Contacts of the helix formed by residues 78 - 108 (chain M) in PDB entry 3Q84
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 78 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77M TYR* 1.3 81.4 - - - +
79M SER* 1.3 65.1 + - - +
81M GLU* 3.3 21.8 + - - +
82M ARG* 3.7 20.2 + - - +
282M GLU* 5.9 1.6 - - - -
283M ASP* 4.2 6.1 - - - -
286M TRP* 5.2 9.5 - - - -
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Residues in contact with SER 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M GLY* 1.3 69.5 - - - -
80M LEU* 1.3 70.5 + - - +
81M GLU 3.0 1.6 - - - -
82M ARG* 2.8 45.0 + - - +
83M ALA* 3.0 11.1 + - - +
277M GLY 4.6 4.5 - - - -
278M ALA* 3.7 7.8 - - - +
279M ASP* 3.2 27.7 + - - -
282M GLU* 3.8 12.8 + - - -
283M ASP* 3.2 19.7 + - - -
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Residues in contact with LEU 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76M GLN* 4.2 12.7 - - - +
79M SER* 1.3 81.3 + - - +
81M GLU* 1.3 60.2 + - - +
83M ALA* 3.9 3.6 - - - +
84M TRP* 3.2 23.2 + - - +
278M ALA* 4.0 18.2 - - + -
279M ASP 4.7 7.6 - - - +
280M ALA 4.8 5.4 - - - +
283M ASP* 3.2 16.3 + - - +
242N LEU* 3.7 40.4 - - + +
245N LEU* 3.1 32.8 - - + +
246N LYS* 3.8 28.7 - - + +
249N LEU* 4.1 10.1 - - + -
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Residues in contact with GLU 81 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M ILE* 3.6 35.8 - - + +
72M GLU* 4.3 13.9 - - - +
76M GLN* 3.7 26.6 - - + +
77M TYR* 3.7 15.3 + - - -
78M GLY 3.3 23.0 + - - +
79M SER 3.0 0.6 - - - -
80M LEU* 1.3 77.4 - - - +
82M ARG* 1.3 52.2 + - + +
84M TRP* 3.2 5.9 + - - +
85M GLY* 2.7 33.4 + - - -
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Residues in contact with ARG 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M GLY* 3.7 14.2 + - - +
79M SER* 2.8 51.9 + - - +
81M GLU* 1.3 73.5 - - + +
83M ALA* 1.3 66.4 + - - +
85M GLY* 3.2 2.1 + - - +
86M ALA* 2.8 24.9 + - - +
274M ALA* 5.1 2.8 - - - +
277M GLY 5.5 1.8 + - - -
282M GLU* 5.0 7.9 + - - -
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Residues in contact with ALA 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M SER 3.0 7.2 + - - +
80M LEU* 4.0 6.3 - - + +
82M ARG* 1.3 76.9 - - - +
84M TRP* 1.3 68.6 + - - +
86M ALA* 3.0 14.1 + - - +
87M ILE* 3.8 2.4 + - - +
274M ALA 3.9 14.7 + - - +
275M ILE* 3.9 28.3 - - - +
278M ALA* 4.0 20.6 - - + -
246N LYS* 6.4 0.2 - - - -
249N LEU* 3.8 19.0 - - + +
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Residues in contact with TRP 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M TRP* 4.3 6.3 - + - -
71M ILE* 3.5 36.9 - - + +
76M GLN* 4.3 31.0 - - + -
80M LEU 3.2 14.5 + - - +
81M GLU 3.4 3.4 - - - +
83M ALA* 1.3 81.7 - - - +
85M GLY* 1.3 59.7 + - - +
87M ILE* 3.1 11.7 + - + +
88M MSE 2.8 28.7 - - + +
38N LEU* 4.5 14.1 - - + -
41N ASP* 3.7 28.3 - - + -
42N LEU* 3.8 38.8 - - + +
45N CYS* 3.8 19.7 - - + -
245N LEU* 5.4 9.2 - - + -
249N LEU* 3.6 27.5 - - + +
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Residues in contact with GLY 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M ARG* 3.7 11.3 + - - -
71M ILE* 4.3 9.8 - - - +
81M GLU 2.7 19.1 + - - -
82M ARG* 3.2 3.6 + - - -
84M TRP* 1.3 70.4 - - - +
86M ALA* 1.3 66.4 + - - +
87M ILE 3.1 0.2 - - - -
88M MSE 2.9 31.0 + - - +
89M THR 3.5 4.0 + - - -
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Residues in contact with ALA 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82M ARG 2.8 16.2 + - - +
83M ALA* 3.0 12.8 + - - +
85M GLY* 1.3 72.7 - - - +
87M ILE* 1.3 58.1 + - - +
89M THR* 2.8 29.1 + - - -
90M GLU 2.9 10.2 + - - -
271M LEU* 3.7 15.6 - - + +
274M ALA* 3.6 30.1 - - + -
275M ILE* 5.1 0.2 - - + -
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Residues in contact with ILE 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M TRP* 3.7 25.5 - - + -
83M ALA 4.6 1.8 - - - +
84M TRP* 3.1 9.6 + - + +
86M ALA* 1.3 76.2 - - - +
88M MSE 1.3 66.9 + - + +
90M GLU* 3.0 21.2 - - + +
91M ALA* 3.2 8.0 + - - +
271M LEU* 3.7 25.8 - - + -
275M ILE* 4.3 13.0 - - + -
249N LEU* 4.1 25.6 - - + +
252N ILE* 3.9 26.5 - - + -
256N LEU* 4.1 20.0 - - + -
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Residues in contact with MSE 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M TRP* 4.5 12.6 - - + -
64M ALA* 3.5 32.1 - - + +
67M TRP* 3.5 32.1 - - - -
68M ARG* 3.7 26.2 - - + +
71M ILE* 4.0 6.5 - - - -
84M TRP* 2.8 49.1 - - + +
85M GLY* 2.9 20.2 + - - +
87M ILE* 1.3 90.7 - - + +
89M THR* 1.3 65.1 + - - +
91M ALA* 3.4 6.4 + - - +
92M ASP* 3.1 19.9 + - - +
45N CYS* 4.8 1.1 - - - -
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Residues in contact with THR 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68M ARG* 2.9 27.6 + - - +
85M GLY 3.5 2.4 + - - -
86M ALA* 2.8 18.0 + - - +
88M MSE 1.3 75.4 - - - +
90M GLU* 1.3 66.4 + - - +
92M ASP* 2.8 16.2 + - + +
93M LYS* 3.0 41.2 + - + +
270M GLU* 4.4 11.0 - - - +
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Residues in contact with GLU 90 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M ALA 2.9 9.8 + - - +
87M ILE* 3.0 26.5 - - + +
89M THR* 1.3 75.2 - - - +
91M ALA* 1.3 73.7 + - - +
93M LYS* 3.5 1.4 + - - +
94M VAL* 2.9 29.9 + - - +
267M VAL* 4.1 21.5 - - + +
268M TYR* 2.4 36.0 + - + -
271M LEU* 4.1 26.5 - - + -
49N ARG* 2.3 35.8 + - - -
256N LEU* 4.1 7.7 - - + +
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Residues in contact with ALA 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M LEU* 3.4 27.9 - - + +
63M TRP* 3.7 28.9 - - + -
64M ALA* 4.4 0.7 - - + -
87M ILE 3.2 4.3 + - - +
88M MSE 3.7 8.3 - - - +
89M THR 3.1 0.6 - - - -
90M GLU* 1.3 96.5 + - - +
92M ASP* 1.3 62.4 + - - +
94M VAL* 4.6 3.1 - - - -
95M SER* 3.1 22.7 + - - -
49N ARG* 4.7 0.9 - - - +
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Residues in contact with ASP 92 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M THR* 4.2 20.1 + - - +
64M ALA* 3.6 17.5 - - - +
68M ARG* 3.5 23.7 + - - -
88M MSE 3.1 10.1 + - - +
89M THR* 2.8 12.1 + - + +
91M ALA* 1.3 75.4 - - - +
93M LYS* 1.3 61.4 + - + +
95M SER* 3.0 6.6 + - - -
96M GLU* 2.8 30.0 + - - +
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Residues in contact with LYS 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M THR* 3.0 32.5 + - + +
90M GLU* 4.0 2.9 - - - +
92M ASP* 1.3 76.7 - - + +
94M VAL* 1.3 60.6 + - - +
96M GLU* 3.5 16.5 + - - +
97M LEU* 3.1 30.0 + - + +
267M VAL* 4.1 26.7 - - + -
270M GLU* 2.5 36.8 + - - +
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Residues in contact with VAL 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M TYR* 4.2 7.9 - - - +
60M LEU* 3.3 24.9 - - + -
90M GLU* 2.9 23.8 + - - +
91M ALA* 4.2 1.8 - - - +
93M LYS* 1.3 71.4 - - - +
95M SER* 1.3 66.5 + - - +
97M LEU* 3.4 7.8 + - - +
98M HIS* 2.9 45.7 + - + +
264M TYR* 4.0 23.8 - - + +
267M VAL* 4.5 6.7 - - + -
268M TYR* 3.6 26.7 - - + +
49N ARG* 5.5 2.0 - - - +
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Residues in contact with SER 95 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M GLY* 2.7 35.2 + - - -
60M LEU* 3.9 10.1 - - - -
61M THR* 2.7 16.8 + - - -
91M ALA 3.1 16.6 + - - -
92M ASP* 3.0 11.7 + - - -
94M VAL* 1.3 75.3 - - - +
96M GLU* 1.3 55.7 + - - +
98M HIS* 2.9 22.6 + - - +
99M GLN* 2.9 22.0 + - - +
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Residues in contact with GLU 96 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M ASP 2.8 14.6 + - - +
93M LYS* 3.6 17.0 - - - +
94M VAL 3.3 0.2 - - - -
95M SER* 1.3 75.1 + - - +
97M LEU* 1.3 57.8 + - + +
99M GLN* 3.3 10.4 + - + +
100M GLU* 3.0 46.3 + - + +
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Residues in contact with LEU 97 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93M LYS* 3.1 18.1 + - + +
94M VAL* 3.6 12.6 - - - +
96M GLU* 1.3 80.6 - - + +
98M HIS* 1.3 61.7 + - - +
100M GLU* 3.2 18.4 + - - +
101M VAL* 3.1 25.6 + - - +
258M LEU* 4.6 18.8 - - + +
261M ASN* 3.4 30.1 - - + +
263M SER* 4.2 12.1 - - - +
264M TYR* 3.7 41.7 - - + +
267M VAL* 4.5 5.4 - - + -
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Residues in contact with HIS 98 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M GLU* 2.8 45.2 + - - +
56M TYR* 3.5 28.8 - + - -
57M GLY* 4.6 6.1 - - - -
60M LEU* 4.9 0.2 - - + -
94M VAL* 2.9 38.4 + - + +
95M SER 2.9 12.5 + - - +
97M LEU* 1.3 69.4 - - + +
99M GLN* 1.3 64.4 + - - +
101M VAL* 3.2 8.9 + - - +
102M LYS* 3.0 21.8 + - - +
258M LEU* 3.6 28.4 - - + +
264M TYR* 5.7 1.2 - - - -
56N TYR* 3.8 15.7 - + - -
98N HIS* 5.6 2.7 - + - -
264N TYR* 6.0 0.2 - - - -
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Residues in contact with GLN 99 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M LYS* 3.7 29.1 - - - +
57M GLY* 3.8 15.4 - - - -
58M GLN* 3.9 8.8 + - - -
95M SER* 2.9 24.7 + - - +
96M GLU* 3.6 10.1 - - - +
98M HIS* 1.3 76.5 - - - +
100M GLU* 1.3 64.1 + - + +
102M LYS* 3.2 36.6 + - - +
103M ASN* 2.9 29.3 + - - +
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Residues in contact with GLU 100 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M GLU* 3.0 30.3 + - + +
97M LEU* 3.4 24.9 - - - +
98M HIS 3.1 0.2 - - - -
99M GLN* 1.3 75.6 - - + +
101M VAL* 1.3 64.9 + - + +
103M ASN* 3.1 7.4 + - - +
104M ASN* 2.9 34.8 + - - +
261M ASN* 4.6 5.4 - - - +
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Residues in contact with VAL 101 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M GLU* 4.3 23.3 - - + +
97M LEU 3.1 15.9 + - - +
98M HIS* 3.2 12.8 + - - +
100M GLU* 1.3 75.4 - - + +
102M LYS* 1.3 64.1 + - - +
104M ASN* 3.2 6.3 + - - +
105M LEU* 2.9 32.6 + - + +
255M HIS* 3.4 30.9 - - - +
256M LEU* 4.4 11.4 - - + +
258M LEU* 4.1 22.2 - - + -
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Residues in contact with LYS 102 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M ALA* 3.8 32.0 - - + +
53M GLU* 4.2 7.0 - - + -
54M LYS* 3.7 28.8 - - + +
98M HIS 3.0 9.7 + - - +
99M GLN* 3.3 36.6 - - - +
101M VAL* 1.3 82.2 - - - +
103M ASN* 1.3 88.4 + - - +
105M LEU* 3.2 4.2 + - - +
106M LEU* 3.0 35.1 + - + +
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Residues in contact with ASN 103 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99M GLN* 2.9 22.9 + - - +
100M GLU* 3.1 7.2 + - - +
102M LYS* 1.3 97.7 + - - +
104M ASN* 1.3 65.7 + - - +
106M LEU* 4.4 5.7 - - - +
107M ASN* 2.8 42.0 + - - +
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Residues in contact with ASN 104 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M GLU* 2.9 30.3 + - - +
101M VAL* 3.8 5.6 - - - +
103M ASN* 1.3 74.8 - - - +
105M LEU* 1.3 65.9 + - - +
107M ASN* 5.1 0.2 - - - -
108M GLU* 2.9 38.4 + - - +
109M ASP* 3.5 6.4 + - - +
255M HIS* 3.4 38.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 105 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M VAL* 3.8 24.1 - - + +
49M ARG* 4.3 15.5 - - + -
50M ALA* 4.0 31.4 - - + +
53M GLU* 4.9 1.1 - - + -
101M VAL* 2.9 30.2 + - + +
102M LYS* 3.6 4.5 - - - +
104M ASN* 1.3 79.4 - - - +
106M LEU* 1.3 61.3 + - - +
109M ASP* 3.5 21.5 - - - +
110M LEU 3.3 19.1 + - - -
252M ILE* 4.4 17.0 - - + -
255M HIS* 4.2 13.0 - - + -
256M LEU* 4.3 13.7 - - + -
----------------------------------------------------------
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Residues in contact with LEU 106 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M VAL 5.0 0.2 - - - +
47M GLN* 4.1 17.7 - - + +
50M ALA* 3.9 24.7 - - + -
102M LYS* 3.0 35.3 + - + +
103M ASN* 4.0 5.6 - - - +
105M LEU* 1.3 80.7 - - - +
107M ASN* 1.3 70.1 + - - +
108M GLU 3.7 0.2 + - - -
110M LEU* 3.5 39.6 - - + +
111M GLU* 3.6 12.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 107 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M ASN* 2.8 33.9 + - - +
104M ASN* 5.1 0.2 - - - -
106M LEU* 1.3 83.8 + - - +
108M GLU* 1.3 76.0 + - + +
111M GLU* 3.6 23.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU 108 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M ASN* 2.9 32.9 + - - +
107M ASN* 1.3 94.7 - - + +
109M ASP* 1.3 60.2 + - - +
110M LEU 3.6 0.2 - - - -
111M GLU* 3.9 0.7 - - - +
112M LYS* 2.9 31.5 + - - +
255M HIS* 4.4 15.7 - - + +
----------------------------------------------------------
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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