Contacts of the helix formed by residues 89 - 111 (chain B) in PDB entry 3N4E
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 GLY 89 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS 4.6 3.6 - - - -
85A LEU* 3.4 16.8 - - - -
86A GLY* 3.8 3.6 - - - -
88B GLU* 1.3 70.7 - - - +
90B ILE* 1.3 65.2 + - - -
91B ALA 3.4 0.2 - - - -
92B THR* 3.1 11.1 + - - -
93B ALA* 3.0 28.8 + - - +
252B TYR* 3.5 20.2 - - - -
274B LYS* 4.0 1.2 - - - +
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Residues in contact with ILE 90 (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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54A VAL* 4.3 0.9 - - + -
85A LEU* 3.0 52.7 + - + +
90A ILE* 3.6 48.7 - - + -
91A ALA 5.0 1.1 - - - +
50B ALA* 3.6 32.1 - - + +
51B SER* 2.7 45.1 + - - +
54B VAL* 4.0 6.1 - - + -
85B LEU 5.7 0.4 - - - +
88B GLU 3.2 3.4 + - - +
89B GLY* 1.3 70.8 - - - -
91B ALA* 1.3 62.7 + - - +
94B ALA* 3.2 11.6 + - - +
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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
----------------------------------------------------------
90A ILE* 5.0 1.2 - - + +
54B VAL* 4.9 3.1 - - - -
82B LEU* 4.5 17.0 - - + -
85B LEU* 4.4 21.7 + - + +
87B PRO* 3.0 34.0 + - + +
90B ILE* 1.3 79.8 - - - +
92B THR* 1.3 59.6 + - - +
94B ALA* 3.2 6.6 + - - +
95B LEU* 2.9 34.7 + - + +
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Residues in contact with THR 92 (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 MSE 5.4 1.6 - - + -
87B PRO* 3.1 33.5 + - + +
88B GLU* 3.9 3.6 - - + -
89B GLY 3.1 18.4 + - - -
91B ALA* 1.3 77.0 - - - +
93B ALA* 1.3 56.4 + - - +
95B LEU* 4.0 10.8 - - + +
96B ALA* 2.9 29.3 + - - +
252B TYR* 3.6 28.0 - - - +
253B THR* 5.0 1.3 - - + -
274B LYS 2.8 21.8 + - - +
275B MSE 3.6 6.7 - - - -
276B GLY 4.2 2.2 + - - -
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Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 3.5 6.1 - - + +
43B SER* 4.0 17.0 - - - +
51B SER* 3.5 13.5 - - - +
89B GLY 3.0 19.3 + - - +
92B THR* 1.3 74.0 - - - +
94B ALA* 1.3 61.3 + - - +
96B ALA* 3.6 1.4 - - - +
97B ALA* 2.9 32.1 + - - +
273B VAL 3.4 22.4 - - - +
274B LYS* 3.2 8.2 + - - +
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 4.7 0.7 - - - -
51B SER* 3.6 26.4 + - - +
54B VAL* 4.0 10.8 - - + -
55B VAL* 3.8 13.8 - - + +
59B ILE* 4.0 13.2 - - + -
90B ILE 3.2 13.7 + - - +
91B ALA 3.2 8.7 + - - +
93B ALA* 1.3 79.3 - - - +
95B LEU* 1.3 61.1 + - - +
97B ALA* 3.5 4.6 + - - +
98B CYS* 3.3 27.0 + - - -
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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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59B ILE* 4.0 16.8 - - + -
75B LEU* 3.8 23.8 - - + +
78B MSE 3.8 31.0 - - + -
79B MSE 3.6 35.0 - - + +
82B LEU* 4.2 8.7 - - + -
87B PRO* 5.2 0.2 - - + -
91B ALA* 2.9 29.7 + - + +
92B THR* 4.0 9.4 - - + +
94B ALA* 1.3 73.9 - - - +
96B ALA* 1.3 59.3 + - - +
98B CYS* 3.2 5.6 + - - +
99B ASP* 2.8 29.7 + - - +
276B GLY* 5.7 1.3 - - - +
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Residues in contact with ALA 96 (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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92B THR 2.9 23.2 + - - +
93B ALA 3.3 4.5 + - - +
95B LEU* 1.3 72.5 - - - +
97B ALA* 1.3 57.4 + - - +
99B ASP* 3.2 3.2 + - - +
100B ILE* 3.0 35.7 + - - +
272B ILE 3.4 22.4 - - - +
273B VAL* 4.0 6.1 - - - -
275B MSE 3.6 13.2 - - - +
276B GLY 4.2 3.3 - - - +
277B GLY* 3.5 18.0 - - - +
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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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28B VAL* 3.8 22.4 - - + +
40B GLY* 3.1 12.5 - - - -
41B GLU 3.3 34.5 + - - +
42B ALA* 3.6 7.6 - - + +
93B ALA 2.9 15.5 + - - +
94B ALA* 3.6 6.3 - - - +
96B ALA* 1.3 76.2 - - - +
98B CYS* 1.3 57.8 + - - +
100B ILE* 3.5 0.9 + - - -
101B ALA* 3.1 23.4 + - - +
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Residues in contact with CYS 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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8B VAL* 4.8 2.5 - - - -
28B VAL* 4.2 13.7 - - - -
30B ILE* 4.0 7.8 - - + +
55B VAL* 4.2 19.1 - - - -
59B ILE* 3.6 26.0 - - - -
63B LEU* 4.2 16.6 - - + -
75B LEU* 3.9 14.1 - - + -
94B ALA 3.3 13.9 + - - +
95B LEU* 3.2 8.6 + - - +
97B ALA* 1.3 77.0 - - - +
99B ASP* 1.3 68.3 + - - +
101B ALA* 3.4 2.4 + - - +
102B LEU* 3.0 27.2 + - - +
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Residues in contact with ASP 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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71B HIS* 4.0 7.3 + - - +
72B ALA* 5.6 0.9 - - - -
75B LEU* 3.4 19.8 - - + +
95B LEU 2.8 14.3 + - - +
96B ALA 3.4 8.1 - - - +
98B CYS* 1.3 76.3 - - - +
100B ILE* 1.3 57.1 + - - +
102B LEU* 3.1 5.7 + - - +
103B TRP* 3.0 41.5 + - - -
276B GLY 3.6 18.5 - - - +
278B ILE 2.7 27.7 + - - -
279B THR* 2.9 26.2 + - - -
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Residues in contact with ILE 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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39B TRP 3.5 13.2 - - - +
40B GLY* 4.1 1.3 - - - -
41B GLU 4.0 9.9 - - - +
96B ALA 3.0 19.1 + - - +
97B ALA 3.8 4.0 - - - +
99B ASP* 1.3 74.9 - - - +
101B ALA* 1.3 57.9 + - - +
103B TRP* 3.3 6.7 + - - +
104B ASP* 3.0 26.5 + - - +
272B ILE 3.6 23.8 - - - +
273B VAL* 3.9 20.0 - - + -
277B GLY* 4.0 11.4 - - - -
278B ILE* 4.2 6.3 - - + +
304B VAL* 3.9 9.9 - - + -
308B ALA* 4.1 26.5 - - + -
355B LEU* 3.9 20.1 - - + +
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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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28B VAL* 3.9 4.5 - - + +
30B ILE* 3.5 28.7 - - + -
38B GLY* 3.4 23.6 - - - +
39B TRP 3.3 12.4 + - - +
40B GLY 3.6 17.5 - - - +
97B ALA 3.1 13.5 + - - +
98B CYS 3.8 0.2 - - - +
99B ASP 3.4 0.2 - - - -
100B ILE* 1.3 75.4 - - - +
102B LEU* 1.3 57.7 + - - +
104B ASP 3.4 0.3 + - - -
105B LEU* 3.1 24.6 + - - +
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Residues in contact with LEU 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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5B ILE* 3.7 31.0 - - + -
30B ILE* 4.0 15.5 - - + -
63B LEU* 4.6 16.6 - - + -
68B VAL* 3.7 19.1 - - + +
71B HIS* 3.6 36.5 - - + -
74B LEU* 5.1 0.9 - - + -
75B LEU* 4.0 19.3 - - + -
98B CYS 3.0 18.6 + - - +
99B ASP 3.6 5.8 - - - +
101B ALA* 1.3 73.3 - - - +
103B TRP* 1.3 61.1 + - - +
105B LEU* 3.4 10.1 + - + +
106B LYS* 2.8 28.6 + - - +
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Residues in contact with TRP 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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71B HIS* 3.2 20.1 - + - -
99B ASP* 3.0 38.7 + - - +
100B ILE 3.7 4.0 - - - +
102B LEU* 1.3 74.4 - - - +
104B ASP* 1.3 60.0 + - - +
106B LYS* 3.2 40.0 + - + +
107B GLY* 2.8 27.4 + - - -
114B ILE* 3.9 25.1 - - + +
117B LEU* 3.8 31.2 - - + -
118B LEU* 3.7 29.8 - - + -
278B ILE* 3.7 33.0 - - + -
279B THR* 2.9 26.9 + - - +
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Residues in contact with ASP 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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38B GLY* 3.5 5.8 - - - -
39B TRP* 3.1 34.0 + - - +
100B ILE 3.0 13.2 + - - +
101B ALA 3.5 9.0 - - - +
102B LEU 3.3 0.2 - - - -
103B TRP* 1.3 76.9 - - - +
105B LEU* 1.3 62.6 + - - +
107B GLY 3.3 1.2 + - - -
108B LYS* 3.2 44.5 + - - +
114B ILE* 4.1 3.5 - - - +
354B GLY* 3.5 7.7 - - - -
355B LEU* 2.8 39.5 + - + +
356B GLY 4.5 1.0 + - - -
357B ILE* 4.6 3.6 - - - +
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Residues in contact with LEU 105 (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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3B LEU* 4.7 2.4 - - + +
5B ILE* 5.4 0.2 - - + -
30B ILE* 3.6 39.7 - - + +
32B ALA* 4.2 8.7 - - + +
36B THR* 3.5 32.7 + - - +
37B VAL 3.5 7.6 - - - +
38B GLY* 3.5 20.1 - - - +
68B VAL* 3.9 28.4 - - + +
101B ALA 3.1 12.7 + - - +
102B LEU* 3.5 11.2 - - + +
104B ASP* 1.3 76.1 - - - +
106B LYS* 1.3 64.9 + - - +
108B LYS* 3.4 5.4 + - + +
109B LEU* 3.0 25.1 + - - +
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Residues in contact with LYS 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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68B VAL* 4.0 10.3 - - + +
69B LEU* 3.8 24.7 - - + -
71B HIS* 3.0 37.4 + - + +
102B LEU 2.8 18.1 + - - +
103B TRP* 3.2 43.4 + - + +
105B LEU* 1.3 76.9 - - - +
107B GLY* 1.3 61.4 + - - +
109B LEU* 3.4 4.4 + - - +
110B LEU* 3.1 45.4 + - + +
117B LEU* 4.1 8.7 - - + -
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Residues in contact with GLY 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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103B TRP 2.8 14.8 + - - -
105B LEU 3.3 0.4 - - - -
106B LYS* 1.3 75.6 - - - +
108B LYS* 1.3 56.8 + - - +
110B LEU 3.5 0.6 + - - -
111B GLY 2.9 23.2 + - - -
112B GLN 2.9 29.7 + - - +
114B ILE* 5.0 0.2 - - - -
117B LEU* 3.7 13.7 - - - +
353B PRO* 3.4 1.4 - - - +
354B GLY* 3.6 13.0 - - - -
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Residues in contact with LYS 108 (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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36B THR* 5.0 15.9 - - + -
37B VAL* 2.5 40.0 + - - +
39B TRP* 4.9 6.9 - - - +
104B ASP* 3.2 35.3 + - - +
105B LEU* 3.8 5.6 - - - +
107B GLY* 1.3 74.4 - - - +
109B LEU* 1.3 65.7 + - - +
110B LEU 3.4 0.5 + - - -
111B GLY* 3.4 9.4 + - - -
353B PRO* 4.1 27.6 - - + +
356B GLY 6.2 0.2 - - - +
357B ILE 5.7 3.5 + - - -
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Residues in contact with LEU 109 (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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3B LEU* 4.1 44.6 - - + +
34B ASP* 5.8 1.3 - - - +
36B THR* 5.7 2.6 + - - -
68B VAL* 5.0 3.8 - - + -
69B LEU* 4.1 38.4 - - + -
105B LEU 3.0 17.9 + - - +
106B LYS* 3.7 4.3 - - - +
108B LYS* 1.3 76.9 - - - +
110B LEU* 1.3 70.0 + - + +
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Residues in contact with LEU 110 (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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69B LEU* 4.6 12.1 - - + -
106B LYS* 3.1 39.8 + - + +
107B GLY 4.3 1.3 - - - +
109B LEU* 1.3 95.6 - - + +
111B GLY* 1.3 63.1 + - - +
112B GLN* 3.6 10.4 + - + +
117B LEU* 3.8 30.3 - - + -
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Residues in contact with GLY 111 (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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107B GLY 2.9 6.8 + - - -
108B LYS 3.4 10.3 + - - -
109B LEU 3.5 0.2 - - - -
110B LEU* 1.3 79.8 - - - +
112B GLN* 1.3 70.4 + - - +
113B PRO* 4.4 2.4 - - - +
353B PRO* 3.9 14.1 - - - +
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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) + - + + + + + -
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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