Contacts of the helix formed by residues 62 - 94 (chain M) in PDB entry 1Q90
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 GLU 62 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 5.0 9.8 + - - +
953D LMG 3.8 32.4 - - - +
2G VAL* 4.1 23.0 - - - +
4G PRO* 4.5 12.7 - - + +
63M ALA* 1.3 69.5 + - - +
64M GLU* 2.9 12.8 - - - +
65M PHE* 2.8 38.6 + - + +
66M ILE* 3.2 13.1 + - - +
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Residues in contact with ALA 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953D LMG 3.3 63.7 - - - +
62M GLU* 1.3 86.6 + - - +
64M GLU* 1.3 62.3 + - + +
66M ILE* 3.8 3.6 - - - +
67M ALA* 3.1 20.3 + - - +
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Residues in contact with GLU 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M GLU* 4.7 4.9 - - - +
63M ALA* 1.3 81.4 - - + +
65M PHE* 1.3 52.3 + - - +
67M ALA* 3.3 6.2 + - - +
68M GLY* 2.6 34.7 + - - -
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Residues in contact with PHE 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G PRO* 3.6 35.2 - - + -
5G LEU* 3.8 17.3 - - + -
951L LMG 3.6 44.2 - - - -
62M GLU* 2.8 25.7 + - + +
64M GLU* 1.3 80.3 - - - +
66M ILE* 1.3 51.6 + - - -
68M GLY* 3.2 1.2 + - - +
69M THR* 2.6 54.4 + - - -
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Residues in contact with ILE 66 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953D LMG 3.3 56.5 - - + +
4G PRO* 4.2 30.1 - - + +
7G CYS* 4.3 4.9 - - + -
8G GLY* 3.7 6.2 - - - -
11G LEU* 3.5 21.8 - - + -
62M GLU* 3.2 25.3 + - - +
63M ALA* 3.8 8.3 - - - +
64M GLU 3.3 0.2 - - - -
65M PHE* 1.3 72.5 - - - +
67M ALA* 1.3 61.6 + - - +
69M THR* 3.1 7.0 + - - -
70M ALA* 2.6 37.8 + - + +
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Residues in contact with ALA 67 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953D LMG 4.2 21.5 - - + +
63M ALA 3.1 15.7 + - - +
64M GLU* 3.6 6.5 - - - +
66M ILE* 1.3 84.0 - - - +
68M GLY* 1.3 62.2 + - - +
70M ALA* 3.4 6.4 - - - +
71M LEU* 2.9 27.3 + - - +
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Residues in contact with GLY 68 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M GLU 2.6 21.8 + - - -
65M PHE* 3.6 2.0 - - - -
66M ILE 3.0 0.2 - - - -
67M ALA* 1.3 73.9 - - - +
69M THR* 1.3 57.1 + - - +
71M LEU* 3.1 8.4 + - - +
72M THR* 2.6 33.6 + - - -
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Residues in contact with THR 69 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LEU* 3.6 28.9 - - + +
8G GLY* 3.8 21.5 - - - -
9G ILE* 4.0 3.8 - - + +
951L LMG 3.6 20.4 + - + -
65M PHE* 2.6 51.3 + - - -
66M ILE* 3.5 4.3 - - - -
68M GLY* 1.3 70.0 - - - +
70M ALA* 1.3 63.1 + - - +
72M THR* 3.0 11.7 + - - -
73M MET* 3.0 22.1 + - + +
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Residues in contact with ALA 70 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953D LMG 5.4 7.4 - - + -
8G GLY 3.3 21.0 + - - +
11G LEU* 4.1 12.6 - - + +
12G GLY* 3.5 15.7 - - - +
66M ILE 2.6 21.1 + - - +
67M ALA* 3.4 9.6 - - - +
69M THR* 1.3 72.8 - - - +
71M LEU* 1.3 64.1 + - - +
73M MET* 3.0 15.6 + - - +
74M VAL* 3.2 15.0 + - - +
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Residues in contact with LEU 71 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951L LMG 6.1 4.0 - - + -
67M ALA 2.9 16.2 + - - +
68M GLY* 3.5 6.3 - - - +
70M ALA* 1.3 78.9 - - - +
72M THR* 1.3 57.8 + - - +
74M VAL* 3.1 14.7 + - + +
75M GLY* 2.9 27.6 + - - +
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Residues in contact with THR 72 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951L LMG 3.5 49.1 + - + +
68M GLY 2.6 26.2 + - - -
69M THR* 3.1 11.3 + - - -
71M LEU* 1.3 77.2 - - - +
73M MET* 1.3 51.6 + - - +
75M GLY* 3.0 3.6 + - - -
76M MET* 2.7 51.5 + - + +
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Residues in contact with MET 73 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G GLY 4.8 0.2 - - - +
9G ILE* 4.1 27.1 - - + +
12G GLY* 4.3 8.7 - - - -
13G LEU* 3.7 24.5 - - + +
16G VAL* 5.6 0.2 - - - -
951L LMG 3.8 33.4 - - + -
69M THR 3.0 15.7 + - - +
70M ALA 3.0 8.1 + - - +
72M THR* 1.3 72.4 - - - +
74M VAL* 1.3 69.5 + - - +
75M GLY 3.0 0.3 + - - -
76M MET* 3.0 28.0 + - + +
77M THR* 2.8 29.4 + - - -
84N PHE* 3.6 39.7 - - + -
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Residues in contact with VAL 74 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G GLY* 4.0 18.5 + - - +
15G PRO* 5.2 4.5 - - + -
16G VAL* 4.1 27.8 - - + +
70M ALA 3.2 17.3 - - - +
71M LEU* 3.3 16.8 - - + +
73M MET* 1.3 76.2 - - - +
75M GLY* 1.3 65.3 - - - +
77M THR* 3.4 1.9 + - - -
78M LEU* 3.2 37.9 + - + +
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Residues in contact with GLY 75 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951L LMG 4.0 21.3 - - - -
71M LEU* 2.9 16.2 + - - +
72M THR 3.3 4.5 - - - -
74M VAL* 1.3 79.4 - - - +
76M MET* 1.3 63.8 + - - +
78M LEU* 3.2 5.0 + - - +
79M VAL* 3.0 29.9 + - - +
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Residues in contact with MET 76 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L TYR* 3.9 15.7 - - + +
951L LMG 3.6 30.3 - - + +
72M THR* 2.7 41.4 + - + +
73M MET* 3.0 39.0 + - - +
75M GLY* 1.3 71.0 - - - +
77M THR* 1.3 64.5 + - - +
79M VAL* 3.3 1.9 + - - +
80M GLY* 2.9 20.4 + - - -
81N CYS* 3.5 35.4 - - - +
84N PHE* 4.1 12.6 - - + -
85N SER* 3.2 23.7 + - - +
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Residues in contact with THR 77 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B BCR 3.6 44.0 - - + -
13G LEU* 4.0 11.8 - - - +
16G VAL* 3.7 13.8 - - + +
73M MET 2.8 21.7 + - - -
74M VAL 3.6 4.0 - - - -
76M MET* 1.3 72.0 - - - +
78M LEU* 1.3 65.0 + - + +
80M GLY* 3.1 3.8 + - - -
81M LEU* 3.1 22.3 + - + +
84N PHE* 3.7 17.3 - - - -
88N LEU* 3.9 17.9 - - + +
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Residues in contact with LEU 78 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B BCR 4.0 44.6 - - + -
16G VAL* 4.5 5.8 - - + -
74M VAL* 3.2 26.7 + - + +
75M GLY* 3.2 7.9 + - - +
77M THR* 1.3 75.9 - - - +
79M VAL* 1.3 64.6 + - + +
80M GLY 3.2 0.2 + - - -
81M LEU* 3.2 10.5 + - + +
82M ALA* 2.9 24.9 + - - +
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Residues in contact with VAL 79 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L TYR* 3.6 10.8 - - + +
11L LEU* 3.4 32.5 - - + -
951L LMG 3.8 24.0 - - + -
75M GLY 3.0 15.0 + - - +
76M MET 3.5 7.0 - - - +
78M LEU* 1.3 75.3 - - + +
80M GLY* 1.3 65.1 + - - +
82M ALA* 3.2 6.0 + - - +
83M ILE* 2.9 34.0 + - + +
85N SER* 5.1 0.2 - - - +
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Residues in contact with GLY 80 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76M MET 2.9 14.5 + - - -
77M THR 3.1 4.0 + - - -
79M VAL* 1.3 78.7 - - - +
81M LEU* 1.3 62.7 + - - +
83M ILE* 3.1 1.7 + - - -
84M GLY 3.0 9.7 + - - -
85N SER* 3.6 27.3 - - - -
88N LEU* 4.5 2.0 - - - -
89N SER* 2.8 27.2 + - - -
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Residues in contact with LEU 81 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 5.1 2.2 - - + -
904B BCR 3.5 62.8 - - + -
77M THR* 3.1 15.3 + - + +
78M LEU* 3.7 10.1 - - + +
80M GLY* 1.3 72.8 - - - +
82M ALA* 1.3 59.4 + - - +
84M GLY* 2.8 17.8 + - - -
85M PHE* 3.1 29.8 + - + -
88N LEU* 4.2 14.1 - - + -
92N VAL* 3.8 25.6 - - + +
98N LEU* 4.4 13.5 - - - +
----------------------------------------------------------
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Residues in contact with ALA 82 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M LEU 2.9 13.2 + - - +
79M VAL* 3.4 12.3 - - - +
81M LEU* 1.3 76.1 - - - +
83M ILE* 1.3 64.3 + - + +
85M PHE* 2.9 13.8 + - - +
86M VAL* 2.9 26.6 + - + +
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Residues in contact with ILE 83 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L LEU* 3.1 47.1 - - + -
15L LEU* 4.1 30.1 - - + -
79M VAL* 2.9 24.3 + - + +
80M GLY* 3.7 1.1 - - - +
82M ALA* 1.3 72.9 - - + +
84M GLY* 1.3 62.6 + - - +
86M VAL* 3.2 12.2 - - + +
87M LEU* 3.0 22.5 + - + +
86N PHE* 4.2 17.0 - - + -
89N SER* 3.6 16.6 - - - +
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Residues in contact with GLY 84 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M GLY 3.0 5.7 + - - -
81M LEU 2.8 12.2 + - - -
83M ILE* 1.3 77.2 - - - +
85M PHE* 1.3 62.4 + - - -
87M LEU* 3.0 15.8 + - - +
88M LEU* 3.0 14.0 + - - +
89N SER* 3.7 29.1 + - - -
92N VAL* 4.1 11.9 - - - -
93N TRP* 4.4 1.4 - - - +
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Residues in contact with PHE 85 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81M LEU* 3.1 34.5 + - + -
82M ALA* 2.9 9.4 + - - +
84M GLY* 1.3 74.6 - - - +
86M VAL* 1.3 52.9 + - - +
88M LEU* 3.1 19.7 + - + +
89M ARG* 2.7 36.3 + - - +
92N VAL* 4.0 11.2 - - + -
97N GLY* 4.4 12.8 - - - -
98N LEU* 3.9 27.4 - - - -
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Residues in contact with VAL 86 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L LEU* 4.4 22.0 - - + -
19L LEU* 6.3 0.4 - - + -
82M ALA* 2.9 22.3 + - + +
83M ILE* 3.2 20.4 - - + +
85M PHE* 1.3 77.4 - - + +
87M LEU* 1.3 63.9 + - - +
89M ARG* 3.2 7.6 + - - +
90M VAL* 3.0 33.1 + - + +
----------------------------------------------------------
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Residues in contact with LEU 87 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L LEU* 3.6 26.0 - - + -
18L THR* 3.7 24.5 - - + -
19L LEU* 4.0 13.0 - - + -
83M ILE* 3.0 23.6 + - + +
84M GLY* 3.0 11.9 + - - +
86M VAL* 1.3 73.7 - - - +
88M LEU* 1.3 67.3 + - - +
90M VAL* 2.8 10.6 + - - +
91M GLU* 2.8 23.9 + - - +
86N PHE* 4.4 13.2 - - + -
89N SER* 4.3 14.8 - - - +
90N LEU* 4.7 0.7 - - + -
93N TRP* 3.7 38.9 + - + -
----------------------------------------------------------
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Residues in contact with LEU 88 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 4.6 0.4 - - - +
84M GLY 3.0 6.9 + - - +
85M PHE* 3.4 34.5 - - + +
87M LEU* 1.3 77.9 - - - +
89M ARG* 1.3 57.5 + - - +
91M GLU* 3.4 10.3 + - - +
92M SER* 2.8 28.7 + - - -
92N VAL* 3.9 5.4 - - + +
93N TRP* 3.5 41.0 - - + +
96N SER* 3.8 38.1 - - - +
97N GLY 3.9 3.1 - - - +
----------------------------------------------------------
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Residues in contact with ARG 89 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85M PHE 2.7 11.9 + - - +
86M VAL* 3.3 13.0 - - - +
88M LEU* 1.3 75.0 - - - +
90M VAL* 1.3 57.2 + - + +
92M SER* 3.0 16.3 + - - -
93M LEU* 2.7 77.3 + - + +
----------------------------------------------------------
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Residues in contact with VAL 90 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L LEU* 3.7 34.3 - - + -
22L TYR* 4.9 3.1 - - + -
23L LEU* 5.6 4.9 - - + -
86M VAL* 3.0 27.1 + - + +
87M LEU* 2.8 13.4 + - - +
89M ARG* 1.3 73.9 - - + +
91M GLU* 1.3 52.8 + - - +
93M LEU* 2.9 10.6 + - + +
94M VAL* 2.6 51.6 + - + +
----------------------------------------------------------
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Residues in contact with GLU 91 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 3.1 36.5 + - - +
22L TYR* 3.2 33.8 + - + +
87M LEU 2.8 14.3 + - - +
88M LEU* 3.4 13.4 - - - +
90M VAL* 1.3 73.2 - - - +
92M SER* 1.3 66.7 + - - +
94M VAL* 3.2 5.0 + - - +
95M GLU* 3.2 14.9 + - - -
93N TRP* 2.7 31.5 + - - +
----------------------------------------------------------
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Residues in contact with SER 92 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88M LEU 2.8 15.3 + - - -
89M ARG* 3.0 25.4 + - - -
91M GLU* 1.3 75.6 - - - +
93M LEU* 1.3 59.2 + - - +
95M GLU* 2.6 47.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 93 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M ARG* 2.7 62.8 + - + +
90M VAL* 3.5 9.2 - - + +
92M SER* 1.3 68.5 - - - +
94M VAL* 1.3 56.6 + - + +
95M GLU* 2.5 39.1 + - - +
----------------------------------------------------------
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Residues in contact with VAL 94 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L TYR* 4.0 10.8 - - + +
23L LEU* 4.0 17.3 - - + -
26L LEU* 3.6 31.2 - - + -
27L LYS* 4.0 25.4 + - - +
90M VAL* 2.6 40.9 + - + +
91M GLU 3.2 8.7 + - - +
93M LEU* 1.3 70.0 - - + +
95M GLU* 1.3 63.5 + - - +
----------------------------------------------------------
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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