Contacts of the helix formed by residues 3 - 34 (chain 5) 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 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15 MET 3.7 2.2 + - - -
25 LEU* 1.3 74.7 - - - +
45 GLU* 1.3 65.7 + - - +
55 ARG* 3.8 2.8 + - - -
65 MET* 3.0 16.7 + - - +
75 LEU* 3.0 23.1 + - - +
1115 GLU* 2.7 34.9 + - - -
1135 ASP* 5.4 1.2 + - - -
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Residues in contact with GLU 4 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25 LEU 3.9 0.6 + - - -
35 SER* 1.3 73.1 - - - +
55 ARG* 1.3 60.5 + - - +
75 LEU* 3.9 8.8 + - + +
85 LYS* 3.6 19.9 + - - +
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Residues in contact with ARG 5 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35 SER* 3.1 1.9 + - - +
45 GLU* 1.3 77.8 - - - +
65 MET* 1.3 62.8 + - - +
85 LYS* 3.6 6.5 + - - +
95 ALA* 3.3 21.4 + - - +
1075 LEU* 4.4 22.8 - - + +
1115 GLU* 3.7 22.2 - - - +
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Residues in contact with MET 6 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25 LEU* 3.8 14.6 - - + -
35 SER* 3.0 25.9 + - - +
55 ARG* 1.3 77.8 - - - +
75 LEU* 1.3 64.7 + - - +
95 ALA* 3.3 4.3 + - - +
105 LEU* 3.0 26.0 + - + +
1045 LEU* 4.1 16.6 - - - +
1075 LEU* 3.8 16.8 - - + -
1085 ALA* 3.6 38.4 - - + +
1115 GLU* 3.7 15.0 + - - +
1135 ASP* 3.6 21.3 - - + +
1165 THR* 3.8 19.5 - - - +
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Residues in contact with LEU 7 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25 LEU* 3.9 25.1 - - + +
35 SER 3.0 15.3 + - - +
45 GLU* 4.1 9.6 - - + +
65 MET* 1.3 75.9 - - - +
85 LYS* 1.3 58.1 + - - +
105 LEU* 3.4 3.4 + - - +
115 ASN* 2.9 40.6 + - - +
615 ILE* 3.8 16.2 - - + -
665 GLY* 4.0 3.1 - - - -
675 ARG* 3.6 42.6 - - + +
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Residues in contact with LYS 8 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45 GLU 3.6 13.7 + - - +
55 ARG* 3.6 6.0 + - - +
65 MET 3.3 0.4 - - - -
75 LEU* 1.3 79.9 - - - +
95 ALA* 1.3 56.6 + - - +
115 ASN* 3.5 7.9 + - + +
125 ASP* 2.9 60.4 + - - +
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Residues in contact with ALA 9 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55 ARG 3.3 12.0 + - - +
65 MET 3.3 9.3 + - - +
85 LYS* 1.3 80.5 - - - +
105 LEU* 1.3 55.9 + - - +
125 ASP* 3.7 7.3 + - - +
135 GLN* 3.3 25.5 + - - +
165 ARG* 4.6 2.1 + - - -
1045 LEU* 3.7 25.3 - - + +
1075 LEU* 3.8 17.7 - - + -
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Residues in contact with LEU 10 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25 LEU* 3.9 37.0 - - + -
65 MET* 3.0 27.4 + - + +
75 LEU* 3.8 4.5 - - - +
85 LYS 3.3 0.2 - - - -
95 ALA* 1.3 74.1 - - - +
115 ASN* 1.3 61.4 + - - +
125 ASP 3.3 0.4 - - - -
135 GLN* 3.5 0.8 + - - -
145 LEU* 3.0 27.9 + - - +
575 PHE* 3.7 36.2 - - + -
605 TYR* 3.9 15.9 - - + -
615 ILE* 3.9 18.6 - - + +
1045 LEU* 4.2 7.9 - - + -
1165 THR* 3.9 19.5 - - + -
1195 PHE* 4.2 8.3 - - + -
1205 LEU* 5.2 0.9 - - + -
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Residues in contact with ASN 11 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75 LEU* 2.9 34.3 + - - +
85 LYS* 3.7 8.8 - - + +
105 LEU* 1.3 77.4 - - - +
125 ASP* 1.3 60.5 + - - +
145 LEU* 3.4 8.1 - - - +
155 ASN* 3.2 24.9 + - - +
615 ILE* 3.6 10.4 - - - +
675 ARG 3.3 18.0 + - - -
685 VAL* 3.3 13.5 - - - +
695 GLU* 3.2 42.9 + - + +
715 ASP* 4.8 3.0 - - - +
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Residues in contact with ASP 12 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85 LYS* 2.9 51.3 + - - +
95 ALA* 3.9 8.8 - - - +
105 LEU 3.3 0.2 - - - -
115 ASN* 1.3 75.9 - - - +
135 GLN* 1.3 59.5 + - - +
155 ASN* 3.2 9.1 + - - +
165 ARG* 3.0 49.7 + - - +
715 ASP* 3.6 16.8 - - - +
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Residues in contact with GLN 13 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95 ALA 3.3 7.0 + - - +
105 LEU 4.0 4.0 - - - +
115 ASN 3.4 0.2 - - - -
125 ASP* 1.3 76.4 - - - +
145 LEU* 1.3 60.4 + - - +
155 ASN 3.2 0.4 - - - -
165 ARG* 3.0 30.9 + - - +
175 GLU* 3.0 59.8 + - - +
575 PHE* 3.4 29.2 - - + -
975 ILE* 3.9 9.3 - - - +
1005 SER* 3.0 25.9 + - - +
1015 ILE* 3.7 14.8 - - + +
1045 LEU* 3.6 22.4 - - + -
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Residues in contact with LEU 14 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105 LEU 3.0 16.1 + - - +
115 ASN* 3.4 8.5 - - - +
135 GLN* 1.3 76.3 - - - +
155 ASN* 1.3 61.8 + - - +
175 GLU* 3.6 5.8 + - - +
185 LEU* 3.3 41.9 + - + +
545 ALA* 3.6 18.0 - - + +
575 PHE* 4.0 13.1 - - + -
585 TYR* 3.6 33.4 - - + +
615 ILE* 4.1 14.1 - - + -
685 VAL* 4.1 15.0 - - + -
705 LEU* 3.8 17.9 - - + -
25N PHE* 4.3 7.6 - - + -
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Residues in contact with ASN 15 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115 ASN 3.2 13.2 + - - +
125 ASP* 3.4 12.6 - - - +
135 GLN 3.2 0.4 - - - -
145 LEU* 1.3 76.9 - - - +
165 ARG* 1.3 58.8 + - - +
185 LEU* 3.4 7.5 + - - +
195 TYR* 3.0 26.7 + - - +
705 LEU* 6.0 0.4 - - - +
715 ASP* 3.1 44.5 + - + +
725 GLU 3.4 18.0 + - - +
735 ILE* 4.1 5.7 - - - +
745 PRO* 4.7 7.3 - - - +
22N TYR* 3.5 9.9 + - - -
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Residues in contact with ARG 16 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95 ALA 4.6 2.0 + - - -
125 ASP* 3.0 33.2 + - - +
135 GLN* 3.0 55.5 + - - +
155 ASN* 1.3 75.9 - - + +
175 GLU* 1.3 60.1 + - - +
195 TYR* 3.3 8.8 + - - +
205 SER* 2.9 32.1 + - - -
965 PHE* 4.1 27.3 - - + -
975 ILE* 4.1 9.0 - - + +
1005 SER* 3.9 23.8 + - - -
1035 GLU* 5.8 2.0 + - - -
1045 LEU* 5.3 1.4 - - - +
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Residues in contact with GLU 17 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135 GLN* 3.0 41.9 + - - +
145 LEU 3.9 1.3 - - - +
155 ASN 3.4 0.4 - - - -
165 ARG* 1.3 76.2 - - - +
185 LEU* 1.3 57.0 + - - +
205 SER* 3.4 3.1 + - - -
215 ALA* 3.1 20.1 + - - +
505 GLU* 2.9 51.4 - - - +
535 HIS* 3.4 24.4 - - + +
545 ALA* 3.8 12.1 - - + +
575 PHE* 4.3 12.2 - - + -
975 ILE* 3.9 14.5 - - - +
1015 ILE* 4.5 1.7 - - - +
1235 PHE* 4.2 15.4 - - - -
1275 GLN* 4.8 3.7 + - - -
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Residues in contact with LEU 18 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145 LEU* 3.3 36.4 + - + +
155 ASN* 3.7 8.3 - - - +
165 ARG 3.3 0.4 - - - -
175 GLU* 1.3 77.4 - - - +
195 TYR* 1.3 58.6 + - - +
215 ALA* 3.4 6.6 + - + +
225 TYR* 3.0 25.1 + - - +
515 ILE* 5.0 20.0 - - + -
545 ALA* 3.8 15.7 - - + -
705 LEU* 4.2 2.2 - - + -
735 ILE* 4.0 19.1 - - + +
22N TYR* 3.6 39.3 - - + +
25N PHE* 4.3 10.1 - - + -
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Residues in contact with TYR 19 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155 ASN* 3.0 17.4 + - - +
165 ARG* 3.7 7.2 - - - +
185 LEU* 1.3 74.0 - - - +
205 SER* 1.3 55.3 + - - +
225 TYR* 3.0 3.8 + - + -
235 LEU* 2.6 50.3 + - + +
735 ILE* 4.0 13.4 - - + +
745 PRO* 3.5 49.8 - - + -
755 LYS 4.4 3.0 + - - -
765 PRO* 3.8 14.7 - - + +
775 PRO* 3.7 23.9 - - - +
935 HIS* 3.9 27.6 - + - -
965 PHE* 5.9 3.1 - + - -
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Residues in contact with SER 20 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165 ARG 2.9 19.7 + - - -
175 GLU* 3.4 7.7 - - - -
195 TYR* 1.3 76.0 - - - +
215 ALA* 1.3 61.0 + - - +
235 LEU* 3.7 2.4 - - - +
245 TYR* 3.0 35.7 + - - -
505 GLU* 3.4 26.9 + - - -
935 HIS* 2.8 33.2 + - - -
945 GLU* 5.8 0.4 - - - -
975 ILE* 3.4 14.2 - - - +
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Residues in contact with ALA 21 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175 GLU 3.1 11.5 + - - +
185 LEU* 3.5 12.8 - - + +
195 TYR 3.2 0.2 - - - -
205 SER* 1.3 77.9 - - - +
225 TYR* 1.3 57.3 + - - +
255 PHE* 3.1 27.4 + - - +
475 ALA* 3.4 32.7 - - + +
505 GLU* 3.6 10.2 - - + +
515 ILE* 3.8 19.3 - - + +
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Residues in contact with TYR 22 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185 LEU 3.0 13.8 + - - +
195 TYR* 3.0 9.5 + + + +
215 ALA* 1.3 74.3 - - - +
235 LEU* 1.3 60.7 + - - +
255 PHE* 3.5 9.3 + + + +
265 ALA* 3.0 26.0 + - - +
735 ILE* 3.8 24.5 - - + -
745 PRO 3.9 5.2 - - - -
765 PRO* 3.6 31.8 - - + +
15N ASN* 3.7 8.8 + - - +
18N LEU* 3.6 28.8 - - + +
70N LEU* 3.4 32.0 - - + +
71N ASP 2.6 31.8 + - - -
72N GLU* 4.7 0.7 - - - -
73N ILE* 3.7 20.1 - - + +
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Residues in contact with LEU 23 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195 TYR* 2.6 33.9 + - + +
205 SER 3.7 4.0 - - - +
215 ALA 3.4 0.2 - - - -
225 TYR* 1.3 73.0 - - - +
245 TYR* 1.3 62.4 + - + +
265 ALA* 3.1 4.7 + - - +
275 MET* 2.9 42.2 + - + +
765 PRO* 4.2 8.2 - - + +
775 PRO* 3.8 30.3 - - + -
805 TRP* 4.3 15.0 - - + -
895 ALA 5.3 0.9 - - - +
935 HIS* 3.5 47.8 - - + +
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Residues in contact with TYR 24 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205 SER* 3.0 26.1 + - - +
235 LEU* 1.3 78.8 - - + +
255 PHE* 1.3 59.6 + - - +
275 MET* 3.8 12.3 - - + -
285 ALA* 2.9 27.7 + - - +
425 TRP* 6.0 0.2 - + - -
435 MET* 3.4 44.7 - - + +
465 GLN* 3.7 21.5 - - + -
475 ALA* 4.2 5.8 - - + -
505 GLU* 3.8 30.5 - - + -
905 ALA* 3.8 29.3 + - + +
935 HIS* 3.8 9.9 - + - -
945 GLU* 2.5 34.8 + - - +
1345 VAL* 4.9 5.0 - - + +
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Residues in contact with PHE 25 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215 ALA 3.1 18.5 + - - +
225 TYR* 3.7 15.9 - + + +
235 LEU 3.3 0.2 - - - -
245 TYR* 1.3 76.6 - - - +
265 ALA* 1.3 58.9 + - - +
285 ALA* 3.7 9.6 - - + +
295 ALA* 3.3 23.4 + - - +
435 MET 5.8 0.2 - - - -
445 LYS* 4.8 7.6 - - + -
475 ALA* 4.2 9.8 - - + +
14N LEU* 4.2 11.4 - - + -
18N LEU* 4.2 13.2 - - + -
54N ALA* 5.1 3.4 - - + -
55N LEU* 3.7 31.4 - - + -
58N TYR* 3.7 38.1 - + + -
70N LEU* 3.5 38.7 - - + +
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Residues in contact with ALA 26 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225 TYR 3.0 15.2 + - - +
235 LEU 3.1 9.4 + - - +
255 PHE* 1.3 75.9 - - - +
275 MET* 1.3 63.8 + - - +
285 ALA 3.3 0.2 - - - -
295 ALA* 3.4 7.0 + - - +
305 TYR* 3.2 19.2 + - - +
765 PRO* 3.6 23.8 - - + -
775 PRO 3.8 15.7 - - - +
785 LYS* 4.4 4.8 - - - +
805 TRP* 4.1 6.5 - - + -
67N ARG* 4.9 0.2 + - - -
70N LEU* 3.6 11.6 - - + +
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Residues in contact with MET 27 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235 LEU* 2.9 34.5 + - + +
245 TYR* 3.5 12.8 + - + +
265 ALA* 1.3 73.5 - - - +
285 ALA* 1.3 60.2 + - - +
305 TYR* 3.2 3.4 + - - +
315 PHE* 3.0 40.8 + - + -
435 MET* 3.8 30.1 - - + -
805 TRP* 3.5 39.7 - - + -
865 ALA* 3.4 28.9 - - + +
895 ALA* 4.1 5.8 - - + -
905 ALA* 3.7 24.5 - - + +
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Residues in contact with ALA 28 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245 TYR 2.9 19.2 + - - +
255 PHE* 3.7 11.2 - - + +
275 MET* 1.3 77.0 - - - +
295 ALA* 1.3 56.0 + - - +
315 PHE 3.5 0.3 + - - -
325 GLU* 3.0 22.7 + - - +
405 ALA* 3.6 30.1 - - - +
435 MET* 3.7 9.8 - - + +
445 LYS* 3.9 16.6 - - + +
58N TYR* 3.0 15.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 29 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255 PHE 3.3 12.4 + - - +
265 ALA* 3.5 11.7 - - - +
275 MET 3.2 0.2 - - - -
285 ALA* 1.3 78.8 - - - +
305 TYR* 1.3 61.4 + - - +
335 ASP* 3.3 9.0 + - - +
58N TYR* 3.4 19.2 + - + -
62N TYR* 2.5 34.9 + - - +
67N ARG* 3.5 13.9 + - - +
68N VAL* 4.1 14.1 - - + +
70N LEU* 5.3 1.3 - - + -
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Residues in contact with TYR 30 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265 ALA 3.2 11.2 + - - +
275 MET 3.2 11.0 + - - +
295 ALA* 1.3 77.4 - - - +
315 PHE* 1.3 71.2 - + - +
335 ASP* 3.4 18.4 + - - +
345 LEU* 3.5 37.2 + - + +
785 LYS 4.1 3.8 - - - +
795 GLU* 4.3 6.3 - - + -
805 TRP* 2.9 54.2 + + + -
815 GLU 3.8 1.9 + - - -
825 SER* 3.3 24.2 - - - -
835 PRO* 3.7 1.7 - - - +
865 ALA* 4.0 23.8 - - + -
67N ARG* 3.8 25.7 - - - +
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Residues in contact with PHE 31 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275 MET* 3.0 31.3 + - + +
285 ALA* 4.0 2.2 - - - +
305 TYR* 1.3 83.3 - + - +
325 GLU* 1.3 62.3 + - - +
335 ASP 3.2 0.7 - - - -
345 LEU* 3.3 7.2 + - + +
365 LEU* 3.0 55.2 + - + +
395 PHE* 3.5 37.0 - + + -
405 ALA 3.8 6.1 - - - +
435 MET* 4.2 15.0 - - + -
835 PRO* 3.8 25.6 - - + -
865 ALA* 4.0 24.9 - - + -
875 PHE* 3.9 31.0 - + - -
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Residues in contact with GLU 32 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285 ALA 3.0 7.6 + - - +
295 ALA 3.8 4.5 - - - +
315 PHE* 1.3 76.3 - - - +
335 ASP* 1.3 61.4 + - - +
355 GLY* 3.3 12.5 + - - -
365 LEU 4.6 2.0 - - - +
375 GLU* 3.6 30.7 - - - +
405 ALA* 3.4 14.3 - - - +
415 ASN* 5.1 0.3 - - - +
445 LYS* 3.0 29.3 + - - -
58N TYR* 3.1 23.4 + - - +
59N ASN* 5.8 0.9 - - - -
62N TYR* 3.6 36.7 - - + +
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Residues in contact with ASP 33 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295 ALA 3.3 11.6 + - - +
305 TYR* 3.4 13.2 - - - +
315 PHE 3.2 0.4 - - - -
325 GLU* 1.3 80.8 - - - +
345 LEU* 1.3 62.2 + - - +
355 GLY 3.1 5.3 + - - -
795 GLU* 5.3 2.8 - - - +
62N TYR* 3.7 7.1 - - + -
66N GLY 4.3 9.4 - - - +
67N ARG* 3.5 33.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305 TYR* 3.5 49.7 + - + +
315 PHE* 3.3 9.1 + - + +
335 ASP* 1.3 82.5 - - + +
355 GLY* 1.3 57.7 + - - +
365 LEU* 3.2 31.6 + - + +
835 PRO* 4.2 12.1 - - + -
139L ASP* 6.0 1.7 - - - +
143L PHE* 5.3 10.5 - - + -
----------------------------------------------------------
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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