Contacts of the helix formed by residues 302 - 327 (chain E) in PDB entry 3EXG
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 SER 302 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E PHE* 4.0 17.9 - - - -
296E VAL* 4.4 4.0 - - - -
301E ALA* 1.3 75.3 - - - +
303E VAL* 1.3 65.6 + - - +
304E GLU* 2.8 22.7 + - - +
305E GLU* 3.0 35.6 + - - +
306E LEU* 3.2 12.3 + - - +
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Residues in contact with VAL 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292E LYS* 3.2 32.8 + - - +
296E VAL* 3.9 20.5 - - + +
302E SER* 1.3 71.1 - - - +
304E GLU* 1.3 83.0 + - + +
306E LEU* 3.7 3.1 + - - +
307E LYS* 2.9 29.8 + - + +
206L HIS* 6.2 4.5 - - + -
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Residues in contact with GLU 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E SER* 2.8 26.1 + - - +
303E VAL* 1.3 93.4 - - + +
305E GLU* 1.3 59.5 + - - +
307E LYS* 3.4 6.7 + - - +
308E GLU* 2.9 39.8 + - + +
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Residues in contact with GLU 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E PHE* 3.7 8.0 - - + -
29E ARG* 2.9 31.3 + - - -
33E LEU* 4.2 10.4 - - - +
301E ALA* 3.2 28.1 - - - +
302E SER* 3.0 24.4 + - - +
304E GLU* 1.3 75.6 - - - +
306E LEU* 1.3 63.3 + - + +
308E GLU* 3.1 25.0 + - - +
309E ILE* 3.1 22.1 + - + +
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Residues in contact with LEU 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 4.3 8.7 - - + -
36E TYR* 3.7 39.6 + - + +
292E LYS* 3.6 40.4 - - + +
295E MET* 4.0 28.7 - - + -
296E VAL* 4.6 7.9 - - + -
301E ALA* 4.3 7.9 - - + -
302E SER 3.2 13.2 + - - +
303E VAL* 3.9 4.0 - - - +
305E GLU* 1.3 79.5 - - + +
307E LYS* 1.3 58.5 + - - +
309E ILE* 3.0 31.1 + - + +
310E ASP* 3.1 17.7 + - - +
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Residues in contact with LYS 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E LYS* 5.7 4.0 - - - +
303E VAL* 2.9 24.0 + - + +
304E GLU* 3.6 8.3 - - - +
305E GLU 3.3 0.2 - - - -
306E LEU* 1.3 75.7 - - - +
308E GLU* 1.3 58.1 + - - +
310E ASP* 3.3 29.0 - - - +
311E VAL* 3.2 22.0 - - + +
205L THR* 3.8 25.6 + - - +
206L HIS* 5.0 11.5 + - + +
255L LYS 3.6 21.8 + - - -
256L THR 4.8 1.8 + - - -
257L ASN* 4.2 18.4 + - - -
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Residues in contact with GLU 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304E GLU* 2.9 32.2 + - + +
305E GLU* 3.3 13.4 - - - +
306E LEU 3.1 0.6 - - - -
307E LYS* 1.3 75.6 - - - +
309E ILE* 1.3 62.6 + - + +
310E ASP 3.2 0.2 - - - -
311E VAL* 3.1 11.9 + - + +
312E GLU* 3.0 36.5 + - + +
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Residues in contact with ILE 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 4.2 27.4 - - + +
36E TYR* 4.3 10.3 - - + -
37E ARG* 3.5 59.9 - - + +
40E GLN* 5.7 0.4 - - + -
305E GLU* 3.3 16.6 - - + +
306E LEU* 3.0 26.4 + - + +
308E GLU* 1.3 75.8 - - + +
310E ASP* 1.3 58.4 + - - +
312E GLU* 3.2 5.1 + - - +
313E VAL* 2.9 31.9 + - + +
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Residues in contact with ASP 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E TYR* 3.2 21.1 + - - -
40E GLN* 3.0 33.2 - - - +
44E ARG* 5.4 0.7 - - - +
306E LEU 3.1 6.4 + - - -
307E LYS* 3.3 44.9 - - + +
309E ILE* 1.3 75.0 - - - +
311E VAL* 1.3 57.6 + - - +
313E VAL* 3.4 6.7 + - - +
314E ARG* 3.0 30.7 + - - +
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Residues in contact with VAL 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E LYS* 3.2 24.5 - - + +
308E GLU* 3.1 11.8 + - + +
310E ASP* 1.3 77.1 - - - +
312E GLU* 1.3 69.0 + - + +
314E ARG* 3.5 4.5 + - - +
315E LYS* 3.2 24.0 + - + +
254L MET 4.1 18.4 - - - +
255L LYS* 3.9 36.1 - - + +
287L PHE* 5.6 0.9 - - - -
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Residues in contact with GLU 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ARG* 2.7 39.9 + - - +
308E GLU* 3.0 22.7 + - - +
309E ILE* 3.6 9.6 + - - +
311E VAL* 1.3 79.5 - - + +
313E VAL* 1.3 64.2 + - - +
315E LYS* 3.4 5.5 + - - +
316E GLU* 3.0 24.4 + - - +
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Residues in contact with VAL 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ARG* 4.1 24.9 - - + +
40E GLN* 3.7 23.6 - - + +
41E THR* 3.7 26.9 - - + +
44E ARG* 3.6 27.4 - - + -
309E ILE* 2.9 21.9 + - + +
310E ASP* 3.6 5.6 - - - +
312E GLU* 1.3 77.0 - - - +
314E ARG* 1.3 58.5 + - - +
316E GLU* 2.8 30.2 - - + +
317E ILE* 2.9 12.1 + - + +
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Residues in contact with ARG 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ARG* 3.2 49.2 - - + +
310E ASP 3.0 17.7 + - - +
311E VAL* 4.2 4.0 - - - +
312E GLU 3.4 0.2 - - - -
313E VAL* 1.3 77.8 - - - +
315E LYS* 1.3 61.7 + - - +
317E ILE* 3.5 7.9 + - - +
318E GLU* 3.0 31.1 + - - +
257L ASN* 3.3 23.5 + - - +
286L ASN 3.0 28.2 + - - -
287L PHE* 3.1 37.8 + - + -
288L LEU 4.0 1.4 + - - -
289L ASP* 3.0 26.5 + - - -
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Residues in contact with LYS 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E VAL* 3.2 15.8 + - + +
312E GLU* 3.7 9.4 - - - +
314E ARG* 1.3 73.5 - - - +
316E GLU* 1.3 66.1 + - - +
318E GLU* 3.1 3.7 + - + +
319E ASP* 2.9 61.4 + - - +
254L MET* 5.7 8.0 - - - -
287L PHE* 4.2 16.4 - - + -
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Residues in contact with GLU 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ARG* 5.5 5.5 + - - +
41E THR* 5.7 4.9 - - + -
102E VAL* 5.6 9.2 - - + -
312E GLU 3.0 15.6 + - - +
313E VAL* 2.8 20.2 - - + +
315E LYS* 1.3 76.2 - - - +
317E ILE* 1.3 64.4 + - + +
319E ASP* 3.3 13.0 + - - +
320E ALA* 3.1 22.9 + - - +
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Residues in contact with ILE 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E THR* 4.2 10.1 - - + +
44E ARG* 3.6 28.5 - - + +
45E MET* 3.8 16.4 - - + +
48E LYS* 3.6 39.0 - - + -
102E VAL* 3.6 32.5 - - + -
106E LEU* 4.8 3.6 - - + -
313E VAL* 2.9 18.5 + - + +
314E ARG* 3.8 9.4 - - + +
316E GLU* 1.3 76.8 - - + +
318E GLU* 1.3 62.0 + - - +
320E ALA* 3.0 4.3 + - - +
321E ALA* 2.7 29.1 + - - +
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Residues in contact with GLU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E LYS* 3.0 38.2 + - - -
314E ARG* 3.0 23.7 + - - +
315E LYS* 3.6 4.5 - - + +
317E ILE* 1.3 83.3 - - - +
319E ASP* 1.3 62.1 + - - +
321E ALA* 4.1 4.0 - - - +
322E GLN* 3.2 24.4 + - - +
283L PRO 5.2 2.9 - - - +
286L ASN* 3.6 27.8 + - + +
287L PHE* 3.8 27.5 - - + -
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Residues in contact with ASP 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ARG* 4.9 7.8 + - - +
315E LYS* 2.9 48.2 + - - +
316E GLU* 3.4 16.0 + - - +
318E GLU* 1.3 75.1 - - - +
320E ALA* 1.3 59.0 + - - +
322E GLN* 3.5 12.9 + - - +
323E PHE* 3.2 23.7 + - - +
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Residues in contact with ALA 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E VAL* 4.0 28.0 - - + +
103E ARG* 4.2 28.9 - - + +
106E LEU* 4.4 4.3 - - + -
316E GLU 3.1 12.5 + - - +
317E ILE 3.0 6.7 + - - +
319E ASP* 1.3 73.5 - - - +
321E ALA* 1.3 54.5 + - - +
322E GLN 3.1 0.9 - - - -
323E PHE* 2.7 8.7 + - - +
324E ALA* 2.7 33.8 + - - +
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Residues in contact with ALA 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E LYS* 3.7 39.7 - - + -
52E LEU* 4.3 6.1 - - + -
106E LEU* 3.7 13.4 - - + +
317E ILE 2.7 18.4 + - - +
318E GLU* 4.1 4.9 - - - +
320E ALA* 1.3 72.3 - - - +
322E GLN* 1.3 61.7 + - - +
324E ALA* 3.7 3.8 - - - +
325E THR* 3.0 29.7 + - + +
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Residues in contact with GLN 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ARG* 5.9 1.2 - - - +
318E GLU 3.2 15.2 + - - +
319E ASP* 3.5 15.4 + - - +
320E ALA 3.1 1.4 - - - -
321E ALA* 1.3 79.8 - - - +
323E PHE* 1.3 73.4 + - - +
325E THR* 3.6 6.9 + - - +
326E ALA* 3.3 26.7 + - - +
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Residues in contact with PHE 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ARG* 3.3 66.0 - - + +
107E ALA* 3.9 21.3 - - + -
114E GLY* 4.4 13.5 - - - -
319E ASP 3.2 13.7 + - - +
320E ALA 2.7 9.2 + - - +
322E GLN* 1.3 87.9 - - - +
324E ALA* 1.3 66.2 + - - +
326E ALA* 3.2 2.8 + - - +
327E ASP* 3.0 53.5 + - + +
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Residues in contact with ALA 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 5.8 1.1 - - + -
103E ARG 4.9 0.2 - - - +
106E LEU* 3.9 13.2 - - + -
107E ALA* 3.7 32.1 - - + +
110E THR* 3.2 21.9 + - + +
112E ARG* 3.3 17.8 + - - +
320E ALA 2.7 18.5 + - - +
321E ALA* 3.7 6.1 - - - +
323E PHE* 1.3 81.8 - - + +
325E THR* 1.3 59.5 + - + +
326E ALA 3.4 0.5 + - - -
327E ASP* 4.0 1.1 + - - -
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Residues in contact with THR 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LEU* 3.7 30.5 - - + -
57E ILE* 4.6 15.0 - - + -
110E THR* 4.6 4.9 - - + -
112E ARG* 3.0 21.7 + - - +
321E ALA* 3.0 23.3 + - + +
322E GLN* 3.6 8.3 + - - -
324E ALA* 1.3 77.2 - - - +
326E ALA* 1.3 59.0 + - - +
328J ASN* 5.8 4.3 - - - +
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Residues in contact with ALA 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E ARG* 4.4 0.6 + - - -
322E GLN* 3.3 25.7 + - - +
323E PHE* 3.2 3.9 + - - +
325E THR* 1.3 83.6 + - - +
327E ASP* 1.3 68.2 + - - +
328E PRO* 3.5 4.2 - - - +
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Residues in contact with ASP 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ALA* 5.6 0.4 - - + -
112E ARG* 3.1 38.8 + - + +
113E LYS* 3.5 12.8 + - - +
114E GLY* 2.8 35.6 + - - -
323E PHE* 3.0 41.1 + - + +
324E ALA* 4.2 1.3 - - - +
325E THR 3.7 0.2 - - - -
326E ALA* 1.3 76.7 - - - +
328E PRO* 1.3 78.7 - - - +
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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
------------------------------------------------------------
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