Contacts of the helix formed by residues 3 - 34 (chain 8) in PDB entry 2X17
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 3 (chain 8).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18 MET 3.8 1.0 + - - -
28 LEU* 1.3 77.1 - - - +
48 GLU* 1.3 64.2 + - - +
58 ARG* 3.7 2.9 + - - -
68 MET* 3.2 17.4 + - - +
78 LEU* 3.1 23.6 + - - +
1118 GLU* 2.7 33.4 + - - -
1138 ASP* 5.5 0.4 + - - -
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Residues in contact with GLU 4 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28 LEU 4.1 0.2 + - - -
38 SER* 1.3 74.3 - - - +
58 ARG* 1.3 61.6 + - - +
78 LEU* 4.0 10.6 - - + +
88 LYS* 3.3 22.9 + - - +
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Residues in contact with ARG 5 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38 SER* 3.2 2.3 - - - +
48 GLU* 1.3 77.8 - - - +
68 MET* 1.3 59.6 + - - +
88 LYS* 3.4 8.6 + - - +
98 ALA* 3.1 27.0 + - + +
1078 LEU* 4.2 27.6 - - + -
1118 GLU* 3.9 17.5 - - - +
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Residues in contact with MET 6 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28 LEU* 3.8 23.8 - - + -
38 SER* 3.2 27.0 + - - +
58 ARG* 1.3 75.7 - - - +
78 LEU* 1.3 61.0 + - - +
98 ALA* 3.2 2.4 + - - +
108 LEU* 2.9 32.9 + - + +
1048 LEU* 4.2 16.4 - - - -
1078 LEU* 3.6 39.5 - - + +
1088 ALA* 3.7 20.6 - - + +
1118 GLU* 4.0 11.2 + - + +
1138 ASP* 4.1 10.3 - - - +
1168 THR* 3.8 19.7 - - + +
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Residues in contact with LEU 7 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28 LEU* 3.9 23.0 - - + +
38 SER 3.1 16.7 + - - +
48 GLU* 4.0 10.1 - - + +
68 MET* 1.3 76.2 - - - +
88 LYS* 1.3 56.9 + - - +
108 LEU* 3.5 4.6 + - - +
118 ASN* 2.9 45.7 + - - +
618 ILE* 3.8 16.6 - - + -
668 GLY* 4.0 3.6 - - - -
678 ARG* 3.6 43.7 - - + +
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Residues in contact with LYS 8 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48 GLU* 3.3 16.9 + - - +
58 ARG* 3.6 8.5 - - + +
68 MET 3.2 0.6 - - - -
78 LEU* 1.3 80.4 - - - +
98 ALA* 1.3 55.7 + - - +
118 ASN* 3.6 6.4 + - - +
128 ASP* 3.1 52.6 + - - +
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Residues in contact with ALA 9 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58 ARG 3.1 16.2 + - - +
68 MET 3.2 4.7 + - - +
88 LYS* 1.3 74.4 - - - +
108 LEU* 1.3 63.9 + - - +
128 ASP* 3.5 7.5 + - - +
138 GLN* 3.2 22.9 + - - +
168 ARG* 4.5 2.1 + - - +
1048 LEU* 3.8 25.5 - - + +
1078 LEU* 3.8 18.6 - - + -
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Residues in contact with LEU 10 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28 LEU* 3.9 33.7 - - + -
68 MET* 2.9 28.4 + - + +
78 LEU 3.9 3.8 - - - +
98 ALA* 1.3 75.0 - - - +
118 ASN* 1.3 58.0 + - - +
138 GLN* 3.4 3.8 + - - +
148 LEU* 3.1 26.3 + - - +
578 PHE* 3.8 35.0 - - + -
608 TYR* 3.9 20.6 - - + -
618 ILE* 3.9 19.7 - - + +
1048 LEU* 4.2 9.0 - - + -
1168 THR* 4.1 17.5 - - + -
1198 PHE* 4.2 8.1 - - + -
1208 LEU* 5.3 0.9 - - + -
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Residues in contact with ASN 11 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78 LEU* 2.9 35.9 + - - +
88 LYS* 3.8 7.1 - - - +
108 LEU* 1.3 76.6 - - - +
128 ASP* 1.3 61.1 + - - +
148 LEU* 3.4 8.4 - - - +
158 ASN* 3.2 24.3 + - - +
618 ILE* 4.0 7.3 - - - +
678 ARG 3.2 20.8 + - - -
688 VAL* 3.3 12.6 - - - +
698 GLU* 2.8 46.4 + - + +
718 ASP* 4.8 3.3 - - - +
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Residues in contact with ASP 12 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88 LYS* 3.1 43.8 + - - +
98 ALA* 3.8 8.2 - - - +
108 LEU 3.3 0.2 - - - -
118 ASN* 1.3 77.2 - - - +
138 GLN* 1.3 58.9 + - - +
158 ASN* 3.3 7.2 + - - +
168 ARG* 2.9 48.5 + - - +
718 ASP* 3.5 19.4 - - - +
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Residues in contact with GLN 13 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98 ALA 3.2 8.7 + - - +
108 LEU 3.8 4.3 - - - +
128 ASP* 1.3 71.5 - - - +
148 LEU* 1.3 58.3 + - - +
158 ASN 3.1 1.8 - - - -
168 ARG* 3.0 27.0 + - - +
178 GLU* 2.8 60.8 + - - +
578 PHE* 3.3 30.1 - - + -
978 ILE* 3.9 9.5 - - - +
1008 SER* 3.0 29.3 + - - -
1018 ILE* 3.7 14.3 - - + +
1048 LEU* 3.6 26.2 - - + +
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Residues in contact with LEU 14 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108 LEU 3.1 11.9 + - - +
118 ASN* 3.4 13.0 - - - +
138 GLN* 1.3 76.3 - - - +
158 ASN* 1.3 60.6 + - - +
178 GLU* 3.6 6.6 + - - +
188 LEU* 3.3 31.4 + - + +
548 ALA* 3.5 19.4 - - + +
578 PHE* 4.0 13.5 - - + -
588 TYR* 3.6 31.2 - - + +
618 ILE* 4.1 6.5 - - + -
688 VAL* 3.9 24.5 - - + -
698 GLU 6.0 0.4 - - - +
708 LEU* 3.8 27.6 - - + -
25Q PHE* 4.3 7.4 - - + -
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Residues in contact with ASN 15 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118 ASN 3.2 11.8 + - - +
128 ASP* 3.4 12.6 - - - +
138 GLN 3.1 0.4 - - - -
148 LEU* 1.3 78.8 - - - +
168 ARG* 1.3 62.9 + - - +
188 LEU* 3.5 7.1 + - - +
198 TYR* 3.2 22.5 + - - +
708 LEU* 5.2 1.0 - - - +
718 ASP* 3.0 49.6 + - - +
728 GLU 3.4 16.4 + - - +
738 ILE* 4.5 5.4 - - - +
748 PRO* 4.9 5.4 - - - +
22Q TYR* 3.5 9.9 + - - -
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Residues in contact with ARG 16 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98 ALA* 4.5 3.0 + - - +
128 ASP* 2.9 32.4 + - - +
138 GLN* 3.0 54.8 + - - +
158 ASN* 1.3 75.1 - - + +
178 GLU* 1.3 63.3 + - - +
198 TYR* 3.5 7.1 + - - +
208 SER* 3.1 26.0 + - - -
938 HIS* 4.8 0.7 + - - -
968 PHE* 4.2 28.5 - - + -
978 ILE* 3.8 9.3 - - + +
1008 SER* 3.8 23.4 + - - -
1038 GLU* 5.5 3.8 + - - -
1048 LEU* 5.2 2.0 - - - +
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Residues in contact with GLU 17 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138 GLN* 2.8 37.3 + - - +
148 LEU 3.8 4.5 - - - +
158 ASN 3.3 0.2 - - - -
168 ARG* 1.3 76.3 - - - +
188 LEU* 1.3 63.2 + - - +
208 SER* 3.3 7.3 + - - -
218 ALA 3.3 16.6 + - - -
508 GLU* 3.0 38.3 - - - +
538 HIS* 3.3 26.5 + - + +
548 ALA* 3.9 18.4 - - + +
578 PHE* 4.2 15.2 - - + -
978 ILE* 3.8 15.0 - - - +
1018 ILE* 4.6 1.4 - - - +
1238 PHE* 4.3 10.0 - - - -
1278 GLN* 4.2 6.1 + - - -
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Residues in contact with LEU 18 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148 LEU* 3.3 34.8 + - + +
158 ASN* 3.9 7.0 - - - +
168 ARG 3.4 0.2 - - - -
178 GLU* 1.3 75.6 - - - +
198 TYR* 1.3 64.0 + - - +
218 ALA* 3.5 7.7 - - + +
228 TYR* 3.2 21.1 + - - +
508 GLU 5.3 0.4 - - - -
518 ILE* 4.9 21.1 - - + -
548 ALA* 3.8 15.9 - - + -
708 LEU* 4.1 2.2 - - + -
738 ILE* 4.2 17.4 - - + +
22Q TYR* 3.6 39.3 - - + +
25Q PHE* 4.3 10.3 - - + -
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Residues in contact with TYR 19 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158 ASN* 3.2 17.0 + - - +
168 ARG* 3.9 6.3 - - - +
178 GLU 3.3 0.2 - - - -
188 LEU* 1.3 73.2 - - - +
208 SER* 1.3 54.8 + - - +
228 TYR* 3.2 2.7 + - + -
238 LEU* 2.7 48.8 + - + +
738 ILE* 4.0 14.1 - - + +
748 PRO* 3.4 51.4 - - + -
758 LYS 4.4 2.2 + - - -
768 PRO* 3.8 14.9 - - + +
778 PRO* 3.7 24.4 - - - +
938 HIS* 3.9 27.8 - + - -
968 PHE* 6.0 1.6 - + - -
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Residues in contact with SER 20 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168 ARG 3.1 13.1 + - - -
178 GLU* 3.3 12.1 + - - -
198 TYR* 1.3 77.5 - - - +
218 ALA* 1.3 57.2 + - - +
238 LEU* 3.3 3.1 + - - +
248 TYR* 2.9 43.0 + - - -
508 GLU* 3.4 23.3 + - - -
938 HIS* 2.9 30.1 + - - -
948 GLU* 5.7 0.4 - - - -
978 ILE* 3.4 12.8 - - - +
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Residues in contact with ALA 21 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178 GLU 3.3 5.4 + - - +
188 LEU* 3.5 12.1 - - + +
198 TYR 3.3 0.2 - - - -
208 SER* 1.3 78.0 - - - +
228 TYR* 1.3 56.3 + - - +
248 TYR 3.3 1.0 + - - -
258 PHE* 2.9 27.0 + - - +
478 ALA* 3.3 37.7 - - + +
508 GLU* 3.6 14.3 - - + +
518 ILE* 3.8 19.3 - - + +
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Residues in contact with TYR 22 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188 LEU 3.2 10.0 + - - +
198 TYR* 3.2 8.8 + - + +
218 ALA* 1.3 77.2 - - - +
238 LEU* 1.3 60.0 + - - +
258 PHE* 3.4 10.8 + + + +
268 ALA* 3.0 26.2 + - - +
738 ILE* 3.8 24.2 - - + -
748 PRO 4.0 4.9 - - - -
768 PRO* 3.6 29.5 - - + +
15Q ASN* 3.9 7.6 + - - -
18Q LEU* 3.6 31.2 - - + +
70Q LEU* 3.4 32.8 - - + +
71Q ASP 2.7 31.5 + - - -
73Q ILE* 3.6 21.9 - - + +
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Residues in contact with LEU 23 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198 TYR* 2.7 35.2 + - + +
208 SER* 3.7 4.3 - - - +
228 TYR* 1.3 74.2 - - - +
248 TYR* 1.3 61.6 + - + +
268 ALA* 3.2 4.0 + - - +
278 MET* 2.9 52.4 + - + +
768 PRO* 4.1 7.3 - - + +
778 PRO* 3.8 29.6 - - + -
808 TRP* 4.1 8.5 - - + -
898 ALA 5.3 0.7 - - - +
938 HIS* 3.6 46.0 - - + +
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Residues in contact with TYR 24 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208 SER* 2.9 27.8 + - - +
218 ALA 3.8 4.3 - - - +
238 LEU* 1.3 78.3 - - + +
258 PHE* 1.3 60.4 + - - +
278 MET* 3.5 11.2 + - + -
288 ALA* 2.9 22.0 + - - +
428 TRP* 5.8 0.9 - + - -
438 MET* 3.3 53.0 - - + +
468 GLN* 3.8 18.8 - - + -
478 ALA* 4.0 2.9 - - + -
508 GLU* 3.4 35.9 - - + -
908 ALA* 3.9 28.8 + - + +
938 HIS* 4.5 9.1 - + - -
948 GLU* 2.6 35.1 + - - +
1348 VAL* 4.6 6.1 - - + +
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Residues in contact with PHE 25 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218 ALA 2.9 16.8 + - - +
228 TYR* 3.6 17.0 - + + +
238 LEU 3.3 0.2 - - - -
248 TYR* 1.3 77.4 - - - +
268 ALA* 1.3 61.5 + - - +
288 ALA* 3.6 9.1 - - + +
298 ALA* 3.3 20.3 + - - +
438 MET 5.3 0.2 - - - -
448 LYS* 4.7 9.2 - - + -
478 ALA* 4.2 8.0 - - + +
14Q LEU* 4.2 11.0 - - + -
18Q LEU* 4.3 12.6 - - + -
54Q ALA* 5.0 3.8 - - + -
55Q LEU* 3.8 28.5 - - + -
58Q TYR* 3.7 41.3 - + + -
68Q VAL* 5.6 0.2 - - + -
70Q LEU* 3.7 37.2 - - + +
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Residues in contact with ALA 26 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228 TYR 3.0 13.9 + - - +
238 LEU 3.2 9.4 + - - +
258 PHE* 1.3 76.5 - - - +
278 MET* 1.3 58.6 + - - +
298 ALA* 3.4 7.8 + - - +
308 TYR* 3.1 23.2 + - - +
768 PRO* 3.8 20.0 - - + -
778 PRO 3.7 20.9 - - - +
788 LYS* 4.6 4.0 - - - +
808 TRP* 4.1 6.5 - - + -
67Q ARG* 5.0 0.2 + - - -
70Q LEU* 3.7 10.3 - - + +
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Residues in contact with MET 27 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238 LEU* 2.9 32.9 + - + +
248 TYR* 3.8 13.5 - - + +
258 PHE 3.4 0.2 - - - -
268 ALA* 1.3 73.2 - - - +
288 ALA* 1.3 66.4 + - - +
308 TYR* 3.1 3.7 + - + +
318 PHE* 3.0 37.3 + - + -
438 MET* 3.7 31.6 - - + -
808 TRP* 3.6 39.3 - - + -
868 ALA* 3.5 27.8 - - + +
898 ALA* 4.3 4.9 - - + -
908 ALA* 3.8 24.5 - - + +
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Residues in contact with ALA 28 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248 TYR 2.9 18.3 + - - +
258 PHE* 3.6 12.1 - - + +
278 MET* 1.3 76.7 - - - +
298 ALA* 1.3 56.2 + - - +
318 PHE 3.5 0.2 + - - -
328 GLU* 3.0 21.7 + - - +
408 ALA* 3.5 29.3 - - - +
438 MET* 3.8 10.2 - - + +
448 LYS* 3.9 17.0 - - + +
58Q TYR* 3.0 16.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 29 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258 PHE 3.3 11.1 + - - +
268 ALA* 3.5 11.7 - - - +
278 MET 3.2 0.2 - - - -
288 ALA* 1.3 79.4 - - - +
308 TYR* 1.3 61.4 + - - +
328 GLU 3.5 0.3 + - - -
338 ASP* 3.1 16.3 + - - +
58Q TYR* 3.6 19.0 + - + -
62Q TYR* 2.6 31.3 + - - +
67Q ARG* 3.7 11.6 + - - +
68Q VAL* 4.1 14.6 - - + +
70Q LEU* 5.6 1.6 - - + -
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Residues in contact with TYR 30 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268 ALA 3.1 13.6 + - - +
278 MET* 3.1 8.0 + - - +
298 ALA* 1.3 78.0 - - - +
318 PHE* 1.3 72.1 + + - +
338 ASP* 3.5 7.7 + - + +
348 LEU* 3.5 47.8 + - + +
798 GLU* 4.4 4.7 - - + -
808 TRP* 2.9 61.8 + + + -
818 GLU 3.7 1.9 + - - -
828 SER* 3.3 22.8 - - - -
838 PRO* 3.6 4.4 - - - +
868 ALA* 3.8 26.0 - - + -
67Q ARG* 3.9 21.9 - - - +
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Residues in contact with PHE 31 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278 MET* 3.0 32.6 + - + +
288 ALA 4.1 1.8 - - - +
308 TYR* 1.3 82.8 - + - +
328 GLU* 1.3 63.2 + - - +
348 LEU* 3.1 9.2 + - + +
368 LEU* 2.9 56.1 + - + +
398 PHE* 3.4 26.7 - + + -
408 ALA 3.8 4.7 - - - +
438 MET* 3.9 30.3 - - + -
838 PRO* 3.6 29.2 - - + -
868 ALA* 4.0 17.0 - - + -
878 PHE* 3.8 26.0 - + - -
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Residues in contact with GLU 32 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288 ALA 3.0 8.1 + - - +
298 ALA 3.7 4.7 - - - +
308 TYR 3.4 0.2 - - - -
318 PHE* 1.3 76.6 - - - +
338 ASP* 1.3 62.1 + - - +
358 GLY* 3.2 13.1 + - - +
368 LEU 4.5 2.7 - - - +
378 GLU* 3.4 31.5 - - - +
408 ALA* 3.5 13.6 - - - +
418 ASN* 4.9 0.7 - - - +
448 LYS* 2.9 29.5 + - - -
58Q TYR* 3.0 26.9 + - - +
59Q ASN* 6.0 0.2 - - - -
62Q TYR* 3.7 34.6 - - + -
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Residues in contact with ASP 33 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298 ALA 3.1 14.5 + - - +
308 TYR* 3.5 12.1 - - - +
328 GLU* 1.3 79.0 - - - +
348 LEU* 1.3 62.6 + - - +
358 GLY* 3.1 3.9 + - - -
798 GLU* 5.4 3.1 - - - +
62Q TYR* 3.6 7.8 - - + -
66Q GLY 4.2 9.9 - - - +
67Q ARG* 3.6 35.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308 TYR* 3.5 50.6 + - + +
318 PHE* 3.1 10.1 + - + +
338 ASP* 1.3 80.1 - - + +
358 GLY* 1.3 60.4 + - - +
368 LEU* 3.5 28.1 + - + +
838 PRO* 4.1 10.8 - - + -
139N ASP* 6.1 0.3 - - - +
143N PHE* 5.4 9.2 - - - -
----------------------------------------------------------
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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