Contacts of the helix formed by residues 184 - 204 (chain A) in PDB entry 1OJ7
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 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A THR 3.4 6.5 - - - +
183A LEU* 1.3 90.0 - - + +
185A PRO* 1.3 75.3 - - + +
186A ARG* 4.4 8.7 - - + +
187A GLN* 2.9 29.0 + - + -
188A VAL* 3.1 8.0 + - - +
1388A NZQ 3.8 19.5 - - + +
24C GLU* 6.1 4.7 - - + -
28C HIS* 4.5 8.5 - - + +
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Residues in contact with PRO 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU 3.6 3.3 - - - +
184A PRO* 1.3 85.5 - - + +
186A ARG* 1.3 63.4 + - - +
188A VAL* 4.1 5.2 - - + -
189A ALA* 2.9 26.6 + - - +
232A LEU* 3.6 26.3 - - + +
337A LEU 5.7 0.4 - - - -
23C ARG* 3.4 55.4 - - + +
28C HIS* 4.5 4.5 - - + +
55C LYS 5.7 1.3 - - - +
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Residues in contact with ARG 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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184A PRO* 3.1 7.2 - - + +
185A PRO* 1.3 80.9 - - - +
187A GLN* 1.3 70.4 + - + +
189A ALA* 3.6 1.1 - - - +
190A ASN* 2.9 17.5 + - - -
278A GLY 5.7 1.4 + - - -
280A ASP* 2.8 39.1 + - - +
283A GLN* 4.0 13.2 + - - +
1389A BO3 2.8 41.8 + - - +
125B LYS* 5.7 5.3 - - - +
24C GLU* 3.6 38.4 + - + +
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Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.0 16.5 - - + +
183A LEU* 4.0 19.1 - - + -
184A PRO* 2.9 25.0 + - + +
186A ARG* 1.3 83.3 + - + +
188A VAL* 1.3 65.4 + - - +
190A ASN* 3.2 27.3 + - - +
191A GLY* 3.0 20.1 + - - -
280A ASP* 4.0 11.7 - - - +
1388A NZQ 3.5 47.4 + - - +
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PRO 5.3 0.2 - - - +
183A LEU* 3.6 29.6 - - + +
184A PRO 3.1 13.2 + - - +
185A PRO* 3.6 10.3 - - + +
187A GLN* 1.3 75.0 - - - +
189A ALA* 1.3 64.3 + - - +
191A GLY* 3.2 3.1 + - - -
192A VAL* 3.1 29.3 + - + +
231A ALA* 3.8 30.1 - - + +
232A LEU* 3.8 19.3 - - + -
235A PRO* 6.5 0.4 - - + -
241A ARG* 3.6 20.2 - - - +
244A VAL* 5.6 3.8 - - + +
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A PRO 2.9 15.6 + - - +
186A ARG* 3.6 4.9 - - - +
188A VAL* 1.3 76.7 - - - +
190A ASN* 1.3 66.4 - - - +
192A VAL* 3.2 7.5 + - - +
193A VAL* 3.0 26.7 + - - +
232A LEU* 4.3 4.9 - - + +
337A LEU* 3.3 35.2 - - + +
338A GLY 5.2 0.2 - - - -
339A VAL* 3.8 16.8 - - + -
1389A BO3 3.8 2.0 - - - +
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Residues in contact with ASN 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 6.1 0.2 - - + -
141A ALA* 4.9 0.7 - - - -
186A ARG* 2.9 16.4 + - - +
187A GLN* 3.2 26.7 + - - +
188A VAL 3.3 0.2 - - - -
189A ALA* 1.3 75.6 - - - +
191A GLY* 1.3 58.0 + - - +
193A VAL* 3.3 1.1 + - - -
194A ASP* 2.9 27.5 + - - +
280A ASP* 3.0 28.0 - - - +
282A ALA* 3.2 33.2 - - + +
283A GLN* 4.2 5.9 - - - +
339A VAL* 4.5 2.2 - - - +
1388A NZQ 5.3 5.6 - - - +
1389A BO3 2.6 33.4 + - - -
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Residues in contact with GLY 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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140A PRO 3.3 24.0 - - - +
141A ALA* 3.4 19.0 - - - -
187A GLN 3.0 13.0 + - - -
188A VAL 3.7 3.1 - - - -
190A ASN* 1.3 75.3 - - - +
192A VAL* 1.3 64.2 + - - +
194A ASP 3.4 0.2 + - - -
195A ALA* 3.0 25.8 + - - +
244A VAL* 5.7 2.0 - - - -
248A ALA* 5.2 0.2 - - - +
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Residues in contact with VAL 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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188A VAL* 3.1 21.2 + - + +
189A ALA* 3.2 8.3 + - - +
191A GLY* 1.3 75.9 - - - +
193A VAL* 1.3 61.7 + - - +
195A ALA* 3.5 2.1 + - - +
196A PHE* 3.0 22.7 + - - +
224A LEU* 4.0 20.7 - - + +
228A GLY* 3.8 31.2 - - - +
244A VAL* 4.1 20.0 - - + -
333A PHE* 3.9 18.6 - - + -
337A LEU* 3.7 22.9 - - + -
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA 3.0 19.9 + - - +
190A ASN 3.6 4.0 - - - +
192A VAL* 1.3 76.4 - - - +
194A ASP* 1.3 56.8 + - - +
196A PHE* 3.2 7.1 + - - +
197A VAL* 2.8 48.3 + - + +
282A ALA* 3.7 28.9 - - + +
285A LEU* 4.5 2.9 - - + -
286A ALA* 4.5 5.2 - - + +
334A PHE* 3.8 31.2 - - + -
337A LEU* 3.9 13.0 - - + -
339A VAL* 3.9 18.4 - - + -
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Residues in contact with ASP 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ALA* 3.7 14.7 - - + +
142A THR* 3.7 14.2 - - - +
190A ASN 2.9 17.2 + - - +
191A GLY 3.8 2.2 - - - +
192A VAL 3.3 0.2 - - - -
193A VAL* 1.3 76.6 - - - +
195A ALA* 1.3 57.5 + - - +
197A VAL 3.3 0.5 + - - -
198A HIS* 2.9 60.0 + - - -
267A HIS* 3.5 0.2 + - - -
281A HIS* 3.2 35.1 + - + -
282A ALA* 4.7 2.5 - - + -
285A LEU* 3.3 14.0 - - + +
1388A NZQ 3.6 8.1 + - - +
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ALA 3.6 6.2 + - - +
191A GLY 3.0 17.1 + - - +
192A VAL 3.9 0.4 - - - +
194A ASP* 1.3 75.9 - - - +
196A PHE* 1.3 62.1 + - - +
198A HIS* 3.5 1.7 + - - -
199A THR* 2.9 28.1 + - - -
224A LEU* 3.8 21.1 - - + -
248A ALA* 3.8 31.6 - - + +
251A ALA* 3.6 13.1 - - + +
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Residues in contact with PHE 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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192A VAL 3.0 19.3 + - - +
193A VAL* 3.3 8.5 - - - +
195A ALA* 1.3 76.9 - - - +
197A VAL* 1.3 62.3 + - + +
199A THR* 3.3 5.4 + - - -
200A VAL* 3.1 31.3 + - + +
221A LEU* 3.6 26.4 - - + +
224A LEU* 3.5 18.8 - - + +
225A ILE* 3.8 30.1 - - + -
289A LEU* 5.1 0.7 - - + -
293A TRP* 4.9 0.9 - + - -
307A TYR* 3.2 30.7 - + - -
312A TRP* 4.7 2.0 - + - -
330A THR* 4.0 16.6 - - + -
333A PHE* 3.7 22.2 - + + -
334A PHE* 3.9 17.3 - + + -
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Residues in contact with VAL 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 VAL* 2.8 22.1 + - + +
194A ASP 4.0 0.4 - - - +
196A PHE* 1.3 73.5 - - - +
198A HIS* 1.3 65.5 + - - +
200A VAL* 3.2 12.4 + - + +
201A GLU* 2.9 37.5 + - + +
266A THR* 4.3 9.6 - - + -
267A HIS* 3.6 23.3 - - + +
285A LEU* 3.9 33.9 - - + +
289A LEU* 4.2 10.5 - - + -
334A PHE* 4.0 23.8 - - + -
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Residues in contact with HIS 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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141A ALA 3.8 5.5 + - - -
142A THR* 3.3 28.7 + - - -
194A ASP* 2.9 35.6 + - - +
195A ALA* 3.6 7.8 - - - +
197A VAL* 1.3 76.4 - - - +
199A THR* 1.3 62.9 + - - +
201A GLU* 3.5 7.7 + - - +
202A GLN* 2.8 26.3 + - - +
251A ALA* 4.0 16.4 - - + +
252A LEU* 3.6 15.7 - - + +
264A TRP* 3.7 18.1 - + + -
267A HIS* 3.3 19.5 - + - -
1388A NZQ 2.5 32.8 + - - +
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Residues in contact with THR 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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195A ALA 2.9 13.7 + - - -
196A PHE 3.4 9.0 - - - -
197A VAL 3.1 0.6 - - - -
198A HIS* 1.3 78.2 - - - +
200A VAL* 1.3 62.3 + - - +
202A GLN* 3.1 13.7 + - - +
203A TYR* 3.1 16.2 + - - +
217A ALA* 3.3 42.8 - - + +
220A ILE* 3.3 19.1 - - + +
221A LEU* 3.7 16.4 - - + -
251A ALA* 3.6 8.4 - - - +
256A ILE* 4.0 12.8 - - + +
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Residues in contact with VAL 200 (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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196A PHE* 3.1 20.4 + - + +
197A VAL* 3.2 23.0 + - + +
199A THR* 1.3 72.2 - - - +
201A GLU* 1.3 64.3 + - + +
203A TYR* 4.4 1.6 - - - -
204A VAL* 2.9 44.7 + - + +
221A LEU* 4.0 22.0 - - + -
263A ASP* 5.3 0.2 - - - +
289A LEU* 4.0 19.5 - - + -
293A TRP* 3.6 39.2 + - + +
307A TYR* 4.3 1.6 - - + -
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Residues in contact with GLU 201 (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 VAL* 2.9 30.6 + - + +
198A HIS 3.6 6.5 - - - +
199A THR 3.2 0.2 - - - -
200A VAL* 1.3 78.3 - - + +
202A GLN* 1.3 59.3 + - - +
205A THR* 4.8 2.6 - - - -
261A PRO 4.6 0.2 - - - +
262A GLN* 3.6 4.2 - - - +
263A ASP* 2.9 42.3 + - - +
264A TRP* 2.8 56.6 + - + -
265A ALA 3.9 0.5 + - - -
266A THR* 3.4 13.8 + - - -
267A HIS* 2.7 43.4 + - - +
289A LEU* 5.6 1.6 - - - +
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Residues in contact with GLN 202 (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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198A HIS 2.8 19.9 + - - +
199A THR 3.1 6.1 + - - +
200A VAL 3.1 0.2 - - - -
201A GLU* 1.3 81.3 - - - +
203A TYR* 1.3 56.5 + - - +
205A THR* 4.1 8.2 - - - +
251A ALA 2.7 28.7 + - - +
252A LEU* 3.7 21.9 - - - +
254A GLY* 5.2 5.2 - - - +
256A ILE* 3.7 18.1 - - + +
257A GLY* 3.4 31.1 + - - -
260A VAL* 3.6 20.4 - - - +
261A PRO 4.0 3.2 - - - +
262A GLN* 4.0 25.7 + - + +
264A TRP* 4.0 6.7 - - + -
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Residues in contact with TYR 203 (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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199A THR 3.1 14.8 + - - +
200A VAL* 4.8 0.4 - - - -
201A GLU 3.6 0.4 - - - -
202A GLN* 1.3 80.0 - - - +
204A VAL* 1.3 81.2 + - + +
205A THR* 3.2 8.3 + - - +
213A HIS 5.4 0.4 - - - -
214A ASP* 3.4 27.4 - - - -
217A ALA* 3.6 22.7 - - + -
218A GLU* 2.6 42.0 + - + +
221A LEU* 4.0 27.1 - - + -
303A LYS* 2.6 45.6 + - - +
306A GLN* 3.8 3.1 - - - +
307A TYR* 3.6 31.1 + + + -
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A VAL* 2.9 37.0 + - + +
203A TYR* 1.3 91.7 - - + +
205A THR* 1.3 60.2 + - - +
263A ASP* 4.8 1.0 - - - +
293A TRP* 3.8 22.4 + - + +
300A LYS* 2.9 29.0 + - + -
303A LYS* 3.9 5.6 - - + +
304A LEU* 3.7 42.8 - - + +
307A TYR* 4.2 13.5 - - + -
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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
------------------------------------------------------------
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