Contacts of the helix formed by residues 247 - 276 (chain B) in PDB entry 3N1Y
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 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B HIS* 3.3 19.7 - - - -
113B LEU* 3.7 11.8 - - + +
117B TRP* 3.0 34.3 + - + +
121B LEU* 3.8 14.4 - - - +
172B ARG* 5.1 4.6 + - - -
242B ALA* 2.8 22.8 + - + +
243B GLN* 3.8 1.4 + - - -
245B GLU 3.4 1.6 + - - -
246B GLY* 1.3 76.2 - - - +
248B THR* 1.3 58.8 + - - +
249B LEU* 3.7 0.9 - - - +
250B LEU* 2.8 33.9 + - - +
251B GLY 3.3 12.3 + - - -
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Residues in contact with THR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LEU* 4.3 10.2 - - - +
107B ARG* 5.4 9.3 + - - +
109B HIS* 3.3 12.4 + - + -
243B GLN* 4.9 16.4 - - + +
246B GLY* 3.2 14.5 + - - +
247B ASP* 1.3 69.7 - - - +
249B LEU* 1.3 61.3 + - - +
251B GLY* 3.4 1.1 + - - +
252B LEU* 3.0 43.8 + - - +
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.8 6.0 - - + +
101B PHE* 4.0 28.5 - - + +
104B LEU* 3.5 37.7 - - + -
105B ASN 5.8 0.4 - - - +
109B HIS* 3.3 22.7 + - + +
110B ASP* 4.5 0.9 - - - +
172B ARG* 3.6 50.0 - - - +
175B GLU* 4.9 0.9 - - - +
247B ASP* 3.2 1.5 - - - +
248B THR* 1.3 79.3 + - - +
250B LEU* 1.3 63.5 + - + +
252B LEU* 3.2 4.9 + - - +
253B LEU* 2.8 33.1 + - + +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TRP* 4.2 1.8 - - + -
121B LEU* 3.7 28.9 - - + -
125B TYR* 3.6 40.4 - - + -
172B ARG* 6.3 0.4 - - - +
234B LEU 5.9 1.3 - - - +
238B LEU* 4.2 15.5 - - + -
239B GLY* 5.0 3.8 - - - -
242B ALA* 3.9 18.4 - - + -
247B ASP* 2.8 25.5 + - - +
249B LEU* 1.3 75.0 - - + +
251B GLY* 1.3 61.9 + - - +
253B LEU* 4.1 13.5 - - + -
254B ALA* 2.9 37.8 + - + +
257B GLN* 5.8 1.3 - - - +
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Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B GLY* 3.7 25.5 - - - -
242B ALA* 4.1 0.8 - - - +
243B GLN* 4.7 9.4 - - - -
247B ASP 3.3 11.7 + - - -
248B THR 3.4 3.3 + - - -
249B LEU 3.3 0.8 - - - -
250B LEU* 1.3 77.9 - - - +
252B LEU* 1.3 62.2 + - - +
254B ALA* 4.0 1.9 - - - +
255B GLN* 3.3 23.7 + - - +
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR* 3.7 17.5 + - - +
100B LEU* 3.7 42.0 - - + -
104B LEU* 5.2 0.7 - - + -
248B THR* 3.0 31.6 + - - +
249B LEU* 3.7 1.6 - - - +
251B GLY* 1.3 75.7 - - - +
253B LEU* 1.3 58.9 + - - +
255B GLN* 3.2 20.4 + - - +
256B ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 4.1 23.1 - - + -
100B LEU* 4.7 5.3 - - + +
101B PHE* 4.2 15.3 - - + -
125B TYR* 3.5 24.5 - - + +
168B HIS* 3.8 41.1 - - + +
172B ARG* 4.4 5.6 - - + -
249B LEU* 2.8 28.2 + - + +
250B LEU* 3.7 13.2 - - + +
252B LEU* 1.3 73.4 - - - +
254B ALA* 1.3 62.1 - - - +
256B ALA* 3.0 6.5 + - - +
257B GLN* 2.9 38.4 + - + +
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B LEU 4.9 1.6 - - - +
235B LEU* 3.5 40.2 - - + +
239B GLY* 4.2 8.3 - - - +
250B LEU* 2.9 24.7 + - + +
251B GLY 4.0 3.1 - - - +
253B LEU* 1.3 76.6 - - - +
255B GLN* 1.3 57.3 + - - +
257B GLN* 3.3 13.7 + - - +
258B LYS* 2.9 29.7 + - - +
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Residues in contact with GLN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B GLY 3.3 13.1 + - - +
252B LEU* 3.2 26.5 + - - +
253B LEU 3.2 0.2 - - - -
254B ALA* 1.3 77.9 - - - +
256B ALA* 1.3 62.9 + - - +
258B LYS* 3.3 17.1 + - + +
259B ARG* 3.5 14.9 + - + +
262B GLU* 5.5 0.2 - - - +
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B GLN* 4.7 5.0 - - - +
96B TYR* 4.3 16.6 - - + -
97B VAL* 4.1 25.4 - - + -
164B ARG* 4.0 14.3 + - - +
252B LEU 2.9 13.7 + - - +
253B LEU* 3.0 10.3 + - - +
255B GLN* 1.3 74.9 - - - +
257B GLN* 1.3 65.1 + - + +
259B ARG* 3.3 28.9 + - - +
260B ASP 4.1 0.3 + - - -
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Residues in contact with GLN 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B TYR* 5.7 3.1 + - - -
132B PHE* 4.8 5.2 - - - -
164B ARG* 4.6 0.9 - - - +
165B TRP* 3.4 47.1 + - + +
168B HIS* 3.0 47.3 - - + +
169B THR* 4.8 3.4 + - - -
235B LEU* 3.4 27.1 - - + +
250B LEU* 5.8 1.2 - - - +
253B LEU* 2.9 28.6 + - + +
254B ALA* 3.8 10.3 - - - +
256B ALA* 1.3 72.8 - - + +
258B LYS* 1.3 57.3 + - - +
259B ARG 3.0 5.6 - - - -
260B ASP* 2.9 26.4 + - - +
261B ALA 3.2 6.8 + - - -
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Residues in contact with LYS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B GLU* 4.1 15.7 - - - -
232B GLU* 3.1 29.2 + - - -
235B LEU* 4.1 16.8 - - + +
236B GLN* 3.6 26.6 + - - +
254B ALA 2.9 17.2 + - - +
255B GLN* 3.5 12.1 - - + +
256B ALA 3.3 0.6 - - - -
257B GLN* 1.3 75.1 - - - +
259B ARG* 1.3 56.7 + - - +
261B ALA* 3.6 11.0 - - + -
262B GLU* 3.0 47.3 + - + +
265B ARG* 4.1 19.8 - - - +
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Residues in contact with ARG 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LEU* 6.2 1.0 - - - +
93B GLN* 3.4 39.8 + - + +
96B TYR* 6.5 0.7 - - - -
255B GLN* 3.8 8.3 - - + +
256B ALA* 3.3 19.5 + - - +
257B GLN 3.0 0.8 - - - -
258B LYS* 1.3 80.0 - - - +
260B ASP* 1.3 63.4 + - - +
262B GLU* 3.5 17.1 + - - +
263B ARG* 3.3 26.1 + - - +
266B ARG* 4.9 2.3 + - - -
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Residues in contact with ASP 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLN* 3.0 14.7 + - - +
93B GLN* 5.7 0.7 - - - +
161B ASP* 3.8 14.8 - - - +
164B ARG* 2.6 34.5 + - - -
165B TRP* 3.0 27.7 + - + +
256B ALA 4.7 1.2 - - - +
257B GLN 2.9 8.6 + - - +
259B ARG* 1.3 77.1 - - - +
261B ALA* 1.3 66.0 + - - +
263B ARG* 2.9 30.9 + - - +
264B HIS* 3.0 30.1 + - + -
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Residues in contact with ALA 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B TRP* 3.9 5.3 - - + -
231B GLU* 3.4 37.9 - - + +
235B LEU* 4.7 0.2 - - + -
257B GLN 3.2 3.7 + - - +
258B LYS* 3.5 22.4 - - + +
259B ARG 3.3 0.2 - - - -
260B ASP* 1.3 79.5 - - - +
262B GLU* 1.3 63.1 + - + +
264B HIS* 3.0 15.3 + - - +
265B ARG* 2.9 29.5 + - - +
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Residues in contact with GLU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B GLN 5.5 0.3 - - - +
258B LYS* 3.0 41.9 + - + +
259B ARG* 3.7 14.6 - - - +
260B ASP 3.3 0.2 - - - -
261B ALA* 1.3 75.5 - - + +
263B ARG* 1.3 58.5 + - - +
265B ARG* 3.3 19.2 + - - +
266B ARG* 3.0 45.5 + - - +
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Residues in contact with ARG 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ASP* 5.8 0.4 - - - +
79B ASP* 3.7 23.6 - - + +
81B LEU* 3.6 32.4 - - + +
86B TYR* 4.6 3.0 - - - -
89B LEU* 3.6 24.3 - - - +
90B GLN* 3.4 8.9 + - - +
161B ASP* 3.0 28.7 + - - -
259B ARG* 3.3 13.4 + - - +
260B ASP* 2.9 34.9 + - - +
262B GLU* 1.3 80.2 - - - +
264B HIS* 1.3 63.7 + - + +
266B ARG* 3.2 37.4 + - - +
267B TRP* 3.3 17.2 + - + +
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Residues in contact with HIS 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLU* 3.6 36.7 - - + +
161B ASP* 2.6 45.1 + - + +
162B HIS* 4.3 1.8 - + - -
165B TRP* 4.1 7.6 - + - -
223B ASN* 4.8 0.9 - - - +
227B LYS* 3.0 38.8 + - - -
260B ASP* 3.0 24.8 + - + -
261B ALA* 3.0 8.9 + - - +
263B ARG* 1.3 81.7 - - + +
265B ARG* 1.3 57.8 + - + +
267B TRP* 3.3 13.2 - + - -
268B SER* 2.7 33.9 + - - -
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Residues in contact with ARG 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ASN 5.7 2.7 - - - +
227B LYS* 6.4 0.7 - - - -
228B PRO* 4.0 15.1 - - + +
231B GLU* 2.8 38.9 + - - +
232B GLU* 3.1 27.7 + - - +
258B LYS* 4.1 14.0 - - - +
261B ALA* 2.9 18.1 + - - +
262B GLU* 3.6 19.3 - - - +
263B ARG 3.2 0.2 - - - -
264B HIS* 1.3 77.2 - - + +
266B ARG* 1.3 59.8 + - + +
268B SER* 3.7 6.4 - - - -
269B SER* 2.8 33.5 + - - -
320B ALA 5.4 0.4 + - - -
324B VAL* 3.6 43.9 - - + +
328B MET* 4.2 2.7 - - + +
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Residues in contact with ARG 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PRO* 3.6 12.0 - - + +
79B ASP* 2.8 43.1 + - - +
259B ARG 4.9 1.8 + - - -
262B GLU* 3.0 44.8 + - - +
263B ARG* 3.2 32.5 + - - +
265B ARG* 1.3 76.9 - - - +
267B TRP* 1.3 57.1 + - - +
269B SER* 3.6 6.0 - - - -
270B ALA* 3.1 25.5 + - - +
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Residues in contact with TRP 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PHE* 3.8 11.0 - + + -
77B ASP* 3.9 13.2 - - - +
78B PRO* 3.8 11.2 - - + +
142B ILE* 4.8 7.6 - - + -
151B ILE* 4.3 14.1 - - + -
154B CYS* 3.3 50.4 + - + +
155B ALA* 4.0 17.9 - - + -
158B GLU* 3.1 31.1 + - - +
219B PHE* 3.8 22.9 - + - -
223B ASN* 3.3 15.7 - - - -
263B ARG* 3.3 11.6 + - + +
264B HIS* 3.3 27.6 + + - +
265B ARG 3.3 0.2 - - - -
266B ARG* 1.3 77.2 - - - +
268B SER* 1.3 61.3 + - - +
270B ALA* 3.1 3.5 + - - +
271B LEU* 2.9 39.4 + - + +
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B PHE* 3.5 25.6 - - - -
223B ASN* 2.7 30.0 + - - +
224B LEU* 4.1 14.1 - - - -
264B HIS 2.7 23.6 + - - -
265B ARG* 3.7 7.1 - - - -
267B TRP* 1.3 78.0 - - - +
269B SER* 1.3 63.1 + - - +
271B LEU 3.2 0.9 + - - -
272B VAL* 3.0 27.3 + - - +
328B MET* 4.4 3.8 - - - -
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Residues in contact with SER 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ARG 2.8 18.4 + - - -
266B ARG* 3.6 6.7 - - - -
268B SER* 1.3 77.1 - - - +
270B ALA* 1.3 57.3 + - - +
272B VAL* 3.4 2.4 + - - +
273B LYS* 3.0 27.9 + - - +
327B MET 5.0 2.3 + - - -
328B MET* 3.7 34.5 - - - +
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PHE* 3.8 10.9 - - + -
76B ARG 4.5 3.1 - - - +
78B PRO* 3.7 24.5 - - + -
266B ARG 3.1 14.2 + - - +
267B TRP 3.1 9.2 + - - +
269B SER* 1.3 74.5 - - - +
271B LEU* 1.3 64.4 + - - +
273B LYS* 3.3 10.9 + - - +
274B MET* 3.0 22.5 + - - +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 5.8 1.8 - - + -
72B TRP* 3.7 27.8 - - + -
75B PHE* 3.5 26.2 - - + -
151B ILE* 3.8 17.7 - - + -
215B TRP* 4.0 23.3 - - + -
219B PHE* 3.9 22.4 - - + -
267B TRP* 2.9 34.2 + - + +
268B SER* 3.2 7.8 + - - +
270B ALA* 1.3 73.4 - - - +
272B VAL* 1.3 63.3 + - - +
274B MET* 3.2 5.7 + - - +
275B ALA* 2.9 28.4 + - + +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B PHE* 3.9 19.5 - - + -
224B LEU* 3.9 12.3 - - + -
268B SER 3.0 20.3 + - - +
269B SER 3.7 4.7 - - - +
271B LEU* 1.3 75.0 - - - +
273B LYS* 1.3 65.5 + - - +
275B ALA* 3.1 8.3 + - - +
276B LEU* 3.0 30.6 + - + +
285B LEU* 4.2 19.3 - - + -
328B MET* 3.9 45.3 - - + +
329B GLY 6.1 0.9 - - - -
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Residues in contact with LYS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B SER 3.0 14.7 + - - +
270B ALA* 3.4 12.8 - - - +
271B LEU 3.2 0.2 - - - -
272B VAL* 1.3 77.8 - - - +
274B MET* 1.3 64.9 + - - +
276B LEU* 3.2 21.4 + - - +
277B GLU* 3.8 8.3 + - - +
328B MET 5.7 1.6 - - - -
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Residues in contact with MET 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B HIS* 3.5 30.8 - - + +
71B ASP 3.1 28.0 - - - +
72B TRP* 3.9 19.5 - - + -
74B ALA* 3.8 7.6 - - + -
75B PHE* 3.7 44.4 - - + +
270B ALA 3.0 13.8 + - - +
271B LEU* 3.5 9.2 - - - +
273B LYS* 1.3 77.6 - - - +
275B ALA* 1.3 61.6 + - - +
277B GLU* 3.0 40.5 + - - +
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Residues in contact with ALA 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 4.2 27.1 - - + -
69B HIS* 4.7 1.8 - - - -
72B TRP* 4.3 15.7 - - + -
271B LEU* 2.9 14.3 + - + +
272B VAL* 3.5 11.0 - - - +
274B MET* 1.3 72.1 - - - +
276B LEU* 1.3 57.5 + - - +
277B GLU 2.9 11.1 + - - -
278B LYS* 3.1 6.8 + - - +
281B ASN* 2.9 30.8 + - + +
285B LEU* 4.3 9.0 - - + -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B VAL* 3.0 23.1 + - + +
273B LYS* 3.2 13.8 + - - +
275B ALA* 1.3 75.4 - - - +
277B GLU* 1.3 60.0 + - - +
278B LYS 3.2 6.8 - - - +
281B ASN 4.3 1.6 - - - -
282B ARG* 3.4 78.0 + - + +
285B LEU* 4.4 10.3 - - + -
328B MET 3.9 21.1 - - - +
329B GLY* 4.8 2.7 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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