Contacts of the helix formed by residues 65 - 89 (chain B) in PDB entry 1U8R
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 THR 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLY* 2.9 28.0 + - - -
53B LEU 3.2 5.5 + - - -
54B LEU* 3.3 33.0 - - - +
55B ARG* 3.9 25.6 - - + +
64B LEU* 1.3 74.3 - - - +
66B GLU* 1.3 69.2 + - - +
67B LYS* 3.4 3.5 + - - +
68B GLY 3.2 10.4 + - - -
69B ARG* 2.9 21.4 + - - +
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B THR* 1.3 76.2 - - - +
67B LYS* 1.3 62.6 + - - +
69B ARG* 3.6 4.2 + - - +
70B ALA* 3.4 19.8 + - - +
57H ALA* 5.4 3.1 - - + -
58H GLY* 4.7 21.2 + - - +
59H ASP* 2.3 35.1 + - - +
61H HIS* 4.6 5.7 - - - -
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASP* 3.7 16.9 + - - +
52B GLY 3.7 13.7 - - - +
53B LEU* 4.0 14.4 - - + +
65B THR* 3.1 7.7 + - - +
66B GLU* 1.3 78.6 - - - +
68B GLY* 1.3 65.9 + - - +
70B ALA* 3.0 18.1 + - - +
71B LEU* 3.2 13.9 + - + +
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Residues in contact with GLY 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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12B LEU* 3.9 10.6 - - - +
53B LEU* 3.2 38.0 + - - +
64B LEU* 4.5 4.0 - - - -
65B THR* 3.2 7.9 + - - -
67B LYS* 1.3 79.8 - - - +
69B ARG* 1.3 56.8 + - - +
71B LEU* 3.5 3.7 + - - +
72B ALA* 3.0 27.9 + - - +
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 4.4 15.7 - - + -
19B GLU* 3.1 39.8 + - - -
63B GLU* 5.7 2.4 + - - -
64B LEU* 4.0 37.9 + - + +
65B THR 2.9 16.8 + - - +
66B GLU* 3.9 4.7 - - - +
68B GLY* 1.3 73.5 - - - +
70B ALA* 1.3 68.4 + - - +
72B ALA* 3.1 1.7 + - + +
73B ILE* 2.9 46.1 + - + +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 3.4 11.6 + - - +
67B LYS* 3.0 12.5 + - - +
69B ARG* 1.3 79.0 - - - +
71B LEU* 1.3 57.1 + - - +
73B ILE* 3.5 10.9 + - - +
74B ALA* 3.1 24.3 + - - +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 5.2 5.8 - - + -
9B GLU* 4.1 18.6 - - + +
12B LEU* 3.6 20.2 - - + -
53B LEU* 4.8 12.1 - - + -
67B LYS* 3.2 8.3 + - + +
68B GLY* 3.7 7.6 - - - +
69B ARG 3.2 0.4 - - - -
70B ALA* 1.3 75.6 - - - +
72B ALA* 1.3 66.8 + - - +
73B ILE 3.1 1.6 - - - -
74B ALA* 2.8 24.4 + - + +
75B VAL* 2.9 30.5 + - + +
78B LYS* 6.4 0.4 - - - -
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Residues in contact with ALA 72 (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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12B LEU* 4.1 29.3 - - + +
13B ARG* 4.5 4.6 - - - +
16B TYR* 4.3 13.8 - - + -
64B LEU* 4.0 20.6 - - + -
68B GLY 3.0 18.1 + - - +
69B ARG* 3.5 5.2 - - - +
71B LEU* 1.3 75.8 - - - +
73B ILE* 1.3 61.6 + - - +
75B VAL* 3.5 6.4 + - - +
76B MET* 3.1 23.0 + - - +
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Residues in contact with ILE 73 (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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16B TYR* 4.0 22.4 - - + +
69B ARG* 2.9 37.5 + - + +
70B ALA* 3.6 11.0 - - - +
72B ALA* 1.3 72.9 - - - +
74B ALA* 1.3 69.5 + - - +
76B MET* 2.9 9.2 + - - +
77B ARG* 2.8 22.4 + - + +
133B PRO* 3.5 10.8 - - + -
134B GLY* 3.3 37.2 - - - +
137B GLU* 4.9 11.4 - - + +
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Residues in contact with ALA 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 ALA 3.1 11.1 + - - +
71B LEU* 2.8 23.7 + - + +
73B ILE* 1.3 80.2 - - - +
75B VAL* 1.3 58.8 + - - +
77B ARG* 3.3 28.7 + - - +
78B LYS* 3.2 36.8 + - - +
110B GLU* 5.9 0.2 - - - +
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Residues in contact with VAL 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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9B GLU* 3.3 43.1 - - + +
12B LEU* 5.9 0.4 - - + -
13B ARG* 4.1 14.8 - - + -
71B LEU* 2.9 24.1 + - + +
72B ALA* 3.8 7.9 - - - +
74B ALA* 1.3 76.1 - - + +
76B MET* 1.3 57.8 - - - +
78B LYS* 3.2 12.6 + - - +
79B HIS* 2.9 27.0 + - - +
105B GLU* 3.6 38.3 - - + +
106B HIS* 4.5 4.5 - - + -
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Residues in contact with MET 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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13B ARG* 4.1 19.7 - - + +
16B TYR* 3.5 31.2 - - + -
17B ASP* 3.3 30.7 - - - +
20B GLU* 4.0 0.9 - - - +
72B ALA 3.1 11.8 + - - +
73B ILE* 2.9 10.0 + - - +
75B VAL* 1.3 78.1 - - - +
77B ARG* 1.3 64.0 + - - +
79B HIS* 3.4 8.3 + - - +
80B ARG* 3.1 63.3 + - - +
133B PRO* 3.7 18.8 - - + -
172B GLU* 4.2 7.2 - - + +
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 2.8 11.5 + - - +
74B ALA* 3.4 28.8 + - - +
75B VAL 3.2 0.2 - - - -
76B MET* 1.3 76.3 - - - +
78B LYS* 1.3 65.4 + - - +
80B ARG* 3.3 1.7 + - - +
81B LEU* 2.9 28.7 + - + +
110B GLU* 3.6 22.0 + - - +
113B GLU* 2.6 35.8 + - - +
132B ILE* 3.8 14.8 - - + +
133B PRO* 3.4 22.8 - - - +
134B GLY* 2.9 31.9 + - - -
135B LEU* 4.5 1.3 - - + +
137B GLU* 4.3 7.7 + - - +
138B LEU* 3.2 35.1 - - - +
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Residues in contact with LYS 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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9B GLU* 6.1 2.0 - - - -
71B LEU* 6.4 0.4 - - - -
74B ALA* 3.2 25.9 + - - +
75B VAL* 3.6 8.1 - - - +
77B ARG* 1.3 79.5 - - - +
79B HIS* 1.3 66.2 + - - +
81B LEU* 3.2 5.0 + - - +
82B ALA* 2.9 26.3 + - - +
105B GLU* 3.5 25.6 - - - +
106B HIS 6.4 0.2 - - - -
107B VAL 5.5 0.2 - - - +
108B MET* 3.2 45.4 + - + +
110B GLU* 4.2 11.9 + - - +
113B GLU* 2.7 41.6 + - + +
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Residues in contact with HIS 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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13B ARG* 4.2 4.5 - - - -
75B VAL 2.9 9.1 + - - +
76B MET* 3.4 16.8 - - - +
78B LYS* 1.3 79.1 - - - +
80B ARG* 1.3 61.7 + - + +
82B ALA* 3.2 5.3 + - - +
83B GLU* 2.9 41.4 + - - +
98B HIS* 3.3 30.5 - + - -
101B ALA* 3.5 17.6 + - + +
102B CYS* 3.8 4.0 + - - -
105B GLU* 3.2 35.9 + - - +
172B GLU* 2.9 18.2 + - - -
2001B CO 2.0 33.0 + - - -
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Residues in contact with ARG 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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20B GLU* 2.8 39.2 + - - -
76B MET* 3.1 43.1 + - - +
77B ARG 4.0 0.9 - - - +
79B HIS* 1.3 77.6 - - + +
81B LEU* 1.3 67.0 + - - +
82B ALA 3.1 1.6 - - - -
83B GLU* 3.4 21.6 + - - +
84B ARG* 3.1 24.8 + - - +
126B SER* 3.8 11.6 - - - -
130B ASN* 3.3 32.8 - - - +
131B PRO* 2.8 31.6 + - - +
132B ILE* 4.0 18.8 - - + -
133B PRO* 4.2 2.9 - - - +
172B GLU* 3.1 24.4 + - - +
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Residues in contact with LEU 81 (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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77B ARG* 2.9 24.3 + - + +
78B LYS* 3.7 4.9 - - - +
80B ARG* 1.3 76.5 - - - +
82B ALA* 1.3 57.6 + - - +
84B ARG* 3.1 6.9 - - - +
85B LEU* 3.0 26.5 + - - +
108B MET* 4.9 1.3 - - + -
113B GLU* 3.6 41.3 - - + +
116B LEU* 4.6 18.1 - - + +
117B VAL* 4.4 23.1 - - + +
120B LEU* 4.0 9.3 - - + +
123B PRO* 4.0 18.6 - - + -
132B ILE* 3.7 26.2 - - + +
135B LEU* 5.2 1.3 - - + -
138B LEU* 4.5 2.7 - - + -
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Residues in contact with ALA 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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78B LYS 2.9 12.4 + - - +
79B HIS* 3.2 11.7 - - - +
81B LEU* 1.3 73.9 - - - +
83B GLU* 1.3 60.5 + - - +
84B ARG 3.0 1.6 - - - -
85B LEU* 3.1 8.1 + - - +
86B LEU* 2.8 36.2 + - + +
101B ALA* 4.0 13.0 - - + -
104B TRP* 4.5 20.6 - - + -
108B MET* 4.0 18.5 - - - -
116B LEU* 5.2 1.3 - - - -
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Residues in contact with GLU 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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79B HIS* 2.9 26.7 + - - +
80B ARG* 3.4 19.5 + - - +
82B ALA* 1.3 75.5 - - - +
84B ARG* 1.3 63.0 + - - +
86B LEU* 3.3 9.2 + - - +
87B VAL* 3.0 29.6 + - - +
97B VAL* 4.2 10.3 - - + +
98B HIS* 3.3 12.2 + - - +
101B ALA* 3.5 13.7 - - + +
126B SER* 3.8 9.4 + - - -
127B PRO* 3.8 14.8 - - + -
128B PHE* 4.0 7.6 - - - -
172B GLU* 3.6 2.9 - - - +
175B GLN* 2.7 9.5 - - - +
2001B CO 1.8 33.3 + - - -
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Residues in contact with ARG 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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80B ARG 3.1 13.6 + - - +
81B LEU* 3.1 12.8 - - - +
82B ALA 3.0 0.2 - - - -
83B GLU* 1.3 76.6 - - - +
85B LEU* 1.3 64.3 + - - +
87B VAL* 3.7 1.4 - - - +
88B ASP* 2.8 61.5 + - - +
120B LEU* 3.3 16.6 - - + -
123B PRO* 3.5 29.6 - - + +
125B THR* 2.4 43.4 + - - +
126B SER 3.0 19.0 + - - -
127B PRO* 3.7 29.9 - - + +
132B ILE* 4.8 1.6 - - + -
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Residues in contact with LEU 85 (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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85A LEU* 4.9 3.1 - - + -
89A VAL* 5.3 1.3 - - + -
90A ILE* 3.6 21.8 - - + -
104A TRP* 4.9 3.6 - - + -
81B LEU 3.0 7.3 + - - +
82B ALA* 3.6 9.2 - - - +
84B ARG* 1.3 79.1 - - - +
86B LEU* 1.3 58.7 + - - +
89B VAL* 3.1 36.7 + - + -
90B ILE* 3.0 39.2 + - + +
104B TRP* 4.5 21.3 - - + -
116B LEU* 3.4 41.5 - - + -
119B VAL* 5.6 1.1 - - + -
120B LEU* 3.8 8.7 - - + +
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Residues in contact with LEU 86 (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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112A VAL* 4.1 5.2 - - + -
82B ALA* 2.8 30.9 + - + +
83B GLU 3.7 0.9 - - - +
85B LEU* 1.3 72.8 - - - +
87B VAL* 1.3 53.0 + - - +
90B ILE* 3.4 14.9 - - + +
91B GLY 2.8 11.1 + - - -
92B LEU* 2.8 46.6 + - + -
97B VAL* 3.4 43.5 - - + +
100B GLU* 3.8 24.2 - - + -
101B ALA* 4.0 7.6 - - + +
104B TRP* 4.0 27.8 - - + -
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Residues in contact with VAL 87 (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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83B GLU 3.0 16.1 + - - +
84B ARG* 3.9 2.5 - - - +
86B LEU* 1.3 76.1 - - - +
88B ASP* 1.3 78.0 + - - +
91B GLY* 3.6 12.6 - - - -
92B LEU 3.9 10.0 - - - +
94B TRP* 4.2 16.6 - - + +
97B VAL* 3.4 28.3 - - + -
127B PRO* 3.9 26.2 - - + -
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 2.8 58.6 + - - +
87B VAL* 1.3 85.9 - - - +
89B VAL* 1.3 68.4 + - + +
91B GLY* 4.5 1.2 + - - -
120B LEU* 4.4 10.0 - - + +
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 5.2 0.4 - - + -
89A VAL* 3.7 26.9 - - + -
115A ARG* 5.2 0.5 + - - -
119A VAL* 4.0 22.7 - - + +
85B LEU* 3.1 29.3 + - + -
88B ASP* 1.3 78.9 - - + +
90B ILE* 1.3 73.3 + - + +
91B GLY* 3.0 3.6 + - - -
119B VAL* 4.8 10.5 - - + +
120B LEU* 3.9 20.9 - - + -
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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