Contacts of the helix formed by residues 82 - 108 (chain B) in PDB entry 4NEF
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 SER 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LEU* 3.9 3.8 - - - -
81B VAL* 1.3 79.8 - - - +
83B VAL* 1.3 59.3 + - - +
84B LEU* 3.7 11.0 + - - +
85B ARG* 3.1 25.3 + - - +
86B ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.8 28.2 - - + +
82B SER* 1.3 71.4 - - - +
84B LEU* 1.4 58.7 + - + +
86B ALA* 3.7 1.3 - - + +
87B ALA* 3.1 29.6 + - + +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.8 28.0 - - + -
82B SER* 3.1 10.0 - - - +
83B VAL* 1.4 80.0 - - + +
85B ARG* 1.4 63.6 + - - +
87B ALA* 3.4 5.7 + - + +
88B PHE* 3.1 52.2 + - + -
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA 5.8 0.8 - - - -
9B PHE* 3.8 38.3 - - + +
12B ALA* 3.6 15.4 - - - +
63B SER* 5.5 0.4 - - - +
81B VAL* 3.5 23.1 - - + +
82B SER* 3.1 19.9 + - - +
84B LEU* 1.4 75.7 - - - +
86B ALA* 1.4 55.8 + - - +
88B PHE* 3.3 2.1 + - - +
89B TYR* 2.8 86.2 + - + +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 3.5 21.0 - - + +
73B VAL* 6.4 0.9 - - + -
76B LEU* 3.7 33.7 - - + -
81B VAL* 4.5 6.0 - - + +
82B SER 2.9 16.6 + - - +
83B VAL 3.7 4.7 - - - +
85B ARG* 1.4 76.5 - - - +
87B ALA* 1.4 56.5 + - - +
90B VAL* 3.0 35.9 + - + +
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 3.1 19.0 + - + +
84B LEU* 3.7 7.2 - - + +
85B ARG 3.3 0.2 - - - -
86B ALA* 1.4 72.5 - - - +
88B PHE* 1.4 62.4 + - + +
90B VAL* 3.4 6.3 + - - +
91B ALA* 2.9 32.2 + - - +
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.5 36.6 - + + -
13B VAL* 3.6 24.0 - - + +
84B LEU* 3.1 45.9 + - + +
85B ARG 3.7 2.7 - - - +
87B ALA* 1.4 80.2 - - + +
89B TYR* 1.3 57.2 + - - +
91B ALA* 4.0 5.5 - - - +
92B ALA* 3.1 28.1 + - - +
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 4.8 0.2 - + - -
12B ALA* 3.2 24.7 - - + +
13B VAL* 4.1 11.9 - - + -
16B GLU* 3.7 23.7 - - + +
63B SER* 2.9 19.8 + - - -
66B HIS* 3.3 40.4 - + - -
72B THR* 3.7 19.1 - - + -
81B VAL* 5.8 2.0 - - + -
85B ARG* 2.8 66.1 + - + +
86B ALA* 5.5 0.2 - - - -
88B PHE* 1.3 75.4 - - - +
90B VAL* 1.3 55.6 + - - +
92B ALA* 3.1 6.5 + - - +
93B GLN* 2.8 44.5 + - - +
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 3.9 25.5 - - + +
72B THR* 3.8 20.9 - - + -
73B VAL* 4.7 9.4 - - + -
86B ALA* 3.0 23.0 + - + +
87B ALA* 3.9 5.8 - - - +
89B TYR* 1.3 71.7 - - - +
91B ALA* 1.4 57.0 + - - +
93B GLN* 3.3 9.2 + - - +
94B LEU* 3.0 51.6 + - + +
205B TRP* 6.1 2.5 - - + -
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA 2.9 19.0 + - - +
88B PHE* 4.0 7.2 - - - +
90B VAL* 1.4 75.5 - - - +
92B ALA* 1.4 57.2 + - - +
94B LEU* 3.6 9.4 + - - +
95B LEU* 3.1 42.7 + - + +
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 3.5 33.2 - - + +
16B GLU* 4.2 3.8 - - + -
17B PHE* 3.4 25.6 - - + +
88B PHE 3.1 19.1 + - - +
89B TYR* 3.1 6.1 + - - +
91B ALA* 1.4 73.0 - - - +
93B GLN* 1.3 56.0 + - - +
95B LEU* 4.6 5.8 - - - -
96B GLY 2.8 27.7 + - - -
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Residues in contact with GLN 93 (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 GLU* 2.9 29.2 + - + +
20B THR* 3.4 29.6 - - + +
66B HIS* 3.7 5.7 - - - +
68B ASN 3.8 11.9 - - - +
69B PRO* 3.0 34.7 - - + +
72B THR* 2.8 24.2 + - - -
89B TYR* 2.8 27.3 + - - +
90B VAL* 3.6 7.6 - - - +
92B ALA* 1.3 73.5 - - - +
94B LEU* 1.4 55.7 + - - +
97B ALA* 2.9 35.9 + - - +
186B ALA* 4.1 3.1 - - + -
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 4.3 6.5 - - + -
90B VAL* 3.0 40.1 + - + +
91B ALA* 4.0 7.0 - - - +
93B GLN* 1.4 74.4 - - - +
95B LEU* 1.3 61.3 + - + +
97B ALA* 3.9 2.0 - - - +
98B VAL* 3.2 26.0 + - - +
186B ALA* 4.1 22.2 - - + -
189B LEU* 3.8 25.7 - - + +
205B TRP* 3.8 30.1 - - + -
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Residues in contact with LEU 95 (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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17B PHE* 3.9 15.2 - - + -
91B ALA* 3.1 29.3 + - + +
92B ALA* 3.9 6.3 - - - +
94B LEU* 1.3 75.7 - - + +
96B GLY* 1.3 58.5 + - - +
98B VAL* 3.3 13.3 - - + +
99B ALA* 3.1 29.5 + - - +
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Residues in contact with GLY 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 3.4 36.7 - - - -
21B LEU* 3.1 20.2 - - - +
92B ALA 2.8 13.8 + - - -
93B GLN 3.8 0.9 - - - -
95B LEU* 1.3 73.4 - - - +
97B ALA* 1.3 57.6 + - - +
99B ALA* 3.3 2.0 + - - +
100B GLY 2.9 23.7 + - - -
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Residues in contact with ALA 97 (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 THR* 3.9 5.7 - - + -
24B VAL* 3.3 28.0 - - + +
93B GLN 2.9 19.1 + - - +
94B LEU 3.9 4.3 - - - +
95B LEU 3.4 0.2 - - - -
96B GLY* 1.3 71.7 - - - +
98B VAL* 1.4 59.9 + - - +
100B GLY 3.0 2.3 + - - -
101B ALA 3.0 23.6 + - - -
186B ALA* 3.3 34.1 - - + +
190B ALA* 3.3 8.0 - - + +
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Residues in contact with VAL 98 (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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94B LEU 3.2 13.1 + - - +
95B LEU* 3.3 24.5 - - + +
97B ALA* 1.4 76.1 - - - +
99B ALA* 1.4 56.2 + - + +
101B ALA* 3.4 1.4 + - - +
102B ALA* 2.9 30.4 + - + +
189B LEU* 6.3 2.5 - - + -
190B ALA* 3.7 14.2 - - - +
193B VAL* 3.7 34.3 - - + -
194B VAL* 4.0 13.9 - - + -
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Residues in contact with ALA 99 (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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17B PHE* 4.4 8.5 - - + -
21B LEU* 3.8 20.2 - - + -
95B LEU 3.1 19.5 + - - +
96B GLY* 3.5 5.8 - - - +
97B ALA 3.2 0.2 - - - -
98B VAL* 1.4 76.1 - - + +
100B GLY* 1.3 57.1 + - - +
102B ALA* 3.9 5.1 - - - +
103B LEU* 3.0 33.6 + - + +
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Residues in contact with GLY 100 (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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21B LEU* 3.5 30.3 - - - +
24B VAL* 4.1 5.4 - - - -
25B PHE* 3.7 13.4 - - - -
96B GLY 2.9 11.4 + - - -
97B ALA 3.0 4.0 + - - -
99B ALA* 1.3 77.2 - - - +
101B ALA* 1.4 56.9 + - - +
103B LEU* 3.7 2.6 + - - -
104B LEU* 3.1 28.1 + - - +
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Residues in contact with ALA 101 (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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24B VAL* 3.7 9.1 - - + +
28B LEU* 4.2 9.0 - - + -
97B ALA 3.0 14.8 + - - +
98B VAL 3.8 3.6 - - - +
100B GLY* 1.4 71.8 - - - +
102B ALA* 1.4 59.6 + - - +
104B LEU* 3.9 4.9 - - - +
105B HIS* 3.1 26.0 + - - +
116B LEU* 3.7 12.2 - - + +
190B ALA* 3.6 34.5 - - + +
191B PRO 4.1 2.5 - - - -
194B VAL* 3.8 5.8 - - + +
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Residues in contact with ALA 102 (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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98B VAL* 2.9 20.6 + - + +
99B ALA* 3.9 6.5 - - - +
101B ALA* 1.4 72.4 - - - +
103B LEU* 1.3 63.3 + - - +
105B HIS* 3.5 11.9 + - + +
106B GLU* 3.2 22.2 + - - +
194B VAL* 3.8 14.3 - - + +
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Residues in contact with LEU 103 (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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21B LEU* 4.1 19.7 - - + -
25B PHE* 3.7 19.1 - - + -
99B ALA* 3.0 20.9 + - + +
100B GLY* 3.8 5.6 - - - +
102B ALA* 1.3 74.3 - - - +
104B LEU* 1.4 64.2 + - - +
106B GLU* 3.4 18.5 - - - +
107B ILE* 3.2 25.6 + - + +
132D THR* 4.4 12.8 - - + -
136D PHE* 3.7 41.5 - - + -
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Residues in contact with LEU 104 (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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24B VAL 4.8 0.9 - - - +
25B PHE* 3.8 25.1 - - + +
28B LEU* 3.7 20.2 - - + -
29B GLY* 3.5 36.8 - - - +
32B LEU* 4.5 3.8 - - + -
100B GLY 3.1 18.8 + - - +
101B ALA* 3.9 3.6 - - - +
103B LEU* 1.4 73.6 - - - +
105B HIS* 1.3 62.8 + - - +
107B ILE* 3.2 8.9 + - + +
108B THR* 2.7 48.0 + - - +
116B LEU* 4.1 20.6 - - + -
174D LEU* 4.5 3.1 - - + -
178D TYR* 3.5 13.7 - - - +
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA 3.1 19.4 + - - +
102B ALA* 3.5 9.6 - - - +
103B LEU 3.4 0.2 - - - -
104B LEU* 1.3 74.8 - - - +
106B GLU* 1.3 64.8 + - + +
108B THR 3.2 6.4 - - - +
113B ARG* 2.8 77.4 + - - +
116B LEU* 4.3 14.3 - - + +
194B VAL* 4.1 20.6 - - + +
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Residues in contact with GLU 106 (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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102B ALA 3.2 10.1 + - - +
103B LEU* 3.4 20.4 - - - +
104B LEU 3.3 0.2 - - - -
105B HIS* 1.3 85.3 - - + +
107B ILE* 1.3 66.8 + - - +
113B ARG* 4.3 5.6 + - - +
129D GLN* 2.9 28.2 + - - +
132D THR* 4.5 10.0 + - - +
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Residues in contact with ILE 107 (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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25B PHE* 3.7 25.8 - - + -
103B LEU* 3.3 16.6 - - + +
104B LEU* 3.2 11.9 + - + +
106B GLU* 1.3 91.6 - - + +
108B THR* 1.3 58.7 + - - +
109B PRO* 3.9 1.2 - - - +
125D THR* 4.2 0.3 - - - +
129D GLN* 3.4 52.3 - - + +
132D THR* 3.7 23.6 - - + -
133D VAL* 3.6 17.9 - - + -
178D TYR* 3.5 36.1 - - + +
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.7 22.8 - - + +
34B TRP* 4.1 2.2 - - + -
104B LEU* 2.7 30.8 + - - +
105B HIS 3.2 2.5 + - - +
107B ILE* 1.3 76.8 - - - +
109B PRO* 1.4 84.5 - - + +
110B ALA 3.4 0.3 + - - -
112B ILE* 4.1 8.7 - - + -
113B ARG* 3.0 43.3 + - + +
116B LEU* 5.6 0.7 - - - -
129D GLN* 4.2 2.2 + - - -
178D TYR* 2.8 23.0 + - - +
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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