Contacts of the helix formed by residues 50 - 73 (chain B) in PDB entry 1O0W
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 ASN 50 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 3.1 22.9 + - - +
29B ALA* 3.0 22.3 + - - +
30B LEU 4.6 0.6 - - - -
31B CYS 2.7 22.4 + - - +
32B HIS* 4.5 11.9 - - - +
33B SER 5.0 1.0 + - - -
49B SER* 1.3 72.3 - - - +
51B GLU* 1.3 67.6 + - - +
52B LYS 3.4 2.5 - - - -
53B LEU* 3.4 4.5 + - - -
54B GLU* 2.8 31.4 + - - +
107B LEU* 5.6 0.6 - - - +
124B ILE* 5.3 1.8 + - - +
127B ASP* 4.5 8.9 - - - +
128B ALA* 3.7 22.4 - - - +
131B ALA* 3.7 10.3 - - + -
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 4.0 28.1 - - + +
33B SER* 4.0 18.5 - - - -
49B SER* 2.8 27.4 + - - +
50B ASN* 1.3 84.6 + - - +
52B LYS* 1.3 62.8 + - + +
54B GLU* 3.4 11.8 + - - +
55B PHE* 3.1 20.1 + - - +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.5 25.8 - - + -
73A TYR 5.1 1.8 - - - +
74A PRO* 2.5 32.9 + - + +
75A GLU* 4.2 4.6 + - - +
76A ALA 3.1 26.4 + - - -
77A GLU* 5.2 0.4 - - - +
78A VAL* 4.9 10.1 - - + +
81A LEU* 4.2 15.9 - - + -
48B GLU* 3.4 30.7 + - - +
49B SER 4.6 2.4 + - - +
50B ASN 3.4 0.6 - - - -
51B GLU* 1.3 74.8 - - + +
53B LEU* 1.3 66.6 + - + +
55B PHE* 3.1 10.2 + - - +
56B LEU 3.1 17.5 + - - -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.3 31.9 - - + +
25B LEU* 3.6 19.1 - - + +
28B ARG* 3.7 20.6 - - + -
29B ALA* 3.5 34.8 - - + +
49B SER 5.4 0.4 + - - -
50B ASN* 3.4 7.7 + - - +
51B GLU 3.4 0.4 - - - -
52B LYS* 1.3 78.7 - - + +
54B GLU* 1.3 51.9 + - - +
56B LEU 3.2 0.3 + - - -
57B GLY* 2.6 32.2 + - - -
131B ALA* 3.9 13.2 - - + +
134B ALA* 3.0 26.1 - - + +
135B ALA* 4.0 8.7 - - + +
138B LEU* 3.9 11.9 - - + -
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASN* 2.8 21.1 + - - +
51B GLU* 3.6 11.9 - - - +
52B LYS 3.1 0.2 - - - -
53B LEU* 1.3 79.3 - - - +
55B PHE* 1.3 58.2 + - - +
58B ASP* 2.9 32.4 + - - +
127B ASP* 3.3 56.2 - - - +
130B GLU* 3.7 21.2 - - + +
131B ALA* 3.8 8.5 - - + +
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Residues in contact with PHE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 5.6 0.2 - - - +
66A CYS* 3.6 55.2 - - + -
69A LEU* 3.8 20.0 - - + -
70A TYR* 4.4 4.3 - - + -
78A VAL* 4.2 16.4 - - + -
81A LEU* 3.7 52.0 - - + -
82A ALA* 4.0 11.2 - - + -
85A LYS* 4.3 7.4 - - + -
51B GLU 3.1 12.9 + - - +
52B LYS* 3.1 11.6 + - - +
54B GLU* 1.3 78.5 - - - +
56B LEU* 1.3 69.7 + - + +
58B ASP* 3.7 9.0 + - - +
59B ALA 3.9 5.5 + - - -
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 4.0 17.7 - - + -
66A CYS* 4.1 6.3 - - + +
67A GLU* 3.8 33.9 - - + +
70A TYR* 3.9 22.7 - - + -
52B LYS 3.1 11.5 + - - +
53B LEU 3.7 4.9 - - - +
55B PHE* 1.3 79.4 - - - +
57B GLY* 1.3 66.8 + - - +
59B ALA* 3.0 13.5 + - - +
60B VAL* 3.0 15.3 + - + +
134B ALA* 4.0 9.4 - - + -
137B TYR* 4.4 7.2 - - + -
138B LEU* 3.8 40.2 - - + -
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Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU 2.6 16.3 + - - -
54B GLU 3.7 1.1 - - - -
56B LEU* 1.3 75.0 - - - +
58B ASP* 1.3 56.4 + - - +
60B VAL* 3.5 5.0 - - - +
61B LEU* 2.9 30.5 + - - +
130B GLU* 3.1 30.5 - - - +
133B LEU* 4.5 3.0 - - - +
134B ALA* 3.4 12.3 - - - +
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Residues in contact with ASP 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 3.5 14.2 - - - +
85A LYS* 5.4 3.1 + - - -
54B GLU* 2.9 17.4 + - - +
55B PHE* 3.9 7.9 - - - +
56B LEU 3.1 0.2 - - - -
57B GLY* 1.3 77.8 - - - +
59B ALA* 1.3 56.3 + - - +
61B LEU* 3.4 3.9 + - - +
62B GLU* 2.9 51.3 + - - +
89B ALA 5.7 0.7 - - - +
130B GLU* 3.0 30.4 + - - +
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Residues in contact with ALA 59 (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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59A ALA 4.8 1.2 - - - +
62A GLU* 3.4 29.4 + - + +
63A LEU* 3.7 31.6 - - + +
66A CYS* 3.9 16.4 - - + -
55B PHE 3.9 0.8 + - - -
56B LEU 3.0 10.3 + - - +
58B ASP* 1.3 75.1 - - - +
60B VAL* 1.3 65.6 - - - +
62B GLU* 3.4 2.0 + - - +
63B LEU* 3.1 23.6 + - - +
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.9 19.5 - - + -
56B LEU* 3.0 23.5 + - + +
57B GLY* 3.2 11.0 + - - +
59B ALA* 1.3 78.3 - - - +
61B LEU* 1.3 57.8 + - - +
63B LEU* 3.3 2.6 + - - +
64B PHE* 2.9 27.8 + - + +
133B LEU* 4.5 15.7 - - + +
134B ALA* 4.6 1.3 - - - -
137B TYR* 3.8 48.5 - - + -
142B TYR* 4.6 10.5 - - + -
145B ILE* 4.7 14.8 - - + -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLY 2.9 16.6 + - - +
58B ASP* 3.6 4.9 - - - +
60B VAL* 1.3 77.7 - - - +
62B GLU* 1.3 62.7 + - - +
64B PHE* 3.2 11.8 + - + +
65B VAL* 2.9 44.5 + - + +
89B ALA* 3.7 26.5 - - + +
94B LEU* 3.6 33.7 - - + -
130B GLU* 4.5 11.2 - - + -
133B LEU* 3.8 24.8 - - + +
153B PHE* 4.1 21.3 - - + -
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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
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59A ALA* 4.1 8.3 - - + -
62A GLU* 3.5 31.2 - - - +
58B ASP* 2.9 45.4 + - - +
59B ALA 3.8 3.1 - - - +
60B VAL 3.3 0.2 - - - -
61B LEU* 1.3 77.3 - - - +
63B LEU* 1.3 58.7 + - - +
65B VAL* 4.1 3.5 - - - +
66B CYS* 2.9 37.5 + - - -
85B LYS* 3.8 29.8 + - + +
89B ALA* 3.6 24.2 - - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.7 26.2 - - + -
59A ALA* 3.8 18.3 - - + +
60A VAL* 3.8 22.7 - - + +
63A LEU* 3.4 32.1 - - + -
137A TYR* 3.8 31.2 - - + +
142A TYR* 5.1 2.9 - - + -
59B ALA 3.1 16.9 + - - +
60B VAL 3.8 3.6 - - - +
62B GLU* 1.3 73.4 - - - +
64B PHE* 1.3 60.6 + - - +
67B GLU* 2.8 31.3 + - - +
142B TYR* 3.9 13.2 - - + +
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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
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60B VAL* 2.9 18.6 + - + +
61B LEU* 3.5 13.2 - - + +
63B LEU* 1.3 77.8 - - - +
65B VAL* 1.3 72.7 + - + +
67B GLU* 3.6 1.9 + - - +
68B ILE* 3.2 37.1 + - + +
133B LEU* 5.9 2.7 - - + -
142B TYR* 3.4 20.3 + + + +
145B ILE* 3.9 21.5 - - + -
146B LYS* 3.9 25.1 - - + -
149B PHE* 3.4 11.9 - - + -
150B GLU* 3.4 40.2 - - + -
153B PHE* 3.5 33.9 - + + -
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 2.9 39.2 + - + +
62B GLU* 4.1 3.8 - - - +
64B PHE* 1.3 80.2 - - + +
66B CYS* 1.3 66.1 + - - +
68B ILE* 3.2 3.7 + - - +
69B LEU* 2.9 38.4 + - + +
85B LYS* 4.2 13.7 - - + +
88B ALA* 3.7 30.7 - - + -
89B ALA* 4.9 2.9 - - + +
153B PHE* 4.3 14.8 - - + -
157B ILE* 4.0 13.2 - - + -
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Residues in contact with CYS 66 (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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55A PHE* 3.5 33.3 - - + -
56A LEU* 4.0 10.1 - - + -
59A ALA* 3.8 24.0 - - + -
62B GLU* 2.9 25.9 + - - +
63B LEU 4.0 1.1 - - - +
65B VAL* 1.3 76.6 - - - +
67B GLU* 1.3 56.7 + - - +
69B LEU* 3.6 1.8 - - - +
70B TYR* 2.8 32.1 + - - +
85B LYS* 3.5 31.6 - - - -
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.8 16.7 - - + +
137A TYR* 2.7 34.4 + - + -
63B LEU* 2.8 20.0 + - + +
64B PHE 3.8 4.0 - - - +
66B CYS* 1.3 72.8 - - - +
68B ILE* 1.3 63.6 + - + +
70B TYR* 3.8 1.9 - - - +
71B LYS* 2.9 63.6 + - + +
142B TYR* 2.5 31.2 + - - +
146B LYS* 4.0 15.1 + - + -
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Residues in contact with ILE 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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64B PHE* 3.2 45.9 + - + +
65B VAL 3.2 7.0 + - - +
67B GLU* 1.3 80.7 - - + +
69B LEU* 1.3 58.6 + - - +
71B LYS* 4.9 1.8 - - - -
72B LYS* 2.9 44.5 + - + +
73B TYR* 5.1 0.4 - - + -
150B GLU* 4.2 27.4 - - + +
153B PHE* 4.1 7.2 - - + -
154B GLU* 3.9 22.9 - - + +
157B ILE* 3.9 33.4 - - + -
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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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55A PHE* 3.8 17.9 - - + -
65B VAL* 2.9 29.2 + - + +
66B CYS 3.2 4.7 + - - +
68B ILE* 1.3 78.2 - - - +
70B TYR* 1.3 61.4 + - - +
73B TYR* 3.1 39.6 + - + +
81B LEU* 3.5 34.3 - - + +
84B VAL* 3.6 16.2 - - + -
85B LYS* 3.7 21.3 - - + +
157B ILE* 3.5 28.7 - - + -
161B MET* 4.2 7.9 - - + -
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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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25A LEU* 4.5 3.3 - - - +
28A ARG* 3.9 15.1 + - - -
52A LYS* 3.5 47.3 - - + +
53A LEU* 3.1 26.0 - - + +
55A PHE* 4.5 7.6 - + + -
56A LEU* 3.8 25.1 - - + -
138A LEU* 3.3 24.6 - - + +
66B CYS 2.8 16.9 + - - +
67B GLU 3.8 3.1 - - - +
69B LEU* 1.3 79.1 - - - +
71B LYS* 1.3 73.4 - - + +
73B TYR 4.3 0.6 - - - -
74B PRO* 4.1 17.8 - - - +
81B LEU* 5.1 4.7 - - + -
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.9 21.5 - - - +
67B GLU* 2.9 52.4 + - + +
68B ILE* 4.1 2.0 - - - +
70B TYR* 1.3 89.3 - - + +
72B LYS* 1.3 64.8 + - + +
74B PRO* 3.9 8.0 - - - +
146B LYS* 4.7 7.9 - - - +
150B GLU* 6.2 0.2 - - - +
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 2.9 33.8 + - + +
71B LYS* 1.3 76.7 - - + +
73B TYR* 1.3 85.6 + - + +
74B PRO* 3.3 10.5 - - - +
154B GLU* 3.6 33.8 + - + +
218B ARG* 5.7 3.0 - - - +
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Residues in contact with TYR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS* 4.4 2.4 - - - -
68B ILE* 4.8 1.8 - - + -
69B LEU* 3.1 35.5 + - + +
70B TYR 4.3 0.8 - - - +
72B LYS* 1.3 101.4 - - + +
74B PRO* 1.3 64.1 - - - +
75B GLU 3.1 5.0 + - - +
76B ALA* 3.1 29.6 + - + +
81B LEU* 4.1 3.9 - - + +
154B GLU 4.4 1.9 + - - -
157B ILE* 3.5 23.8 - - + +
158B GLU* 2.4 50.5 + - - +
161B MET* 3.7 31.0 - - + -
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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
------------------------------------------------------------
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