0 - - - +
217A THR* 1.3 67.6 + - - +
218A LEU 3.3 0.2 + - - -
219A GLN* 3.1 41.5 + - - +
220A LEU* 3.0 68.5 + - + +
223A ASP* 4.7 3.4 + - - -
237A GLN* 4.3 22.2 + - - +
238A LEU* 5.0 13.2 - - + -
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Residues in contact with THR 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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213A ILE* 2.6 30.3 + - - +
214A ARG 3.6 3.8 - - - -
216A ARG* 1.3 76.8 - - - +
218A LEU* 1.3 62.1 + - - +
220A LEU* 3.3 11.3 + - - +
221A TRP* 3.0 21.8 + - - +
229A LEU* 3.7 21.5 - - + +
234A THR* 3.8 24.0 - - + +
238A LEU* 5.4 0.3 - - - +
252A VAL* 4.4 4.0 - - - +
253A HIS* 4.1 14.4 + - + +
256A LEU* 3.8 19.3 - - + -
262A ILE* 4.5 3.8 - - + -
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Residues in contact with LEU 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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177A ALA* 3.8 11.2 - - + -
178A ALA* 4.7 4.7 - - - -
181A SER* 3.3 27.6 - - - +
183A LEU* 3.9 15.7 - - + -
214A ARG* 3.1 42.3 + - + +
215A ASN* 3.4 13.5 - - - +
216A ARG 3.2 0.2 - - - -
217A THR* 1.3 72.3 - - - +
219A GLN* 1.3 66.4 + - - +
221A TRP* 2.8 7.1 + - + +
222A LEU* 2.8 26.5 + - + +
256A LEU* 4.3 7.4 - - + -
261A LEU* 4.0 27.8 - - + +
262A ILE* 4.2 10.5 - - + -
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Residues in contact with GLN 219 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A GLY* 3.1 36.0 + - - +
174A VAL* 3.3 19.7 - - - +
177A ALA* 3.4 16.0 - - + +
215A ASN 3.1 9.8 + - - +
216A ARG* 3.1 34.2 + - - +
218A LEU* 1.3 77.1 - - - +
220A LEU* 1.3 56.6 + - - +
222A LEU* 3.0 4.5 + - - -
223A ASP* 2.8 56.3 + - - +
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Residues in contact with LEU 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 ARG* 3.0 53.2 + - + +
217A THR* 3.4 14.8 - - - +
219A GLN* 1.3 81.1 - - - +
221A TRP* 1.3 64.6 + - - +
223A ASP* 3.5 6.8 + - - +
224A ASN* 3.4 17.8 + - - +
229A LEU* 4.1 21.4 - - + +
234A THR* 4.7 19.5 - - + +
237A GLN* 3.8 43.7 - - + +
238A LEU* 6.0 0.7 - - + -
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Residues in contact with TRP 221 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A THR 3.0 7.2 + - - +
218A LEU* 2.8 10.6 + - + +
220A LEU* 1.3 72.2 - - - +
222A LEU* 1.3 83.5 + - + +
224A ASN 3.1 22.9 - - - -
225A PRO* 3.2 40.0 - - + +
227A ILE 3.9 17.5 - - - -
229A LEU* 4.2 13.4 - - + +
261A LEU 3.3 25.9 + - - -
262A ILE* 3.5 22.4 - - + -
263A ASN* 3.4 46.7 - - - -
264A PHE* 3.6 29.7 - + - -
267A TYR* 4.3 5.8 - + + -
344A VAL* 4.0 6.4 - - + +
348A GLN* 3.4 12.8 - - - -
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Residues in contact with LEU 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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177A ALA* 3.8 39.7 - - + +
180A GLN* 3.9 25.6 - - + +
181A SER* 3.9 12.8 - - - +
218A LEU 2.8 16.4 + - - +
219A GLN* 3.6 4.9 - - - +
221A TRP* 1.3 86.2 - - + +
223A ASP* 1.3 64.4 + - - +
224A ASN 2.9 6.1 + - - -
225A PRO* 3.3 17.1 - - - +
261A LEU 5.6 0.4 - - - +
264A PHE* 5.9 0.4 - - + -
344A VAL* 3.4 32.3 - - + +
347A LYS* 4.4 11.0 + - - +
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Residues in contact with ASP 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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216A ARG* 4.7 4.2 + - - -
219A GLN* 2.8 45.8 + - - +
220A LEU* 3.9 6.9 + - - +
222A LEU* 1.3 71.9 - - - +
224A ASN* 1.3 62.9 + - + +
225A PRO* 4.0 2.3 - - - +
347A LYS* 5.5 4.4 + - - +
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Residues in contact with ASN 224 (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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220A LEU 3.4 7.2 + - - +
221A TRP* 3.1 10.7 + - - +
222A LEU 2.9 1.6 - - - -
223A ASP* 1.3 85.8 - - + +
225A PRO* 1.3 60.4 - - - +
226A LYS* 3.1 20.9 + - - +
227A ILE* 3.3 46.7 + - + +
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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