Contacts of the helix formed by residues 3 - 35 (chain 9) 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 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19 MET 3.8 1.6 + - - -
29 LEU* 1.3 76.5 - - - +
49 GLU* 1.3 63.6 + - - +
59 ARG* 3.6 3.4 + - - +
69 MET* 3.1 18.0 + - - +
79 LEU* 3.1 23.6 + - - +
1119 GLU* 2.7 32.0 + - - -
1139 ASP* 5.5 0.8 + - - -
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Residues in contact with GLU 4 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39 SER* 1.3 75.0 - - - +
59 ARG* 1.3 61.0 + - - +
79 LEU* 3.8 8.5 + - + +
89 LYS* 3.8 17.8 + - - +
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Residues in contact with ARG 5 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39 SER* 3.2 3.7 + - - +
49 GLU* 1.3 78.4 - - - +
69 MET* 1.3 64.1 + - - +
89 LYS* 3.7 5.1 + - - +
99 ALA* 3.4 20.6 + - - +
1079 LEU* 4.4 20.1 - - + +
1119 GLU* 3.7 19.1 - - - +
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Residues in contact with MET 6 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29 LEU* 3.8 16.2 - - + -
39 SER* 3.1 29.2 + - - +
59 ARG* 1.3 76.3 - - - +
79 LEU* 1.3 64.4 + - - +
99 ALA* 3.2 4.3 + - - +
109 LEU* 3.0 31.1 + - + +
1049 LEU* 4.2 17.5 - - - -
1079 LEU* 3.9 15.9 - - + +
1089 ALA* 3.7 33.0 - - + +
1119 GLU* 3.7 19.0 + - - +
1139 ASP* 3.7 20.6 - - + +
1169 THR* 3.8 18.6 - - - +
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Residues in contact with LEU 7 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29 LEU* 3.9 19.0 - - + +
39 SER 3.1 15.7 + - - +
49 GLU* 4.1 7.9 - - + +
59 ARG 3.4 0.2 - - - -
69 MET* 1.3 76.5 - - - +
89 LYS* 1.3 54.9 - - - +
109 LEU* 3.5 7.7 + - - +
119 ASN* 2.8 46.1 + - - +
619 ILE* 3.8 16.2 - - + -
669 GLY* 4.0 3.8 - - - -
679 ARG* 3.7 42.0 - - + +
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Residues in contact with LYS 8 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49 GLU 3.8 9.4 + - - +
59 ARG* 3.7 9.0 + - - +
69 MET 3.3 0.4 - - - -
79 LEU* 1.3 76.2 - - - +
99 ALA* 1.3 59.8 + - - +
119 ASN* 3.7 7.0 - - + +
129 ASP* 2.8 52.0 + - - +
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Residues in contact with ALA 9 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59 ARG 3.4 12.2 + - - +
69 MET 3.2 9.1 + - - +
89 LYS* 1.3 78.1 - - - +
109 LEU* 1.3 60.3 + - - +
129 ASP* 4.1 6.3 - - - +
139 GLN* 3.3 23.0 + - - +
169 ARG* 4.2 3.4 + - - +
1049 LEU* 3.7 26.9 - - + +
1079 LEU* 3.8 17.7 - - + -
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Residues in contact with LEU 10 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29 LEU* 3.8 38.8 - - + -
69 MET* 3.0 25.8 + - + +
79 LEU* 3.8 3.8 - - - +
99 ALA* 1.3 75.9 - - - +
119 ASN* 1.3 58.9 + - - +
139 GLN* 3.5 2.9 + - - +
149 LEU* 3.0 28.2 + - - +
579 PHE* 4.0 31.6 - - + -
609 TYR* 4.1 12.1 - - + -
619 ILE* 3.8 21.3 - - + +
1049 LEU* 4.0 12.1 - - + -
1169 THR* 3.9 19.5 - - + -
1199 PHE* 4.3 8.3 - - + -
1209 LEU* 5.3 1.1 - - + -
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Residues in contact with ASN 11 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79 LEU* 2.8 38.4 + - - +
89 LYS* 3.3 8.8 + - + +
109 LEU* 1.3 76.5 - - - +
129 ASP* 1.3 59.7 + - - +
149 LEU* 3.4 9.7 - - - +
159 ASN* 3.2 24.4 + - - +
619 ILE* 4.1 7.3 - - - +
679 ARG 3.3 19.2 + - - -
689 VAL* 3.3 12.3 - - - +
699 GLU* 2.9 43.6 + - + +
719 ASP* 4.8 4.3 - - - +
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Residues in contact with ASP 12 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89 LYS* 2.8 48.8 + - - +
99 ALA* 4.1 5.3 - - - +
119 ASN* 1.3 75.9 - - - +
139 GLN* 1.3 59.2 + - - +
159 ASN* 3.2 8.5 + - - +
169 ARG* 2.8 52.2 + - - +
719 ASP* 3.5 18.2 - - - +
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Residues in contact with GLN 13 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99 ALA 3.3 15.8 + - - +
109 LEU 3.8 3.8 - - - +
119 ASN 3.4 0.2 - - - -
129 ASP* 1.3 75.8 - - - +
149 LEU* 1.3 56.2 + - - +
169 ARG* 3.4 21.4 + - - +
179 GLU* 2.8 62.6 + - - +
579 PHE* 3.4 30.1 - - + -
979 ILE* 3.9 9.3 - - - +
1009 SER* 2.9 38.1 + - - +
1019 ILE* 3.7 14.9 - - + +
1049 LEU* 3.6 13.2 - - + -
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Residues in contact with LEU 14 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109 LEU 3.0 15.4 + - - +
119 ASN* 3.4 10.5 - - - +
139 GLN* 1.3 74.6 - - - +
159 ASN* 1.3 57.0 + - - +
179 GLU* 3.6 6.2 + - - +
189 LEU* 3.2 44.6 + - + +
549 ALA* 3.5 17.5 - - + +
579 PHE* 3.9 14.5 - - + -
589 TYR* 3.5 33.9 - - + +
619 ILE* 4.0 6.3 - - + -
689 VAL* 4.0 21.8 - - + -
699 GLU 5.8 0.9 - - - +
709 LEU* 3.8 19.1 - - + -
25R PHE* 4.5 6.5 - - + -
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Residues in contact with ASN 15 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119 ASN 3.2 9.7 + - - +
129 ASP* 3.2 11.9 + - - +
139 GLN 3.1 0.4 - - - -
149 LEU* 1.3 78.6 - - - +
169 ARG* 1.3 62.0 + - - +
189 LEU* 3.2 7.2 + - - +
199 TYR* 2.9 29.3 + - - +
709 LEU* 6.4 0.2 - - - -
719 ASP* 3.6 31.7 + - + +
729 GLU 3.2 27.7 + - - +
739 ILE* 4.0 8.7 - - - +
749 PRO* 4.8 6.8 - - - +
22R TYR* 4.0 7.4 + - - -
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Residues in contact with ARG 16 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99 ALA* 4.2 4.2 + - - +
129 ASP* 2.8 36.2 + - + +
139 GLN* 3.4 58.4 + - - +
159 ASN* 1.3 74.2 - - - +
179 GLU* 1.3 58.1 + - - +
199 TYR* 3.3 9.2 + - - +
209 SER* 2.9 32.5 + - - -
969 PHE* 4.6 22.0 - - + -
979 ILE* 4.1 10.4 - - + +
1009 SER* 3.7 23.5 + - - -
1039 GLU* 5.3 4.9 + - - -
1049 LEU* 5.2 2.2 - - - +
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Residues in contact with GLU 17 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139 GLN* 2.8 42.1 + - - +
149 LEU 3.8 5.8 - - - +
169 ARG* 1.3 72.1 - - - +
189 LEU* 1.3 60.5 + - - +
209 SER* 3.5 6.6 - - - -
219 ALA* 3.2 16.5 + - - +
509 GLU* 2.9 48.8 - - - +
539 HIS* 3.4 21.6 + - + +
549 ALA* 4.0 8.1 - - + +
579 PHE* 4.0 23.2 - - + -
979 ILE* 3.9 13.9 - - - +
1019 ILE* 4.5 1.6 - - - +
1239 PHE* 4.2 10.0 - - - -
1279 GLN* 4.8 4.5 + - - -
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Residues in contact with LEU 18 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149 LEU* 3.2 39.9 + - + +
159 ASN* 3.2 7.6 + - - +
179 GLU* 1.3 75.8 - - - +
199 TYR* 1.3 64.1 + - - +
219 ALA* 3.4 7.4 + - + +
229 TYR* 3.2 19.8 + - - +
519 ILE* 4.9 20.2 - - + -
549 ALA* 3.8 16.4 - - + -
709 LEU* 4.0 3.4 - - + -
739 ILE* 4.3 17.7 - - + +
22R TYR* 3.7 35.9 - - + +
25R PHE* 4.2 12.1 - - + -
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Residues in contact with TYR 19 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159 ASN* 2.9 18.5 + - - +
169 ARG* 3.7 7.4 - - - +
189 LEU* 1.3 73.4 - - - +
209 SER* 1.3 56.6 + - - +
229 TYR* 2.9 5.0 + - + +
239 LEU* 2.7 49.2 + - + +
739 ILE* 4.0 15.1 - - + +
749 PRO* 3.6 48.9 - - + -
759 LYS 4.3 3.5 + - - -
769 PRO* 3.9 14.6 - - + +
779 PRO* 3.7 23.6 - - - +
939 HIS* 3.9 26.2 - + - -
969 PHE* 5.8 4.3 - + - -
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Residues in contact with SER 20 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169 ARG 2.9 19.1 + - - -
179 GLU* 3.5 11.6 + - - -
199 TYR* 1.3 76.6 - - - +
219 ALA* 1.3 55.9 + - - +
239 LEU* 3.2 4.0 + - - +
249 TYR* 3.0 41.2 + - - -
509 GLU* 3.7 21.4 + - - -
939 HIS* 2.8 32.7 + - - -
949 GLU* 5.8 0.4 - - - -
979 ILE* 3.3 13.9 - - - +
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Residues in contact with ALA 21 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179 GLU 3.2 5.7 + - - +
189 LEU* 3.4 12.6 - - + +
199 TYR 3.2 0.4 - - - -
209 SER* 1.3 78.0 - - - +
229 TYR* 1.3 56.9 + - - +
259 PHE* 3.0 29.1 + - - +
479 ALA* 3.4 33.8 - - + +
509 GLU* 3.7 14.7 - - + +
519 ILE* 3.8 19.3 - - + +
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Residues in contact with TYR 22 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189 LEU 3.2 12.5 + - - +
199 TYR* 2.9 9.5 + - + +
219 ALA* 1.3 75.8 - - - +
239 LEU* 1.3 59.5 + - - +
259 PHE* 3.8 10.2 - + - +
269 ALA* 3.0 26.7 + - - +
739 ILE* 3.8 25.1 - - + -
749 PRO 3.9 5.2 - - - -
769 PRO* 3.6 31.6 - - + +
15R ASN* 3.4 11.6 + - - -
18R LEU* 3.6 29.3 - - + +
70R LEU* 3.4 26.0 - - + +
71R ASP 2.7 30.3 + - - -
72R GLU* 4.8 0.9 - - - -
73R ILE* 3.7 20.2 - - + -
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Residues in contact with LEU 23 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199 TYR* 2.7 33.2 + - + +
209 SER* 3.6 5.4 - - - +
229 TYR* 1.3 73.6 - - - +
249 TYR* 1.3 62.2 + - + +
269 ALA* 3.1 4.9 + - - +
279 MET* 2.9 53.8 + - + +
769 PRO* 4.2 8.2 - - + +
779 PRO* 3.8 30.3 - - + -
809 TRP* 4.4 6.7 - - + -
899 ALA 5.5 0.2 - - - +
939 HIS* 3.5 48.5 - - + +
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Residues in contact with TYR 24 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209 SER* 3.0 31.8 + - - +
219 ALA 4.1 3.6 - - - +
239 LEU* 1.3 76.8 - - + +
259 PHE* 1.3 59.3 + - - +
279 MET* 3.3 12.2 + - + +
289 ALA* 2.8 22.5 + - - +
429 TRP* 5.7 1.1 - + - -
439 MET* 3.4 50.6 - - + +
469 GLN* 4.0 17.9 - - + -
479 ALA* 4.2 2.9 - - + +
509 GLU* 3.7 32.1 - - + -
909 ALA* 3.8 29.4 + - + +
939 HIS* 4.1 10.8 - + - -
949 GLU* 2.5 36.2 + - - +
1349 VAL* 4.8 5.4 - - + +
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Residues in contact with PHE 25 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219 ALA 3.0 19.0 + - - +
229 TYR* 3.8 16.2 - + - +
239 LEU 3.3 0.2 - - - -
249 TYR* 1.3 76.4 - - - +
269 ALA* 1.3 61.9 + - - +
289 ALA* 3.4 8.5 - - + +
299 ALA* 3.3 18.7 + - - +
449 LYS* 4.8 9.0 - - + -
479 ALA* 4.2 9.1 - - + +
14R LEU* 4.5 5.2 - - + -
18R LEU* 4.3 18.8 - - + -
54R ALA* 5.3 3.6 - - + -
55R LEU* 3.7 27.8 - - + -
58R TYR* 3.6 40.2 - + + -
70R LEU* 3.6 37.7 - - + +
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Residues in contact with ALA 26 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229 TYR 3.0 15.2 + - - +
239 LEU 3.1 9.8 + - - +
259 PHE* 1.3 75.8 - - - +
279 MET* 1.3 63.8 + - - +
289 ALA 3.2 0.2 - - - -
299 ALA* 3.2 7.3 + - - +
309 TYR* 3.1 20.3 + - - +
769 PRO* 3.7 26.0 - - + -
779 PRO 3.9 13.5 - - - +
789 LYS* 4.6 3.3 - - - +
809 TRP* 4.1 5.9 - - + -
70R LEU* 3.6 11.6 - - + +
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Residues in contact with MET 27 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239 LEU* 2.9 34.9 + - + +
249 TYR* 3.3 15.0 + - + +
269 ALA* 1.3 71.8 - - - +
289 ALA* 1.3 65.7 + - - +
309 TYR* 3.2 2.6 + - - +
319 PHE* 3.0 36.3 + - + -
439 MET* 3.8 31.9 - - + -
809 TRP* 3.5 37.7 - - + -
869 ALA* 3.4 30.7 - - + +
899 ALA* 4.2 6.5 - - + -
909 ALA* 3.8 23.8 - - + +
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Residues in contact with ALA 28 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249 TYR 2.8 16.8 + - - +
259 PHE* 3.4 13.7 - - + +
269 ALA 3.2 0.2 - - - -
279 MET* 1.3 76.9 - - - +
299 ALA* 1.3 55.3 + - - +
319 PHE 3.5 0.5 + - - -
329 GLU* 2.9 25.5 + - - +
409 ALA* 3.5 28.5 - - - +
439 MET* 3.7 9.4 - - + +
449 LYS* 3.9 17.5 - - + +
58R TYR* 3.0 13.1 + - - +
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Residues in contact with ALA 29 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259 PHE 3.3 9.6 + - - +
269 ALA* 3.2 13.2 + - - +
289 ALA* 1.3 75.8 - - - +
309 TYR* 1.3 66.4 + - - +
329 GLU 3.5 0.2 + - - -
339 ASP* 3.2 12.3 + - - +
58R TYR* 3.4 19.0 + - + -
62R TYR* 2.5 31.4 + - - +
67R ARG* 3.5 13.3 + - - +
68R VAL* 4.1 14.1 - - + +
70R LEU* 5.5 2.9 - - + -
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Residues in contact with TYR 30 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269 ALA 3.1 6.3 + - - +
279 MET* 3.2 9.8 + - - +
299 ALA* 1.3 76.9 - - - +
319 PHE* 1.3 77.9 + + - +
339 ASP* 3.3 13.5 + - + +
349 LEU* 3.4 40.7 + - + +
789 LYS 4.1 3.4 - - - +
799 GLU* 4.4 10.1 - - + -
809 TRP* 3.2 66.8 + + + -
819 GLU 3.9 1.4 + - - -
829 SER* 3.3 22.3 - - - -
839 PRO* 3.5 7.7 - - - +
869 ALA* 3.9 23.1 - - + -
67R ARG* 3.9 14.3 - - - +
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Residues in contact with PHE 31 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279 MET* 3.0 31.8 + - + +
289 ALA 4.0 1.8 - - - +
309 TYR* 1.3 83.3 - + - +
329 GLU* 1.3 61.9 + - - +
349 LEU* 3.3 5.5 + - + +
359 GLY 3.3 4.5 + - - -
369 LEU* 3.0 44.9 + - + +
399 PHE* 3.5 37.5 - + + -
409 ALA 3.8 5.4 - - - +
439 MET* 3.7 33.7 - - + -
839 PRO* 3.7 27.6 - - + -
869 ALA* 3.9 16.8 - - + -
879 PHE* 3.6 27.4 - + - -
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Residues in contact with GLU 32 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289 ALA 2.9 7.0 + - - +
299 ALA 3.7 5.2 - - - +
309 TYR 3.3 0.2 - - - -
319 PHE* 1.3 77.3 - - - +
339 ASP* 1.3 62.3 + - - +
359 GLY* 3.4 11.9 + - - +
369 LEU 4.6 2.7 - - - +
379 GLU* 3.5 30.7 - - - +
409 ALA* 3.3 14.9 - - - +
419 ASN* 4.7 0.9 - - - +
449 LYS* 3.0 28.0 + - - -
58R TYR* 3.1 25.7 + - - +
62R TYR* 3.8 34.4 - - + -
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Residues in contact with ASP 33 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299 ALA 3.2 12.6 + - - +
309 TYR* 3.5 11.6 - - + +
319 PHE 3.2 0.4 - - - -
329 GLU* 1.3 77.6 - - - +
349 LEU* 1.3 65.1 + - - +
359 GLY* 3.1 1.3 + - - -
799 GLU* 5.1 4.3 - - - +
62R TYR* 3.6 11.7 - - + -
66R GLY 4.4 6.1 - - - +
67R ARG* 3.5 35.3 + - - +
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Residues in contact with LEU 34 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309 TYR* 3.4 51.5 + - + +
319 PHE* 3.3 8.8 + - + +
339 ASP* 1.3 83.1 - - + +
359 GLY* 1.3 59.6 + - - +
369 LEU* 4.2 16.9 - - + +
839 PRO* 3.9 20.6 - - + -
139K ASP* 5.8 2.8 - - - +
143K PHE* 5.6 6.9 - - - -
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Residues in contact with GLY 35 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319 PHE 3.3 2.0 + - - -
329 GLU 3.4 10.0 + - - -
339 ASP 3.1 4.9 - - - -
349 LEU* 1.3 79.3 - - - +
369 LEU* 1.3 62.2 + - - +
379 GLU* 3.2 14.1 + - - +
1559 ASP* 4.7 1.9 - - - +
136K LYS* 6.1 0.3 - - - +
139K ASP* 5.9 7.0 - - - -
140K LYS* 4.3 20.7 - - - +
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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) + - + + + + + -
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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