Contacts of the helix formed by residues 181 - 204 (chain D) in PDB entry 4JDA
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 THR 181 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ILE* 4.0 3.0 - - - +
179D GLY 4.7 6.1 - - - +
180D ASN* 1.3 77.6 - - - +
182D GLU* 1.3 67.9 + - - +
183D GLU* 3.6 8.4 + - - +
184D ASP* 2.9 34.8 + - - +
185D THR* 3.2 18.2 + - - -
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Residues in contact with GLU 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D THR 4.7 5.7 - - - +
50D CYS* 4.0 8.4 - - + -
51D THR 5.7 0.2 + - - -
176D ILE* 3.8 29.1 - - + +
181D THR* 1.3 73.2 - - - +
183D GLU* 1.3 57.4 + - - +
185D THR* 2.9 20.4 + - - -
186D ARG* 2.9 51.7 + - - +
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Residues in contact with GLU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D THR* 3.2 8.1 + - - +
182D GLU* 1.3 79.6 - - + +
184D ASP* 1.3 62.9 + - - +
186D ARG* 4.0 18.9 - - - +
187D MET* 3.1 36.8 + - + +
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Residues in contact with ASP 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D ASN* 5.0 7.2 - - + -
181D THR* 2.9 35.8 + - - +
182D GLU 3.3 0.4 - - - -
183D GLU* 1.3 76.9 - - - +
185D THR* 1.3 63.6 + - - +
187D MET* 3.7 14.7 - - - +
188D PHE* 3.3 21.8 + - - +
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Residues in contact with THR 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D CYS* 4.1 17.0 - - - -
141D LEU* 5.9 4.0 - - - -
174D VAL* 5.1 6.7 - - - -
175D ASP 5.9 0.2 - - - -
176D ILE* 4.6 14.6 - - - -
177D PRO* 5.3 5.4 - - - -
180D ASN* 5.6 3.3 - - - +
181D THR 3.2 10.5 + - - -
182D GLU* 2.9 11.3 + - - -
184D ASP* 1.3 73.8 - - - +
186D ARG* 1.3 65.6 + - - +
188D PHE* 3.2 6.5 + - - +
189D VAL* 3.0 30.5 + - - +
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Residues in contact with ARG 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D CYS* 3.7 13.7 - - - -
51D THR 3.9 15.1 + - - +
52D SER* 3.7 33.7 - - - +
172D TYR* 3.5 9.4 - - - +
182D GLU* 2.9 55.1 + - - +
183D GLU* 4.0 17.9 - - - +
185D THR* 1.3 75.6 - - - +
187D MET* 1.3 64.2 + - - +
190D ASP* 2.8 40.4 + - - +
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Residues in contact with MET 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASP* 4.6 21.3 - - + +
183D GLU* 3.1 32.8 + - + +
184D ASP* 3.7 16.6 - - - +
186D ARG* 1.3 77.1 - - - +
188D PHE* 1.3 63.4 + - - +
190D ASP* 4.0 3.4 - - - +
191D THR* 3.2 26.0 + - - +
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Residues in contact with PHE 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 4.3 14.8 - - + -
205C THR* 5.2 3.6 - - - -
207C SER* 3.6 49.6 - - - -
111D LEU* 4.8 10.5 - - + -
141D LEU* 4.1 16.2 - - + -
184D ASP 3.3 9.3 + - - +
185D THR* 3.2 8.3 + - - +
187D MET* 1.3 78.5 - - - +
189D VAL* 1.3 76.0 + - + +
191D THR* 3.4 10.0 - - + -
192D VAL* 3.2 37.9 + - + +
301D A9S 4.0 33.0 - - + -
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Residues in contact with VAL 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 3.9 31.2 - - + -
144D TYR* 3.9 13.0 - - + -
172D TYR* 3.2 51.1 - - + +
174D VAL* 4.5 5.2 - - + -
185D THR* 3.0 16.3 + - - +
188D PHE* 1.3 81.3 - - + +
190D ASP* 1.3 64.7 + - - +
192D VAL* 3.0 7.5 + - - +
193D VAL* 2.9 23.0 + - + +
301D A9S 4.0 9.4 - - + -
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Residues in contact with ASP 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D SER* 2.8 24.9 + - - -
54D ILE* 3.4 29.1 - - + +
172D TYR* 2.9 13.3 + - - -
186D ARG* 2.8 29.8 + - - +
187D MET* 4.0 3.4 - - - +
189D VAL* 1.3 74.5 - - - +
191D THR* 1.3 55.0 + - - +
193D VAL* 3.1 3.7 + - - +
194D LYS* 2.7 50.2 + - + +
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Residues in contact with THR 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C GLN* 5.1 1.9 - - - +
201C ALA* 5.1 6.1 - - + +
202C VAL* 3.1 40.6 - - + +
205C THR* 5.8 3.1 - - + +
187D MET* 3.2 14.7 + - - +
188D PHE* 3.4 16.4 - - + +
190D ASP* 1.3 77.8 - - - +
192D VAL* 1.3 57.2 + - - +
194D LYS* 3.8 9.4 - - - +
195D SER* 2.9 29.1 + - - -
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Residues in contact with VAL 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 4.1 18.8 - - + -
81D PHE* 4.8 7.2 - - + -
188D PHE* 3.2 38.1 + - + +
189D VAL* 3.0 8.5 + - - +
191D THR* 1.3 72.8 - - - +
193D VAL* 1.3 62.6 + - - +
195D SER* 3.3 6.7 + - - -
196D ASN* 2.9 37.6 + - - +
301D A9S 3.8 51.1 - - + -
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Residues in contact with VAL 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ILE* 3.8 29.6 - - + -
144D TYR* 4.0 20.9 - - - +
170D GLU* 3.9 34.8 - - + +
172D TYR* 4.5 9.9 - - + -
189D VAL* 2.9 26.0 + - + +
190D ASP* 3.7 5.8 - - - +
192D VAL* 1.3 74.9 - - - +
194D LYS* 1.3 58.3 + - - +
196D ASN* 2.9 10.5 + - - +
197D LEU* 2.8 30.8 + - + +
301D A9S 4.7 7.0 - - + -
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Residues in contact with LYS 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C GLN* 5.3 4.3 - - + -
54D ILE* 4.1 23.8 - - + -
56D HIS* 5.4 6.0 - - + -
190D ASP* 2.7 38.0 + - + +
191D THR* 3.8 7.9 - - - +
193D VAL* 1.3 72.4 - - - +
195D SER* 1.3 63.3 + - - +
197D LEU* 3.9 5.6 - - - +
198D GLN* 3.0 31.8 + - - +
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Residues in contact with SER 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C SER 5.6 0.3 - - - +
198C GLN* 4.4 15.8 - - - +
199C ASN* 2.4 30.9 + - - +
202C VAL* 4.1 15.0 - - - -
80D HIS* 4.9 0.3 - - - +
81D PHE* 3.6 13.1 - - - -
191D THR 2.9 20.2 + - - -
192D VAL* 3.4 7.1 + - - -
194D LYS* 1.3 77.3 - - - +
196D ASN* 1.3 62.8 + - - +
198D GLN* 3.6 2.1 + - - +
199D ASN* 3.0 31.9 + - - -
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Residues in contact with ASN 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D TYR* 3.2 29.6 - - + +
79D LYS* 3.4 48.2 - - - +
80D HIS 4.1 4.0 + - - -
81D PHE* 5.2 3.3 + - - -
170D GLU* 5.3 4.7 + - - +
192D VAL* 2.9 24.3 + - - +
193D VAL* 2.9 9.7 + - - +
195D SER* 1.3 78.7 + - - +
197D LEU* 1.3 62.4 + - + +
199D ASN* 3.3 1.3 + - - +
200D LEU 2.9 23.6 + - - -
301D A9S 3.6 24.2 + - - +
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Residues in contact with LEU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 3.4 39.9 - - + +
56D HIS* 3.7 32.3 + - + +
58D VAL* 5.3 1.2 - - - +
78D TYR* 5.3 4.3 - - + -
148D THR* 5.4 4.0 - - + -
168D VAL* 4.0 27.9 - - + +
170D GLU* 4.0 22.4 - - + +
193D VAL* 2.8 27.0 + - + +
194D LYS* 3.9 4.3 - - - +
196D ASN* 1.3 74.8 - - + +
198D GLN* 1.3 58.5 + - - +
200D LEU* 3.2 12.3 + - + +
201D ALA* 2.8 29.6 + - - +
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Residues in contact with GLN 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C THR* 4.4 13.5 - - + +
194C LYS* 3.5 39.4 - - - +
195C SER* 3.8 26.9 - - - +
198C GLN* 5.0 7.6 - - + +
56D HIS* 3.3 37.0 + - - +
194D LYS* 3.0 21.3 + - - +
195D SER* 4.0 5.6 - - - +
197D LEU* 1.3 76.8 - - - +
199D ASN* 1.3 62.1 + - - +
201D ALA* 3.3 15.2 + - - +
202D VAL* 3.4 12.6 + - - +
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Residues in contact with ASN 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C HIS* 3.8 19.8 - - - +
81C PHE* 3.6 11.5 - - - -
195C SER* 2.7 29.8 + - - -
199C ASN* 3.3 26.3 + - - +
78D TYR* 3.2 24.8 + - - +
80D HIS* 3.8 14.6 - - - +
195D SER* 3.0 20.6 + - - +
197D LEU 3.2 0.6 - - - -
198D GLN* 1.3 76.4 - - - +
200D LEU* 1.3 65.3 + - - +
202D VAL 3.2 9.9 + - - -
203D ILE* 3.2 16.9 + - - +
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Residues in contact with LEU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D VAL* 5.8 0.9 - - + -
65D ILE* 4.1 27.6 - - + +
68D PHE* 3.6 32.1 - - + -
69D VAL* 4.3 7.6 - - + -
78D TYR* 3.7 28.6 - - + +
168D VAL* 5.0 5.4 - - + -
196D ASN 2.9 14.1 + - - +
197D LEU* 3.2 20.9 - - + +
199D ASN* 1.3 76.4 - - - +
201D ALA* 1.3 55.9 + - - +
202D VAL 3.3 0.2 + - - -
203D ILE* 3.3 9.2 - - + +
204D SER* 2.7 33.1 + - - -
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Residues in contact with ALA 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C THR* 4.3 13.2 - - + -
56D HIS* 3.9 20.9 - - + +
57D ARG 5.0 0.2 - - - +
58D VAL* 3.9 27.6 - - + +
197D LEU 2.8 16.3 + - - +
198D GLN 3.4 11.0 - - - +
199D ASN 3.1 0.2 - - - -
200D LEU* 1.3 75.7 - - - +
202D VAL* 1.3 62.9 + - - +
204D SER* 3.6 4.3 + - - +
205D THR* 3.2 22.5 + - - +
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Residues in contact with VAL 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C PHE* 3.3 41.5 - - + -
111C LEU* 4.6 15.8 - - + +
188C PHE* 4.6 7.5 - - + -
191C THR* 3.5 43.5 - - + +
192C VAL* 4.1 17.5 - - + +
195C SER* 4.3 1.6 - - - -
198D GLN 3.6 9.6 - - - +
199D ASN 3.2 1.6 + - - +
201D ALA* 1.3 73.2 - - - +
203D ILE* 1.3 65.4 + - - +
204D SER 3.3 0.9 + - - -
205D THR* 3.3 25.9 + - - +
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Residues in contact with ILE 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C PHE* 3.7 21.3 - - + -
108C VAL* 5.9 2.5 - - + -
109C SER 5.8 1.6 - - - +
110C GLY* 5.2 16.8 - - - +
111C LEU* 5.1 13.1 - - + +
68D PHE* 3.3 60.6 - - + -
77D LYS* 4.2 14.4 - - + +
78D TYR* 3.8 22.9 - - + -
199D ASN 3.2 17.2 + - - +
200D LEU* 3.3 10.1 - - - +
202D VAL* 1.3 76.9 - - - +
204D SER* 1.3 54.4 + - - +
205D THR 3.2 10.2 + - - +
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Residues in contact with SER 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D VAL* 4.0 3.3 - - - +
60D ALA* 3.0 18.5 - - - +
64D ALA* 3.6 19.3 - - - -
65D ILE* 3.5 24.4 - - - +
68D PHE* 3.6 24.9 - - - -
200D LEU* 2.7 24.3 + - - -
201D ALA 3.6 3.3 + - - +
202D VAL 3.2 0.6 - - - -
203D ILE* 1.3 75.5 - - - +
205D THR* 1.3 65.8 + - - +
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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