Contacts of the helix formed by residues 60 - 96 (chain B) in PDB entry 2YPT
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 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 5.5 0.4 - - - -
56B GLY 5.1 2.0 - - - -
59B MET* 1.3 75.7 - - - +
61B SER* 1.4 55.6 + - - +
62B GLU* 3.4 15.8 + - - +
63B THR* 2.7 38.9 + - - -
64B PHE* 2.8 33.1 + - - +
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 5.1 12.2 + - - +
60B ASP* 1.4 71.9 - - - +
62B GLU* 1.4 56.6 + - - +
64B PHE* 3.8 9.5 - - - +
65B GLU* 3.1 30.3 + - - +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ASP* 3.3 13.0 + - - +
61B SER* 1.4 74.6 - - - +
63B THR* 1.4 59.9 + - - +
65B GLU* 4.0 3.1 - - - +
66B LYS* 3.1 28.6 + - - +
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Residues in contact with THR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B MET* 4.6 10.8 - - + -
60B ASP* 2.7 34.9 + - - +
62B GLU* 1.4 76.3 - - - +
64B PHE* 1.4 57.3 - - - +
66B LYS* 3.4 7.2 + - - +
67B SER* 2.9 28.9 + - - -
440B LYS* 4.2 28.5 - - + +
443B LEU* 3.6 13.9 - - + +
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Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B THR* 3.5 17.9 - - - -
49B THR* 3.5 25.1 - - - -
50B HIS 3.8 16.8 - - - -
51B VAL* 4.3 15.7 - - + -
52B PRO* 4.1 16.8 - - + -
59B MET* 4.7 11.6 - - + +
60B ASP 2.8 23.1 + - - +
61B SER* 3.8 8.5 - - - +
63B THR* 1.4 71.8 - - - +
65B GLU* 1.4 56.4 + - + +
67B SER* 3.3 6.4 + - - -
68B ARG* 2.8 36.4 + - - +
445B PHE* 3.5 35.3 - + - -
446B PRO* 4.2 24.7 - - + -
447B VAL* 4.6 1.8 - - + -
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Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B THR* 3.7 18.7 + - - +
61B SER* 3.1 19.4 + - - +
62B GLU* 4.1 3.8 - - - +
64B PHE* 1.4 73.3 - - + +
66B LYS* 1.4 58.9 + - - +
68B ARG* 2.8 46.9 + - - +
69B LEU* 3.1 34.4 + - + +
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Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU 3.1 18.9 + - - +
63B THR* 3.5 8.5 - - - +
64B PHE 3.3 0.2 - - - -
65B GLU* 1.4 75.2 - - - +
67B SER* 1.4 60.3 + - - +
69B LEU* 4.2 3.7 - - - +
70B TYR* 3.3 23.7 + - - +
153B HIS* 4.6 3.1 + - - -
443B LEU* 3.7 20.5 - - + +
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR* 2.9 18.9 + - - -
64B PHE* 3.5 8.1 - - - -
66B LYS* 1.4 74.8 - - - +
68B ARG* 1.4 58.1 + - - +
70B TYR* 3.7 0.7 - - - +
71B GLN* 3.0 32.7 + - - +
443B LEU* 2.8 38.8 + - - +
444B GLY 3.3 3.6 - - - -
445B PHE* 3.2 25.5 + - - -
446B PRO* 5.7 1.8 - - - -
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Residues in contact with ARG 68 (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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45B TYR* 2.8 28.5 + - - +
46B LYS* 3.2 28.3 + - - +
48B THR 3.6 17.8 + - - -
49B THR* 3.6 21.6 + - - +
64B PHE* 2.8 24.3 + - - +
65B GLU* 2.8 48.2 + - - +
67B SER* 1.4 73.0 - - - +
69B LEU* 1.4 57.6 + - - +
71B GLN* 4.0 2.4 - - - +
72B LEU* 3.1 29.7 + - + +
445B PHE* 3.7 19.7 - - + -
54E GLU* 4.2 6.5 + - - -
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Residues in contact with LEU 69 (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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65B GLU* 3.1 21.7 + - + +
66B LYS* 4.2 4.9 - - - +
68B ARG* 1.4 74.5 - - - +
70B TYR* 1.4 60.1 + - - +
72B LEU* 3.5 5.9 + - - +
73B ASP* 3.1 36.8 + - - +
153B HIS* 3.7 13.0 - - + +
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Residues in contact with TYR 70 (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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66B LYS 3.3 18.7 + - - +
67B SER 3.7 2.7 - - - +
68B ARG 3.4 0.2 - - - -
69B LEU* 1.4 76.3 - - - +
71B GLN* 1.3 87.6 + - - +
73B ASP* 3.5 3.3 + - - +
74B LYS* 3.1 30.8 + - + +
149B ILE* 4.3 10.7 - - + +
150B GLU* 3.1 33.9 + - - -
153B HIS* 3.5 35.8 - + + +
155B PHE* 3.5 26.5 - + - -
263B HIS* 3.3 13.6 - + - -
442B ASN 3.7 10.8 - - - -
443B LEU* 3.7 20.0 - - + -
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Residues in contact with GLN 71 (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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45B TYR* 3.6 38.1 + - + -
67B SER 3.0 20.8 + - - +
68B ARG 4.2 0.7 - - - +
70B TYR* 1.3 90.1 - - - +
72B LEU* 1.4 60.1 + - - +
74B LYS* 3.7 10.8 - - - +
75B SER* 3.0 28.1 + - - -
442B ASN 4.6 1.2 + - - -
443B LEU 3.1 23.3 + - - +
444B GLY* 4.2 6.1 - - - -
445B PHE* 3.9 22.0 - - + -
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TYR* 4.7 14.8 - - + +
68B ARG* 3.1 19.6 + - + +
69B LEU* 3.6 9.2 - - - +
70B TYR 3.3 0.4 - - - -
71B GLN* 1.4 74.6 - - - +
73B ASP* 1.4 56.5 + - - +
75B SER* 3.3 7.2 + - - -
76B THR* 2.7 36.5 + - - -
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Residues in contact with ASP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.1 13.1 + - - +
70B TYR 3.8 2.5 - - - +
72B LEU* 1.4 75.0 - - - +
74B LYS* 1.3 60.7 + - - +
76B THR* 3.6 7.9 + - - -
77B PHE* 3.3 23.4 + - - +
149B ILE* 4.3 17.5 - - + +
152B LYS* 4.7 9.2 - - - +
153B HIS* 2.9 36.1 + - + +
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Residues in contact with LYS 74 (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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70B TYR* 3.1 23.4 + - + +
71B GLN* 3.7 16.6 - - - +
72B LEU 3.3 0.2 - - - -
73B ASP* 1.3 76.1 - - - +
75B SER* 1.4 57.1 + - - +
77B PHE* 3.5 7.1 + - - +
78B SER* 2.9 30.6 + - - -
149B ILE* 4.6 13.2 - - + +
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Residues in contact with SER 75 (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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38B ALA* 4.4 8.0 + - - +
42B ARG* 3.7 24.5 - - - +
45B TYR* 4.5 13.4 - - - -
71B GLN 3.0 19.2 + - - -
72B LEU* 3.3 8.3 + - - -
74B LYS* 1.4 72.5 - - - +
76B THR* 1.4 62.7 + - - +
78B SER* 3.4 8.3 + - - -
79B PHE* 3.1 22.9 + - - +
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Residues in contact with THR 76 (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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72B LEU 2.7 19.7 + - - -
73B ASP* 3.9 7.9 - - - -
74B LYS 3.4 0.2 - - - -
75B SER* 1.4 73.7 - - - +
77B PHE* 1.4 61.4 + - - +
79B PHE* 3.4 12.0 + - + +
80B TRP* 3.2 40.3 + - + +
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Residues in contact with PHE 77 (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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73B ASP 3.3 15.1 + - - +
74B LYS* 3.8 6.1 - - - +
76B THR* 1.4 74.3 - - - +
78B SER* 1.4 57.6 + - - +
79B PHE 3.2 0.3 + - - -
80B TRP* 3.4 4.6 + - + +
81B SER* 2.9 58.0 + - - -
141B TRP* 3.2 52.9 - + + -
142B SER* 5.5 0.2 - - - -
144B TYR* 3.5 32.3 - + + -
145B ASN* 4.0 22.7 - - + -
149B ILE* 3.6 16.6 - - + -
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Residues in contact with SER 78 (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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74B LYS 2.9 19.9 + - - -
75B SER* 3.4 10.5 - - - -
76B THR 3.4 0.2 - - - -
77B PHE* 1.4 78.0 - - - +
79B PHE* 1.4 56.2 + - - +
81B SER* 3.4 6.4 + - - -
82B GLY* 3.1 23.9 + - - -
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Residues in contact with PHE 79 (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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31B TYR* 3.8 20.6 + + - -
35B THR* 4.2 22.4 - - + -
75B SER 3.1 12.5 + - - +
76B THR* 3.6 9.2 - - - +
77B PHE 3.2 0.2 - - - -
78B SER* 1.4 75.4 - - - +
80B TRP* 1.4 102.0 + + - +
82B GLY* 3.2 2.1 + - - -
83B LEU* 2.7 57.3 + - + +
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Residues in contact with TRP 80 (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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144A TYR* 3.7 38.6 - + - -
76B THR* 3.2 39.2 + - + +
77B PHE* 3.4 5.6 + - + +
79B PHE* 1.4 95.9 - + - +
81B SER* 1.4 59.5 + - - +
83B LEU* 3.7 28.1 - - + +
84B TYR* 3.0 30.3 + - - +
141B TRP* 3.9 16.3 - - + -
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 2.9 41.5 + - - -
78B SER* 3.4 10.6 + - - -
80B TRP* 1.4 75.8 - - - +
82B GLY* 1.3 55.8 + - - +
84B TYR* 3.7 3.3 + - - +
85B SER* 2.8 32.3 + - - -
141B TRP* 3.7 32.4 - - - -
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Residues in contact with GLY 82 (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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31B TYR* 3.9 11.6 - - - -
78B SER 3.1 12.6 + - - -
79B PHE 3.5 3.8 - - - -
81B SER* 1.3 82.0 + - - +
83B LEU* 1.3 58.2 + - - +
85B SER* 3.5 7.2 + - - -
86B GLU* 3.1 27.5 + - - +
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Residues in contact with LEU 83 (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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144A TYR* 5.4 6.3 - - + -
28B TRP* 4.9 8.7 - - + -
31B TYR* 3.3 31.3 + - + +
79B PHE* 2.7 44.4 + - + +
80B TRP* 3.7 31.2 - - + +
82B GLY* 1.3 71.2 - - - +
84B TYR* 1.4 55.9 + - - +
86B GLU 3.4 1.2 + - - -
87B THR* 2.8 47.4 + - - +
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Residues in contact with TYR 84 (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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84A TYR* 3.0 23.8 + + - -
137A ALA* 3.1 20.6 + - - +
140A PRO* 3.8 23.3 - - + -
141A TRP* 3.3 27.1 - + - -
80B TRP 3.0 18.2 + - - +
81B SER 3.9 5.8 - - - +
83B LEU* 1.4 74.9 - - - +
85B SER* 1.4 57.3 + - - +
87B THR* 3.4 5.1 + - - -
88B GLU* 2.8 59.4 + - + +
137B ALA* 4.5 12.1 - - + +
141B TRP* 3.6 39.0 - + + -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B SER 2.8 20.2 + - - -
82B GLY* 3.5 10.6 - - - -
83B LEU 3.3 0.2 - - - -
84B TYR* 1.4 81.2 - - - +
86B GLU* 1.4 56.7 + - - +
88B GLU* 3.2 7.6 + - - +
89B GLY* 2.9 28.1 + - - -
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER* 3.2 36.3 - - - +
28B TRP* 3.7 28.4 + - + -
31B TYR* 3.5 37.7 - - + +
82B GLY 3.1 13.8 + - - +
83B LEU 3.8 4.0 - - - +
85B SER* 1.4 78.5 - - - +
87B THR* 1.4 56.7 + - - +
89B GLY* 4.3 1.2 - - - -
90B THR* 2.8 33.8 + - - -
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Residues in contact with THR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PRO* 3.9 16.6 - - + +
143A LEU* 3.7 29.6 - - + -
28B TRP* 4.5 12.3 - - + -
83B LEU* 2.8 35.1 + - - +
84B TYR* 3.7 5.6 - - - -
86B GLU* 1.4 72.6 - - - +
88B GLU* 1.4 54.4 + - - +
90B THR* 3.3 2.9 + - - -
91B LEU* 2.8 53.6 + - + +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU 2.8 29.8 - - - +
137A ALA* 3.3 7.2 - - - -
140A PRO* 3.4 16.8 - - + +
84B TYR* 2.8 54.6 + - + +
85B SER* 3.5 6.5 - - - +
87B THR* 1.4 72.7 - - - +
89B GLY* 1.3 56.5 + - - +
91B LEU* 3.3 3.8 + - - +
92B ILE* 2.9 63.4 + - + +
133B PHE* 4.3 9.1 - - + -
137B ALA* 5.8 1.5 - - + +
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Residues in contact with GLY 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER 2.9 14.8 + - - -
86B GLU* 4.3 1.6 - - - -
88B GLU* 1.3 75.3 - - - +
90B THR* 1.3 62.8 + - - +
92B ILE* 3.5 6.2 + - - +
93B LEU* 3.1 35.1 + - - +
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.9 18.7 - - + +
27B SER* 6.0 0.3 - - - -
28B TRP* 2.7 39.6 + - + +
86B GLU* 2.8 23.7 + - - -
87B THR* 3.3 4.8 + - - -
89B GLY* 1.3 75.5 - - - +
91B LEU* 1.3 58.4 + - + +
93B LEU* 3.4 4.6 + - - +
94B LEU* 3.0 52.1 + - + +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 5.0 2.9 - - + +
139A LEU* 3.7 26.0 - - + +
140A PRO* 3.5 43.7 - - + -
143A LEU* 3.9 21.5 - - + -
164A MET* 3.7 28.1 - - + +
87B THR* 2.8 29.7 + - + +
88B GLU* 3.3 6.7 + - - +
90B THR* 1.3 72.4 - - + +
92B ILE* 1.4 55.5 + - + +
94B LEU* 4.0 7.1 - - + +
95B PHE* 2.8 38.6 + - - +
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 3.9 27.4 - - + -
88B GLU* 2.9 48.3 + - + +
89B GLY* 3.9 6.1 - - - +
91B LEU* 1.4 70.6 - - - +
93B LEU* 1.4 57.7 + - + +
95B PHE 3.8 0.3 - - - -
96B GLY 3.0 8.0 + - - -
97B GLY* 2.8 38.6 + - - -
98B ILE* 4.1 26.4 + - + +
133B PHE* 4.0 24.5 - - + -
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 4.0 22.5 - - + -
23B VAL* 5.4 1.6 - - + -
24B LEU* 4.0 22.2 - - + -
27B SER* 6.2 0.2 - - - +
89B GLY* 3.1 26.4 + - - +
90B THR* 3.7 4.7 - - - +
92B ILE* 1.4 76.9 - - + +
94B LEU* 1.4 61.5 + - - +
96B GLY* 3.3 13.2 + - - -
98B ILE* 3.7 26.0 - - + -
376B PHE* 3.7 33.8 - - + +
394B PHE* 3.7 28.5 - - + -
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A MET* 3.9 31.9 - - + +
168A ILE* 4.5 7.1 - - - +
20B PHE* 4.1 17.0 - - + -
24B LEU* 3.8 21.5 - - + -
90B THR* 3.0 39.5 + - + +
91B LEU* 4.0 4.9 - - + +
93B LEU* 1.4 73.9 - - - +
95B PHE* 1.4 62.0 + - - +
96B GLY* 3.4 0.9 + - - -
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Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 5.1 6.1 - - + -
135A ALA* 4.9 9.0 - - + -
136A LEU* 4.0 22.9 - - + -
139A LEU* 3.7 22.7 - - + -
164A MET* 3.7 10.9 - - + +
167A ALA* 3.8 22.2 - - + -
168A ILE* 3.7 39.1 - - + +
171A PHE* 3.7 50.3 - + + -
91B LEU 2.8 24.3 + - - +
92B ILE 4.1 2.5 - - - +
94B LEU* 1.4 71.8 - - - +
96B GLY* 1.3 60.9 + - - +
97B GLY* 5.0 3.8 - - - -
100B TYR* 6.3 0.4 - + - -
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Residues in contact with GLY 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE 3.0 5.4 + - - -
93B LEU* 3.3 9.4 + - - -
94B LEU 3.2 4.6 - - - -
95B PHE* 1.3 81.4 - - - +
97B GLY* 1.3 65.8 + - - +
99B PRO* 3.5 21.6 - - - +
100B TYR* 3.5 16.3 + - - +
376B PHE 5.4 1.8 - - - -
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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