Contacts of the helix formed by residues 59 - 84 (chain A) in PDB entry 2V1T
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 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLY 4.4 3.3 - - - +
58A SER* 1.3 79.7 - - - +
60A LEU* 1.3 68.3 + - - +
61A LYS* 2.6 63.7 + - - +
62A ASP* 2.8 42.5 + - - +
63A ALA* 4.0 1.6 + - - +
102B GLN* 4.1 10.5 - - - +
24D CY3 3.9 13.5 - - - +
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Residues in contact with LEU 60 (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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58A SER 4.3 1.0 + - - -
59A ASP* 1.3 83.9 + - - +
61A LYS* 1.3 80.6 + - + +
62A ASP 3.4 0.5 + - - -
63A ALA* 3.4 20.2 + - - +
64A GLU* 3.7 23.4 - - - +
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Residues in contact with LYS 61 (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 ASP* 2.6 39.8 + - - +
60A LEU* 1.3 85.0 - - + +
62A ASP* 1.3 58.1 + - - +
63A ALA 3.3 0.2 - - - -
64A GLU* 3.4 17.4 + - + +
65A ALA* 3.0 23.6 + - - +
101B GLY* 3.5 34.7 - - - +
102B GLN* 4.0 24.4 - - - +
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Residues in contact with ASP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.3 22.3 - - + +
57A GLY* 2.7 28.9 + - - +
59A ASP* 2.8 27.1 + - - +
61A LYS* 1.3 78.3 - - - +
63A ALA* 1.3 60.2 + - - +
65A ALA* 3.3 2.6 + - - +
66A VAL* 3.1 25.3 + - - +
66B VAL* 5.9 0.3 - - - +
99B VAL 4.0 3.8 - - - +
101B GLY* 2.8 28.8 + - - +
102B GLN 4.1 0.2 + - - -
24D CY3 3.2 25.1 + - - +
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Residues in contact with ALA 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 ASP 4.0 1.8 + - - +
60A LEU* 3.4 12.4 + - - +
61A LYS 3.3 0.4 - - - -
62A ASP* 1.3 78.5 - - - +
64A GLU* 1.3 63.2 + - + +
66A VAL* 3.3 9.5 - - - +
67A GLN* 3.2 39.7 + - - +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.7 34.7 - - - +
61A LYS* 3.4 15.2 + - + +
62A ASP 3.3 0.6 - - - -
63A ALA* 1.3 78.8 - - + +
65A ALA* 1.3 55.9 + - - +
67A GLN* 3.4 10.7 + - - +
68A LYS* 3.0 54.1 + - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS 3.0 17.2 + - - +
62A ASP 3.3 4.7 + - - +
64A GLU* 1.3 76.8 - - - +
66A VAL* 1.3 56.9 + - - +
68A LYS* 3.4 14.0 + - - +
69A PHE* 2.9 23.9 + - - +
98B ALA 3.4 25.4 - - - +
99B VAL 3.8 14.6 - - - -
100B CYS 4.1 4.5 - - - +
101B GLY* 4.1 9.6 - - - +
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Residues in contact with VAL 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 ASP 3.1 16.0 + - - +
63A ALA* 3.3 17.7 - - - +
65A ALA* 1.3 74.0 - - - +
67A GLN* 1.3 67.8 + - + +
69A PHE* 3.7 4.6 - - - +
70A PHE* 2.9 28.8 + - - +
99A VAL* 3.7 29.8 - - + +
66B VAL* 3.5 41.3 - - + -
99B VAL* 4.4 7.1 - - + +
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Residues in contact with GLN 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 ALA* 3.2 28.5 + - - +
64A GLU* 3.7 9.5 - - - +
65A ALA 3.4 0.2 - - - -
66A VAL* 1.3 86.2 - - + +
68A LYS* 1.3 62.1 + - + +
70A PHE* 3.6 6.7 + - - +
71A LEU* 3.3 23.0 + - - +
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Residues in contact with LYS 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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64A GLU* 3.0 52.0 + - - +
65A ALA* 3.7 10.5 - - - +
67A GLN* 1.3 77.7 - - + +
69A PHE* 1.3 56.6 + - - +
71A LEU* 3.4 7.5 + - - +
72A GLU* 2.9 49.3 + - - +
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Residues in contact with PHE 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 ALA 2.9 18.4 + - - +
66A VAL 3.7 3.8 - - - +
67A GLN 3.4 0.2 - - - -
68A LYS* 1.3 76.6 - - - +
70A PHE* 1.3 57.3 + - - +
72A GLU* 3.3 13.2 + - - +
73A GLU* 2.9 68.8 + - + +
95A ASN* 4.0 11.2 - - + -
99A VAL* 4.0 17.9 - - + -
69B PHE* 3.7 35.9 - + - -
95B ASN* 3.7 22.7 - - - -
98B ALA* 3.6 29.8 + - + +
99B VAL* 3.6 20.4 - - + -
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Residues in contact with PHE 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 VAL* 2.9 17.8 + - + +
67A GLN* 3.8 7.4 - - - +
69A PHE* 1.3 76.6 - - - +
71A LEU* 1.3 68.6 + - + +
73A GLU* 3.4 1.7 + - - +
74A ILE* 3.1 43.4 + - + +
96A ALA* 3.2 38.1 - - + -
99A VAL* 4.3 12.6 - - + -
100A CYS* 4.5 0.4 - - + -
106A LEU* 3.7 25.6 - - + -
19C LEU 4.5 14.6 - - - -
20C SER* 4.6 13.7 - - - -
23C GLY* 4.7 5.4 - - - -
24C CY3 3.6 30.1 - - - -
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Residues in contact with LEU 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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67A GLN 3.3 14.2 + - - +
68A LYS* 3.7 6.3 - - - +
70A PHE* 1.3 85.7 - - + +
72A GLU* 1.3 57.8 + - + +
74A ILE* 3.4 3.9 + - + -
75A GLN* 2.9 63.4 + - + +
16C SER* 5.7 1.3 - - - +
20C SER* 3.4 26.0 - - - +
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Residues in contact with GLU 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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68A LYS* 2.9 38.7 + - - +
69A PHE* 3.4 21.2 + - - +
71A LEU* 1.3 75.4 - - + +
73A GLU* 1.3 64.3 + - - +
75A GLN* 3.4 11.5 + - - +
76A LEU* 2.8 32.4 + - - +
98B ALA* 5.2 4.7 - - - +
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Residues in contact with GLU 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 PHE* 2.9 62.5 + - + +
70A PHE 3.8 3.6 - - - +
72A GLU* 1.3 78.6 - - - +
74A ILE* 1.3 57.7 + - - +
76A LEU* 4.5 7.3 - - - +
77A GLY* 2.8 28.1 + - - -
92A HIS* 2.6 55.8 + - - +
93A LEU 4.3 0.2 + - - -
95A ASN* 3.0 18.5 + - + +
96A ALA* 3.9 8.5 - - + -
95B ASN* 4.8 2.3 - - - +
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Residues in contact with ILE 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 PHE* 3.1 35.1 + - + +
71A LEU* 3.9 5.4 - - + +
72A GLU 3.3 0.2 - - - -
73A GLU* 1.3 73.5 - - - +
75A GLN* 1.3 59.1 + - - +
77A GLY* 5.0 0.7 - - - -
78A GLU* 3.0 30.3 + - - +
93A LEU* 4.8 10.9 - - + +
96A ALA* 3.4 23.1 - - + -
106A LEU* 4.4 12.1 - - + -
110A LEU* 5.6 1.1 - - + -
16C SER* 3.6 20.8 - - - +
19C LEU* 3.3 48.7 - - + -
20C SER* 4.9 4.0 - - - +
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Residues in contact with GLN 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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71A LEU* 2.9 52.2 + - + +
72A GLU* 3.7 10.1 - - - +
74A ILE* 1.3 76.0 - - - +
76A LEU* 1.3 61.7 + - - +
78A GLU* 3.9 1.2 - - - +
79A GLU* 3.0 24.6 + - - +
13C PRO* 4.8 4.2 - - - +
16C SER* 4.0 24.1 + - - +
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Residues in contact with LEU 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 GLU 2.8 20.6 + - - +
73A GLU* 3.9 8.3 - - - +
75A GLN* 1.3 70.0 - - - +
77A GLY* 1.3 66.8 + - - +
79A GLU* 3.3 8.2 + - + +
80A LEU* 3.0 47.4 + - + +
92A HIS* 3.4 37.7 - - + +
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Residues in contact with GLY 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 GLU 2.8 14.6 + - - -
76A LEU* 1.3 78.4 - - - +
78A GLU* 1.3 55.3 - - - +
80A LEU* 3.4 2.8 + - - +
81A LEU* 3.0 31.7 + - - +
89A GLY* 3.6 11.4 - - - -
92A HIS* 3.9 5.1 - - - +
93A LEU* 3.2 28.0 - - - -
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Residues in contact with GLU 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 ILE 3.0 22.2 + - - +
75A GLN 4.2 0.9 - - - +
77A GLY* 1.3 71.7 - - - +
79A GLU* 1.3 60.3 + - - +
81A LEU* 3.6 24.0 - - - +
82A ALA* 2.9 29.3 + - - +
93A LEU* 4.0 5.5 - - + +
110A LEU* 4.4 2.8 - - - +
113A THR* 5.0 3.6 + - - -
114A LEU* 5.2 2.3 - - - +
12C GLY 4.6 0.9 - - - +
13C PRO* 3.7 24.2 - - + +
15C LEU* 3.6 31.6 - - + +
16C SER 3.8 15.5 - - - +
19C LEU* 3.2 31.0 - - + +
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Residues in contact with GLU 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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75A GLN 3.0 17.6 + - - +
76A LEU* 3.7 9.9 - - + +
78A GLU* 1.3 73.4 - - - +
80A LEU* 1.3 63.3 + - + +
82A ALA* 3.2 5.2 + - - +
83A GLN* 3.0 55.4 + - - +
13C PRO* 3.4 32.8 - - + +
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Residues in contact with LEU 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 LEU* 3.0 46.4 + - + +
77A GLY 3.5 4.3 - - - +
79A GLU* 1.3 76.7 - - + +
81A LEU* 1.3 60.7 + - - +
83A GLN* 3.2 20.8 + - - +
84A GLY 3.0 5.2 + - - -
85A ASP* 2.8 40.6 + - + +
88A LYS* 3.8 20.2 - - + +
89A GLY* 3.7 13.7 - - - +
92A HIS* 3.5 25.4 - - + +
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Residues in contact with LEU 81 (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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77A GLY 3.0 18.4 + - - +
78A GLU* 3.6 26.2 - - - +
80A LEU* 1.3 75.7 - - - +
82A ALA* 1.3 61.6 + - - +
84A GLY* 3.2 13.4 + - - +
85A ASP 4.4 1.8 - - - -
86A TYR* 3.5 54.3 - - + +
89A GLY* 4.3 5.8 - - - -
90A VAL* 4.7 2.5 - - + -
93A LEU* 3.7 28.7 - - + -
114A LEU* 3.8 14.8 - - + -
115A PRO* 6.3 0.7 - - + -
118A VAL* 4.4 13.2 - - + -
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Residues in contact with ALA 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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78A GLU 2.9 19.7 + - - +
79A GLU* 3.2 8.7 + - - +
81A LEU* 1.3 76.8 - - - +
83A GLN* 1.3 58.8 + - + +
12C GLY* 4.1 12.3 - - - +
13C PRO* 4.1 22.9 - - + -
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Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.0 39.3 + - - +
80A LEU* 3.2 30.3 + - - +
82A ALA* 1.3 76.4 - - - +
84A GLY* 1.3 58.4 + - - +
85A ASP* 3.6 3.8 - - + +
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Residues in contact with GLY 84 (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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80A LEU 3.0 2.0 + - - -
81A LEU 3.2 11.6 + - - -
82A ALA 3.4 0.8 - - - -
83A GLN* 1.3 78.7 - - - +
85A ASP* 1.3 59.7 + - - +
86A TYR* 3.2 26.0 + - - -
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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
------------------------------------------------------------
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