Contacts of the helix formed by residues 178 - 199 (chain A) in PDB entry 2PE2
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 ASP 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A SER 4.1 1.2 + - - -
177A PHE* 1.3 72.2 - - - +
179A GLU* 1.3 59.8 + - - +
180A THR* 4.0 9.3 - - - -
181A CYS* 2.8 36.1 + - - +
182A THR* 2.8 25.3 + - - -
306A PHE* 3.7 6.5 - - - -
357A LYS 5.1 1.7 - - - +
359A THR* 4.9 11.5 + - - +
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASP* 1.3 75.5 - - - +
180A THR* 1.3 58.5 + - - +
182A THR* 3.6 1.8 - - - -
183A ARG* 2.9 57.5 + - - +
306A PHE* 3.3 46.9 - - + +
307A PRO* 5.7 2.3 - - - +
308A LYS* 5.1 8.7 - - - +
341A PHE* 3.9 18.9 - - + -
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Residues in contact with THR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASP* 3.3 10.7 + - - -
179A GLU* 1.3 78.8 - - - +
181A CYS* 1.3 57.4 + - - +
183A ARG* 3.5 19.4 + - - +
184A PHE* 3.1 28.3 + - + +
356A PRO* 3.7 23.3 - - + -
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Residues in contact with CYS 181 (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 PHE* 4.0 9.5 - - + -
178A ASP* 2.8 34.8 + - - +
180A THR* 1.3 71.8 - - - +
182A THR* 1.3 65.4 + - - +
185A TYR* 3.1 30.9 + - + +
356A PRO* 3.9 23.3 - - + -
357A LYS 3.4 26.5 - - - -
358A LEU* 3.6 31.0 - - + -
359A THR 5.0 2.2 - - - -
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Residues in contact with THR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE* 3.2 25.7 + - - +
178A ASP 2.8 24.9 + - - -
179A GLU* 3.6 7.6 - - - -
181A CYS* 1.3 77.5 - - - +
183A ARG* 1.3 56.1 + - - +
185A TYR* 4.5 0.2 - - - +
186A THR* 2.7 45.2 + - - +
272A ILE* 4.7 5.4 - - + -
275A LEU* 4.3 12.9 + - + +
276A VAL* 3.6 27.1 - - + +
306A PHE* 3.9 4.3 - - - -
341A PHE* 3.7 16.6 - - + -
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Residues in contact with ARG 183 (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 GLU* 2.9 49.2 + - - +
180A THR* 3.9 24.2 + - - +
182A THR* 1.3 77.2 - - - +
184A PHE* 1.3 62.6 + - - +
186A THR* 3.9 0.9 - - - -
187A ALA* 3.0 23.6 + - - +
341A PHE* 3.3 44.3 + - + +
342A PHE* 4.2 6.7 - - + +
344A SER* 3.6 21.9 + - - +
345A VAL* 3.5 27.8 - - + -
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Residues in contact with PHE 184 (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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180A THR* 3.1 19.1 + - + +
181A CYS 3.9 1.3 - - - +
183A ARG* 1.3 79.1 - - - +
185A TYR* 1.3 75.5 + + - +
187A ALA* 3.2 8.0 + - - +
188A GLU* 3.1 58.1 + - - +
218A HIS* 3.8 13.0 - + - -
345A VAL* 5.8 1.1 - - - -
350A LEU* 4.0 20.2 - - + -
353A GLN* 4.2 21.1 - - + -
354A THR 4.6 1.8 - - - -
355A PRO* 3.5 31.9 - - + -
356A PRO* 3.4 25.6 - - + -
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Residues in contact with TYR 185 (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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167A LEU* 5.5 8.3 - - + -
177A PHE* 4.2 14.6 - + + -
181A CYS* 3.1 25.3 + - - +
182A THR 4.5 0.7 - - - +
184A PHE* 1.3 98.0 - + - +
186A THR* 1.3 66.0 + - - +
188A GLU* 3.4 6.6 + - - +
189A ILE* 3.1 32.4 + - + +
213A LEU* 3.7 16.8 - - + -
217A MET* 2.6 45.2 + - - +
219A ILE* 3.8 21.1 - - + -
275A LEU* 4.7 11.4 - - + -
355A PRO* 3.4 11.3 - - - +
356A PRO* 4.4 12.6 + - + -
358A LEU* 4.2 25.2 - - + +
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Residues in contact with THR 186 (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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182A THR* 2.7 32.9 + - - +
183A ARG* 3.9 3.8 - - - -
185A TYR* 1.3 78.1 - - - +
187A ALA* 1.3 56.5 + - - +
189A ILE* 3.2 10.8 + - - +
190A VAL* 2.9 31.9 + - + +
268A LEU* 4.4 3.1 - - + -
272A ILE* 3.6 37.9 - - + +
275A LEU* 4.1 7.7 - - - +
341A PHE* 4.6 4.0 - - + -
342A PHE* 3.5 27.8 - - + -
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Residues in contact with ALA 187 (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 ARG 3.0 19.5 + - - +
184A PHE* 3.2 7.4 + - - +
186A THR* 1.3 76.2 - - - +
188A GLU* 1.3 57.1 + - - +
190A VAL 3.4 0.2 + - - -
191A SER* 2.9 32.9 + - - -
342A PHE* 4.3 2.5 - - + -
345A VAL* 3.9 24.5 - - + -
347A TRP* 3.2 27.9 - - + -
350A LEU* 3.7 9.6 - - + -
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Residues in contact with GLU 188 (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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141A PHE* 3.1 33.9 - - + -
184A PHE* 3.1 35.3 + - + +
185A TYR* 3.7 10.2 - - - +
186A THR 3.3 0.2 - - - -
187A ALA* 1.3 77.5 - - - +
189A ILE* 1.3 60.9 + - - +
191A SER 3.3 0.9 + - - -
192A ALA* 3.0 23.6 + - - +
218A HIS* 2.6 33.9 + - - -
219A ILE* 3.1 42.9 + - + +
350A LEU* 3.7 14.9 - - + +
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Residues in contact with ILE 189 (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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167A LEU* 4.8 7.9 - - + -
185A TYR* 3.1 21.0 + - + +
186A THR* 3.2 10.3 + - - +
188A GLU* 1.3 75.2 - - - +
190A VAL* 1.3 56.9 + - - +
192A ALA* 3.3 3.6 + - - +
193A LEU* 3.0 38.2 + - + +
206A LEU* 4.3 14.1 - - + -
211A ILE* 4.0 26.9 - - + -
219A ILE* 3.9 21.1 - - + -
221A ILE* 4.8 6.7 - - + -
268A LEU* 3.9 20.6 - - + -
271A ILE* 4.2 20.0 - - + -
275A LEU* 5.1 3.8 - - + -
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Residues in contact with VAL 190 (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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186A THR* 2.9 22.1 + - + +
187A ALA 3.6 4.9 - - - +
189A ILE* 1.3 74.5 - - - +
191A SER* 1.3 60.2 + - - +
193A LEU* 3.3 8.4 + - - +
194A GLU* 2.9 26.7 + - - +
268A LEU* 3.8 24.5 - - + -
333A TYR* 3.8 10.5 - - + -
336A LEU* 3.8 24.5 - - + -
337A LYS* 4.1 8.3 - - + -
342A PHE* 4.0 20.4 - - + -
347A TRP* 3.7 20.9 - - + -
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Residues in contact with SER 191 (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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139A HIS* 4.5 3.8 + - - -
141A PHE* 4.0 17.5 - - - -
187A ALA 2.9 17.8 + - - -
188A GLU 3.7 4.9 - - - -
190A VAL* 1.3 77.0 - - - +
192A ALA* 1.3 61.8 + - - +
194A GLU* 3.5 13.2 + - - +
195A TYR* 3.2 22.3 + - - +
337A LYS* 5.5 0.8 - - - +
347A TRP* 3.4 13.5 + - - -
350A LEU* 3.2 16.2 - - - +
604A GOL 4.3 17.3 + - - -
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Residues in contact with ALA 192 (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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139A HIS* 4.9 0.7 - - - -
141A PHE* 3.9 19.7 - - + -
142A PHE* 3.2 27.5 - - + -
188A GLU 3.0 16.7 + - - +
189A ILE* 3.6 5.2 - - - +
190A VAL 3.2 0.2 - - - -
191A SER* 1.3 76.5 - - - +
193A LEU* 1.3 59.9 + - - +
195A TYR* 3.3 2.6 + - - -
196A LEU* 2.9 23.4 + - - +
219A ILE* 4.5 0.7 - - + -
221A ILE* 3.8 25.6 - - + -
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Residues in contact with LEU 193 (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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142A PHE* 6.2 0.2 - - + -
189A ILE* 3.0 24.8 + - + +
190A VAL* 3.8 4.5 - - - +
192A ALA* 1.3 74.0 - - + +
194A GLU* 1.3 60.9 + - - +
196A LEU* 4.2 14.8 - - + -
197A HIS* 2.8 42.3 + - + +
203A HIS* 5.4 1.6 - - + -
206A LEU* 3.9 35.2 - - + -
221A ILE* 5.4 4.7 - - + -
264A ASP* 4.2 32.5 - - + +
265A LEU* 4.7 3.8 - - + -
268A LEU* 4.3 22.0 - - + -
333A TYR* 3.4 17.7 - - + +
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Residues in contact with GLU 194 (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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190A VAL* 2.9 17.6 + - + +
191A SER* 3.7 10.3 - - - +
192A ALA 3.3 0.2 - - - -
193A LEU* 1.3 75.5 - - - +
195A TYR* 1.3 59.5 + - - +
197A HIS* 3.9 0.7 - - - +
198A GLY* 3.0 25.5 + - - -
333A TYR* 3.6 45.1 - - + +
337A LYS* 3.0 32.0 + - - +
604A GOL 5.6 1.4 + - - -
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Residues in contact with TYR 195 (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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136A ARG 3.8 0.5 + - - -
137A LEU* 3.9 22.7 - - + -
138A ASP* 2.9 34.2 + - - +
139A HIS* 3.5 39.5 - + + +
142A PHE* 3.7 17.7 - + + -
191A SER 3.2 11.6 + - - +
192A ALA 3.6 6.1 - - - +
194A GLU* 1.3 80.9 - - - +
196A LEU* 1.3 65.5 + - - +
198A GLY* 3.3 9.9 + - - -
199A LYS* 3.3 43.2 + - + +
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Residues in contact with LEU 196 (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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137A LEU* 3.7 27.1 - - + -
142A PHE* 3.9 13.5 - - + -
192A ALA 2.9 16.4 + - - +
193A LEU* 3.3 18.1 + - + +
195A TYR* 1.3 81.8 - - - +
197A HIS* 1.3 58.0 + - + +
199A LYS* 2.9 20.9 + - - +
201A ILE* 3.2 50.9 + - + +
203A HIS* 4.1 31.2 - - + +
221A ILE* 6.4 0.2 - - + -
224A PHE* 4.0 19.5 - - + -
264A ASP* 4.7 1.1 - - - +
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Residues in contact with HIS 197 (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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193A LEU* 2.8 24.7 + - + +
194A GLU 4.2 1.6 - - - +
196A LEU* 1.3 75.4 - - + +
198A GLY* 1.3 59.9 + - - +
200A GLY 3.0 14.6 + - - +
201A ILE 3.2 22.4 - - - +
261A LYS* 3.2 70.3 + - + +
264A ASP* 2.8 31.4 + - + +
265A LEU* 4.7 7.3 - - + +
333A TYR* 2.7 35.4 + - + +
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Residues in contact with GLY 198 (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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194A GLU 3.0 18.1 + - - -
195A TYR 3.6 4.3 - - - -
196A LEU 3.2 0.4 - - - -
197A HIS* 1.3 78.7 - - - +
199A LYS* 1.3 61.2 + - - +
200A GLY 3.2 1.6 + - - -
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Residues in contact with LYS 199 (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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136A ARG* 2.7 53.8 + - - +
137A LEU* 4.5 2.4 - - + +
195A TYR* 3.3 44.9 + - + +
196A LEU 2.9 10.5 + - - +
198A GLY* 1.3 80.8 - - - +
200A GLY* 1.3 62.4 + - - +
201A ILE* 3.4 20.4 + - + +
229A VAL* 5.3 1.0 - - - +
601A SO4 3.2 37.3 + - - +
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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
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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