Contacts of the helix formed by residues 60 - 96 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 4.6 0.2 - - - -
56A GLY 5.1 2.2 - - - -
59A MET* 1.3 74.6 - - - +
61A SER* 1.4 55.1 + - - +
62A GLU* 3.4 15.9 + - - +
63A THR* 2.7 38.7 + - - +
64A PHE* 2.8 33.3 + - - +
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 3.8 24.1 - - - +
60A ASP* 1.4 72.6 - - - +
62A GLU* 1.4 56.8 + - - +
64A PHE* 3.9 1.0 - - - +
65A GLU* 3.1 30.5 + - - +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASP* 3.3 13.0 + - - +
61A SER* 1.4 75.2 - - - +
63A THR* 1.3 58.9 + - - +
65A GLU* 4.0 4.7 - - - +
66A LYS* 3.1 54.8 + - + +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A MET* 4.5 10.5 - - + -
60A ASP* 2.7 36.0 + - - +
62A GLU* 1.3 75.8 - - - +
64A PHE* 1.4 58.3 + - - +
66A LYS* 3.4 11.1 + - + +
67A SER* 3.0 29.6 + - - -
440A LYS* 4.3 33.2 - - + +
443A LEU* 5.5 2.9 - - + +
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Residues in contact with PHE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A THR* 3.6 19.3 - - - -
49A THR 4.0 9.4 - - - -
50A HIS 3.8 23.3 - - - -
51A VAL* 3.8 31.0 - - + -
52A PRO* 4.0 15.3 - - + -
55A LEU 5.8 0.2 - - - -
59A MET* 4.5 11.3 - - + +
60A ASP 2.8 20.9 + - - +
61A SER 3.9 2.5 - - - +
63A THR* 1.4 71.5 - - - +
65A GLU* 1.3 61.5 + - - +
67A SER* 3.4 6.3 + - - -
68A ARG* 2.8 30.8 + - + +
445A PHE* 3.5 29.9 - + - -
446A PRO* 3.8 33.7 - - + -
447A VAL* 4.5 5.2 - - + -
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR* 3.7 18.7 + - - +
61A SER* 3.1 19.1 + - - +
62A GLU* 4.1 5.4 - - - +
64A PHE* 1.3 75.4 - - + +
66A LYS* 1.4 59.6 + - - +
68A ARG* 2.8 45.9 + - - +
69A LEU* 3.0 34.0 + - + +
46E LYS 5.3 4.7 - - - +
49E THR* 6.2 0.2 - - - +
68E ARG* 5.8 5.8 - - - +
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 3.1 43.6 + - + +
63A THR* 3.5 10.5 - - + +
65A GLU* 1.4 76.4 - - - +
67A SER* 1.4 59.7 + - - +
69A LEU* 4.1 4.3 - - - +
70A TYR* 3.3 22.9 + - - +
153A HIS* 4.6 3.8 + - - +
443A LEU* 4.8 5.2 - - + +
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR* 3.0 18.1 + - - -
64A PHE* 3.5 7.9 - - - -
66A LYS* 1.4 75.5 - - - +
68A ARG* 1.4 57.2 - - - +
70A TYR* 3.4 0.9 + - - +
71A GLN* 3.0 32.9 + - - +
443A LEU* 2.8 39.2 + - - +
444A GLY 3.3 3.1 - - - -
445A PHE* 3.2 25.1 + - - -
446A PRO* 5.7 1.6 - - - -
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TYR* 2.8 28.7 + - - +
46A LYS* 3.1 28.3 + - - +
48A THR 3.6 17.8 + - - -
49A THR* 3.6 21.4 + - - +
64A PHE* 2.8 19.9 + - - +
65A GLU* 2.8 49.1 + - - +
67A SER* 1.4 74.8 - - - +
69A LEU* 1.4 58.3 + - - +
71A GLN* 3.6 2.1 + - - +
72A LEU* 3.1 29.7 + - + +
445A PHE* 3.7 21.7 - - + -
46E LYS 5.3 5.5 + - - -
47E THR* 5.9 8.9 + - - +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLU* 3.0 21.9 + - + +
66A LYS* 4.1 4.5 - - - +
68A ARG* 1.4 75.9 - - - +
70A TYR* 1.3 57.9 + - - +
72A LEU* 3.3 6.2 + - - +
73A ASP* 3.0 36.4 + - - +
153A HIS* 3.8 13.2 - - + +
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LYS 3.3 17.5 + - - +
67A SER* 3.7 3.8 - - - +
68A ARG 3.4 0.2 - - - -
69A LEU* 1.3 78.1 - - - +
71A GLN* 1.3 83.9 + - - +
73A ASP* 3.5 3.3 + - - +
74A LYS* 3.1 50.5 + - + +
149A ILE* 4.3 7.0 - - + -
150A GLU* 3.1 31.1 + - - -
153A HIS* 3.5 38.7 - + + +
155A PHE* 3.4 26.9 - + + -
263A HIS* 3.3 13.9 - + - -
442A ASN 3.7 11.2 - - - -
443A LEU* 3.7 16.4 - - + -
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Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TYR* 3.6 39.0 + - + -
67A SER 3.0 20.9 + - - +
68A ARG 4.2 0.4 - - - +
70A TYR* 1.3 81.4 - - - +
72A LEU* 1.4 59.2 + - - +
74A LYS* 3.6 35.1 + - - +
75A SER* 3.0 27.7 + - - -
442A ASN 4.6 1.0 + - - -
443A LEU 3.1 22.7 + - - +
444A GLY* 4.2 6.1 - - - -
445A PHE* 3.9 21.3 - - + -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TYR* 4.7 14.1 - - + +
68A ARG* 3.1 19.1 + - + +
69A LEU* 3.5 9.2 - - - +
70A TYR 3.3 0.2 - - - -
71A GLN* 1.4 73.9 - - - +
73A ASP* 1.4 60.6 + - - +
75A SER* 3.3 8.1 + - - -
76A THR* 2.7 33.6 + - - -
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Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.0 13.1 + - - +
70A TYR 3.8 2.2 - - - +
71A GLN 3.5 0.2 - - - -
72A LEU* 1.4 76.7 - - - +
74A LYS* 1.3 61.5 + - - +
76A THR* 3.6 7.0 + - - -
77A PHE* 3.3 23.2 + - - +
149A ILE* 4.3 16.3 - - + +
152A LYS* 4.7 8.3 - - - +
153A HIS* 2.9 35.5 + - + +
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A TYR* 3.1 52.3 + - + +
71A GLN* 3.6 36.9 + - - +
73A ASP* 1.3 76.3 - - - +
75A SER* 1.4 57.0 + - - +
77A PHE* 3.5 7.1 + - + +
78A SER* 2.9 31.2 + - - -
145A ASN* 5.1 4.7 - - - +
149A ILE* 4.0 18.4 - - + -
150A GLU* 4.5 4.5 - - - +
263A HIS* 5.7 1.0 - - - -
442A ASN 5.6 0.2 + - - -
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 4.3 7.3 + - - +
42A ARG* 3.7 24.6 - - - +
45A TYR* 4.5 13.8 - - - -
71A GLN 3.0 18.0 + - - -
72A LEU* 3.3 8.9 + - - -
74A LYS* 1.4 73.9 - - - +
76A THR* 1.3 63.7 + - - +
78A SER* 3.4 8.3 + - - -
79A PHE* 3.1 22.3 + - - +
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU 2.7 17.7 + - - -
73A ASP* 3.9 8.3 - - - -
74A LYS 3.4 0.2 - - - -
75A SER* 1.3 75.0 - - - +
77A PHE* 1.4 62.8 + - - +
79A PHE* 3.4 11.3 + - - +
80A TRP* 3.2 38.4 + - + +
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ASP 3.3 15.3 + - - +
74A LYS* 3.8 5.6 - - + +
76A THR* 1.4 75.3 - - - +
78A SER* 1.4 59.1 + - - +
79A PHE 3.2 0.3 + - - -
80A TRP* 3.4 5.3 + - + +
81A SER* 2.9 58.1 + - - -
141A TRP* 3.2 53.6 - + + -
144A TYR* 3.5 32.8 - + + -
145A ASN* 4.0 22.9 - - + -
149A ILE* 3.6 15.9 - - + -
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LYS 2.9 19.9 + - - -
75A SER* 3.4 10.8 - - - -
76A THR 3.4 0.2 - - - -
77A PHE* 1.4 78.2 - - - +
79A PHE* 1.4 56.7 + - - +
81A SER* 3.4 6.5 + - - -
82A GLY* 3.1 24.3 + - - -
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Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TYR* 3.9 20.2 + + - -
35A THR* 4.2 23.1 - - + -
38A ALA* 6.2 4.3 - - + -
75A SER 3.1 12.9 + - - +
76A THR* 3.6 9.0 - - - +
77A PHE 3.2 0.6 - - - -
78A SER* 1.4 73.2 - - - +
80A TRP* 1.4 104.8 + + - +
82A GLY 3.2 1.9 + - - -
83A LEU* 2.7 56.7 + - + +
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Residues in contact with TRP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A THR* 3.2 37.6 + - + +
77A PHE* 3.4 5.6 + - + +
79A PHE* 1.4 97.4 - + - +
81A SER* 1.4 61.1 + - - +
83A LEU* 3.7 27.3 - - + +
84A TYR* 3.0 30.0 + - - +
141A TRP* 3.9 15.8 - - + -
144B TYR* 3.6 38.8 - + - -
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 2.9 41.9 + - - -
78A SER* 3.4 9.9 + - - -
80A TRP* 1.4 74.6 - - - +
82A GLY* 1.3 56.8 + - - +
84A TYR* 3.7 3.3 + - - +
85A SER* 2.8 32.1 + - - -
141A TRP* 3.7 32.7 - - - -
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Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TYR* 3.9 12.1 - - - -
78A SER 3.1 13.6 + - - -
79A PHE 3.2 3.8 + - - -
81A SER* 1.3 80.8 + - - +
83A LEU* 1.3 58.1 + - - +
85A SER* 3.5 7.3 + - - -
86A GLU* 3.1 28.2 + - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TRP* 4.9 8.3 - - + -
31A TYR* 3.3 31.3 + - + +
79A PHE* 2.7 44.0 + - + +
80A TRP* 3.7 30.3 - - + +
81A SER 3.5 0.2 - - - -
82A GLY* 1.3 70.5 - - - +
84A TYR* 1.4 56.2 + - - +
86A GLU* 3.4 1.6 + - - -
87A THR* 2.8 47.7 + - - +
144B TYR* 5.4 6.5 - - + -
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TRP 3.0 19.0 + - - +
81A SER 3.9 4.7 - - - +
83A LEU* 1.4 74.7 - - - +
85A SER* 1.3 57.1 + - - +
87A THR* 3.4 5.8 + - - -
88A GLU* 2.8 59.4 + - + +
137A ALA* 4.5 11.4 - - + +
141A TRP* 3.6 39.7 - + + -
84B TYR* 3.0 24.1 + + - -
137B ALA* 3.1 20.1 + - - +
140B PRO* 3.8 23.6 - - + -
141B TRP* 3.3 28.5 - + - -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER 2.8 19.5 + - - -
82A GLY* 3.5 9.9 - - - -
83A LEU 3.3 0.2 - - - -
84A TYR* 1.3 81.2 - - - +
86A GLU* 1.4 57.2 + - - +
88A GLU* 3.2 6.9 + - - +
89A GLY* 2.9 27.9 + - - -
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A SER* 3.4 37.8 - - - +
28A TRP* 3.7 30.6 + - + -
31A TYR* 3.6 36.6 - - + +
82A GLY 3.1 14.7 + - - +
83A LEU 3.8 3.8 - - - +
85A SER* 1.4 78.2 - - - +
87A THR* 1.3 58.5 + - - +
89A GLY* 4.2 1.0 - - - +
90A THR* 2.9 31.4 + - - -
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Residues in contact with THR 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TRP* 4.5 11.9 - - + -
83A LEU* 2.8 35.6 + - - +
84A TYR* 3.7 4.3 - - - -
86A GLU* 1.3 74.1 - - - +
88A GLU* 1.4 58.4 + - - +
90A THR* 3.3 3.6 + - - -
91A LEU* 2.8 47.7 + - + +
140B PRO* 3.9 16.2 - - + +
143B LEU* 3.7 29.2 - - + -
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 2.8 58.6 + - + +
85A SER* 3.5 6.3 - - - +
87A THR* 1.4 71.9 - - - +
89A GLY* 1.3 57.0 + - - +
91A LEU* 3.3 3.9 + - - +
92A ILE* 2.9 63.2 + - + +
137A ALA* 5.7 3.3 - - + +
136B LEU* 2.9 30.0 - - - +
137B ALA* 3.3 7.4 - - - -
140B PRO* 3.4 16.4 - - + +
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Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A SER 2.9 15.4 + - - -
86A GLU* 4.2 1.8 - - - -
88A GLU* 1.3 74.4 - - - +
90A THR* 1.3 62.5 + - - +
92A ILE* 3.5 7.2 + - - +
93A LEU* 3.1 35.6 + - - +
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Residues in contact with THR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.8 14.9 - - + +
27A SER* 6.0 0.2 - - - -
28A TRP* 2.7 40.1 + - + +
86A GLU* 2.9 20.2 + - - -
87A THR* 3.3 4.4 + - - -
89A GLY* 1.3 74.2 - - - +
91A LEU* 1.4 58.3 + - + +
93A LEU* 3.4 10.3 + - - +
94A LEU* 2.9 53.2 + - + +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A THR* 2.8 32.6 + - + +
88A GLU* 3.8 6.5 - - - +
90A THR* 1.4 71.1 - - + +
92A ILE* 1.4 55.2 + - - +
94A LEU* 4.0 7.8 - - + +
95A PHE* 2.8 39.1 + - - +
136B LEU* 4.9 2.5 - - + +
139B LEU* 3.7 25.8 - - + +
140B PRO* 3.5 40.4 - - + -
143B LEU* 4.0 20.2 - - + -
160B LEU* 6.2 1.3 - - + -
164B MET* 3.7 28.1 - - - +
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLU* 2.9 49.5 + - + +
89A GLY* 3.9 5.8 - - - +
91A LEU* 1.4 70.3 - - - +
93A LEU* 1.4 58.5 + - + +
95A PHE 3.8 0.3 - - - -
96A GLY 3.0 8.3 + - - -
97A GLY* 2.8 38.3 + - - -
98A ILE* 4.1 27.5 + - + +
136B LEU* 3.8 31.6 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.8 22.3 - - + -
23A VAL* 5.3 1.1 - - + -
24A LEU* 3.8 24.2 - - + -
27A SER* 6.1 1.1 - - - +
89A GLY* 3.1 26.7 + - - +
90A THR* 3.6 4.9 - - - +
92A ILE* 1.4 76.0 - - + +
94A LEU* 1.4 60.7 + - - +
96A GLY* 3.3 12.8 + - - -
98A ILE* 3.8 19.1 - - + -
376A PHE* 3.7 37.1 - - + +
394A PHE* 3.8 31.9 - - + -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 4.1 16.2 - - + -
24A LEU* 3.8 22.2 - - + -
90A THR* 2.9 39.4 + - + +
91A LEU* 4.0 5.4 - - + +
93A LEU* 1.4 72.6 - - - +
95A PHE* 1.3 63.2 + - - +
96A GLY 3.2 0.9 + - - -
160B LEU* 4.7 12.8 - - + -
164B MET* 3.9 32.7 - - + +
168B ILE* 4.5 7.3 - - - +
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU 2.8 23.9 + - - +
92A ILE 4.1 2.2 - - - +
94A LEU* 1.3 72.2 - - - +
96A GLY* 1.3 60.9 + - - +
97A GLY 5.0 3.4 - - - -
100A TYR* 6.3 0.4 - + - -
132B LEU* 5.1 7.9 - - + -
135B ALA* 4.8 8.5 - - + -
136B LEU* 4.1 22.2 - - + -
139B LEU* 3.8 22.4 - - + -
164B MET* 3.8 10.9 - - + +
167B ALA* 3.8 29.8 - - + -
168B ILE* 3.7 31.9 - - + +
171B PHE* 3.7 50.3 - + + -
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ILE 3.0 6.0 + - - -
93A LEU* 3.7 8.3 - - - -
94A LEU 3.2 4.8 - - - -
95A PHE* 1.3 79.8 - - - +
97A GLY* 1.3 64.3 + - - +
99A PRO* 3.5 21.6 - - - +
100A TYR* 3.6 15.9 + - - +
376A PHE 5.4 2.0 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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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