Contacts of the helix formed by residues 87 - 116 (chain M) in PDB entry 1NF6
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 ALA 87 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M MET* 5.9 1.1 - - - -
85M GLY 3.5 3.2 + - - -
86M GLN* 1.3 75.2 - - - +
88M VAL* 1.3 57.3 + - - +
89M PRO* 3.4 11.9 - - + -
90M VAL* 2.8 36.4 + - + +
91M ILE* 2.9 10.7 + - - +
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Residues in contact with VAL 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M LEU* 4.5 9.2 - - + -
40M MET* 3.7 35.6 - - + +
42M TYR* 4.4 11.2 - - + -
45M LEU* 5.0 2.7 - - + -
86M GLN 3.8 0.8 + - - -
87M ALA* 1.3 70.0 - - - +
89M PRO* 1.3 71.0 - - + +
91M ILE* 3.2 17.4 + - - +
92M TYR* 3.3 23.1 - - + -
146M ILE* 3.4 26.7 - - + -
154M LEU* 4.2 22.7 - - + -
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Residues in contact with PRO 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M ALA* 3.5 11.9 - - + -
88M VAL* 1.3 95.7 - - + +
90M VAL* 1.3 63.1 + - + +
92M TYR* 3.5 2.9 + - + +
93M GLU* 3.2 23.8 + - - +
143M GLY* 5.7 2.1 - - - -
146M ILE* 4.0 28.7 - - + -
147M LYS* 6.1 3.6 - - + -
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Residues in contact with VAL 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M GLN* 3.5 26.9 - - + +
87M ALA* 2.8 25.6 + - + +
89M PRO* 1.3 79.6 - - + +
91M ILE* 1.3 56.8 + - - +
93M GLU* 3.9 7.1 - - + +
94M SER* 2.8 44.4 + - - +
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Residues in contact with ILE 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M GLN* 3.8 33.2 - - + +
36M SER* 5.1 2.7 - - - -
37M LEU* 4.0 21.8 - - + -
40M MET* 4.9 6.3 - - + -
49M MET* 3.6 24.0 - - + -
86M GLN* 3.9 24.5 - - + +
87M ALA 2.9 10.9 + - - +
88M VAL* 3.2 22.2 + - + +
90M VAL* 1.3 76.9 - - - +
92M TYR* 1.3 76.8 + - + +
94M SER* 3.8 0.6 - - - -
95M ASP* 2.9 38.7 + - - +
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Residues in contact with TYR 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M LEU* 3.5 17.9 - - + +
45M LEU* 3.3 38.2 + - + +
49M MET* 3.9 20.0 - - + +
88M VAL* 3.3 16.8 - - + -
89M PRO 3.5 4.5 + - - +
90M VAL 3.4 0.2 - - - -
91M ILE* 1.3 84.7 - - + +
93M GLU* 1.3 60.1 + - - +
95M ASP* 4.4 2.9 - - - -
96M ALA* 3.0 30.3 + - - +
138M TYR* 4.2 6.4 + + - -
139M TYR* 3.7 36.1 - + - +
142M ILE* 3.7 35.7 - - + -
143M GLY* 3.8 17.5 - - - +
146M ILE* 3.8 14.4 - - + -
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Residues in contact with GLU 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89M PRO 3.2 18.2 + - - +
90M VAL* 3.9 7.9 - - + +
92M TYR* 1.3 76.6 - - - +
94M SER* 1.3 63.9 + - - +
96M ALA* 3.4 4.7 + - - +
97M ASP* 3.2 38.7 + - - +
143M GLY* 5.5 0.8 - - - -
147M LYS* 5.6 7.2 - - - +
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Residues in contact with SER 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M GLN* 6.4 0.2 - - - -
86M GLN* 3.2 26.6 + - - -
90M VAL* 2.8 26.4 + - - +
91M ILE 3.8 2.7 - - - -
93M GLU* 1.3 76.4 - - - +
95M ASP* 1.3 66.7 + - - +
97M ASP* 3.5 8.8 + - - +
98M GLN* 3.1 24.4 + - - +
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Residues in contact with ASP 95 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M GLN* 4.6 2.9 - - - +
30M TYR* 3.2 18.1 - - + -
33M GLN* 2.5 41.7 + - - +
49M MET* 3.3 18.4 - - - +
91M ILE* 2.9 21.5 + - - +
92M TYR 4.2 0.9 - - - +
94M SER* 1.3 75.9 - - - +
96M ALA* 1.3 67.6 + - - +
98M GLN* 3.2 6.6 + - - +
99M GLU* 3.0 27.7 + - - +
139M TYR* 3.6 29.6 - - + -
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Residues in contact with ALA 96 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92M TYR 3.0 21.1 + - - +
93M GLU* 3.9 5.2 - - - +
94M SER 3.3 0.2 - - - -
95M ASP* 1.3 76.3 - - - +
97M ASP* 1.3 59.2 + - - +
99M GLU* 3.5 0.5 + - - +
100M ASP* 3.1 23.8 + - - +
136M LEU* 3.3 16.3 - - + +
139M TYR* 4.0 17.0 - - + +
140M GLU* 4.2 24.5 - - + +
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Residues in contact with ASP 97 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93M GLU* 3.2 26.6 + - - +
94M SER* 3.6 11.0 - - - +
95M ASP 3.2 0.2 - - - -
96M ALA* 1.3 76.8 - - - +
98M GLN* 1.3 54.2 + - - +
100M ASP* 3.1 8.6 + - - +
101M ALA* 2.8 35.4 + - - +
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Residues in contact with GLN 98 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M MET 4.3 4.0 + - - -
25M HIS* 3.0 39.4 + - - -
26M ALA* 3.7 24.2 - - - +
29M GLN* 4.1 12.0 - - - +
30M TYR* 3.6 18.2 - - - +
94M SER 3.1 17.3 + - - +
95M ASP* 3.2 5.7 + - - +
97M ASP* 1.3 72.9 - - - +
99M GLU* 1.3 58.4 + - - +
101M ALA* 3.4 7.7 + - - +
102M THR* 2.7 43.8 + - - +
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Residues in contact with GLU 99 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M ALA* 5.2 1.0 - - - +
30M TYR* 2.4 26.2 + - - +
56M GLU* 3.3 5.6 - - - +
95M ASP 3.0 20.5 + - - +
96M ALA 3.9 1.8 - - - +
98M GLN* 1.3 75.0 - - - +
100M ASP* 1.3 64.5 + - - +
102M THR* 3.1 6.5 + - - -
103M ILE* 3.0 30.0 + - - +
132M GLU* 3.0 18.2 - - - +
135M HIS* 3.1 13.0 - - - +
136M LEU* 3.8 23.6 - - + +
139M TYR* 3.6 21.5 - - + -
200M FE 2.2 30.8 - - - -
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Residues in contact with ASP 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M ALA 3.1 14.9 + - - +
97M ASP* 3.3 11.3 - - - +
99M GLU* 1.3 76.7 - - - +
101M ALA* 1.3 66.5 + - - +
103M ILE* 3.2 12.9 + - - +
104M GLU* 3.1 32.1 + - - +
136M LEU* 4.5 15.2 - - + +
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Residues in contact with ALA 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M MET* 4.5 2.4 - - + +
97M ASP 2.8 20.1 + - - +
98M GLN* 3.7 8.1 - - + +
100M ASP* 1.3 76.3 + - - +
102M THR* 1.3 58.7 + - - +
104M GLU* 3.5 8.2 + - - +
105M ALA* 3.0 28.6 + - - +
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Residues in contact with THR 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M MET* 3.7 21.7 + - + +
23M GLU* 4.8 0.7 - - - +
98M GLN* 2.7 29.9 + - - +
99M GLU* 3.4 7.2 + - - -
100M ASP 3.1 0.2 - - - -
101M ALA* 1.3 75.4 - - - +
103M ILE* 1.3 57.8 + - - +
105M ALA 3.2 0.5 + - - -
106M TYR* 2.7 73.1 + - + +
132M GLU* 3.1 28.3 + - - +
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Residues in contact with ILE 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99M GLU 3.0 18.8 + - - +
100M ASP* 3.2 7.2 + - - +
102M THR* 1.3 76.0 - - - +
104M GLU* 1.3 60.6 + - + +
106M TYR* 3.7 5.5 - - - +
107M SER* 2.8 44.7 + - - +
129M ILE* 4.4 21.6 - - + +
132M GLU* 3.7 21.8 - - + +
133M GLN* 4.0 30.1 - - + +
136M LEU* 3.8 28.0 - - + -
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Residues in contact with GLU 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M ASP* 3.1 27.1 + - - +
101M ALA* 3.6 11.2 - - - +
103M ILE* 1.3 81.2 - - + +
105M ALA* 1.3 63.0 + - - +
107M SER* 3.1 18.4 + - - -
108M GLN* 3.2 19.2 + - - +
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Residues in contact with ALA 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M MET* 3.9 25.1 - - + -
101M ALA 3.0 17.4 + - - +
102M THR 3.2 3.3 + - - +
104M GLU* 1.3 74.8 - - - +
106M TYR* 1.3 63.7 + - - +
108M GLN* 3.0 20.4 + - - +
109M PHE* 3.0 35.4 + - + -
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Residues in contact with TYR 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ALA* 3.4 25.0 + - + -
22M MET* 4.0 12.7 - - + +
23M GLU* 2.6 43.2 + - - +
63M PHE* 3.6 8.9 - + - -
102M THR* 2.7 47.8 + - + +
103M ILE* 3.8 1.6 - - - +
105M ALA* 1.3 72.4 - - - +
107M SER* 1.3 57.7 + - - +
109M PHE* 3.3 17.8 + + - +
110M LEU* 2.9 29.5 + - - +
125M PHE* 4.0 15.3 - + + -
128M ILE* 3.6 25.8 - - + -
129M ILE* 3.8 24.0 - - + +
132M GLU* 4.1 8.3 - - + -
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Residues in contact with SER 107 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M ILE* 2.8 31.4 + - - +
104M GLU* 3.4 12.3 + - - -
105M ALA 3.1 0.6 - - - -
106M TYR* 1.3 78.9 - - - +
108M GLN* 1.3 60.8 + - - +
110M LEU* 3.5 5.8 + - - +
111M LYS* 3.2 21.7 + - - +
129M ILE* 4.1 15.5 - - - +
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Residues in contact with GLN 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M GLU* 3.2 8.1 + - - +
105M ALA* 3.0 28.1 + - - +
107M SER* 1.3 77.0 - - - +
109M PHE* 1.3 74.2 + - + +
111M LYS* 3.2 19.1 + - + +
112M VAL* 3.2 17.5 + - + +
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Residues in contact with PHE 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M VAL* 3.6 45.2 - - + +
18M LYS* 3.6 36.6 - - + -
19M ALA* 3.8 24.9 - - + -
22M MET* 4.1 14.8 - - - -
105M ALA* 3.0 30.0 + - + -
106M TYR* 3.3 11.0 + + - +
108M GLN* 1.3 81.7 - - + +
110M LEU* 1.3 65.6 + - - +
112M VAL* 3.0 7.7 + - + +
113M CYS* 3.0 25.0 + - - -
125M PHE* 3.8 16.8 - + + -
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Residues in contact with LEU 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M TYR 2.9 16.7 + - - +
107M SER* 3.6 7.2 - - - +
109M PHE* 1.3 76.1 - - - +
111M LYS* 1.3 63.0 + - - +
113M CYS* 2.9 17.6 + - - +
114M LYS* 3.0 49.3 + - + +
122M ALA* 3.8 22.2 - - + +
125M PHE* 4.1 9.1 - - + -
126M GLU* 3.3 32.3 - - + +
129M ILE* 3.8 21.5 - - + -
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Residues in contact with LYS 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107M SER 3.2 10.5 + - - +
108M GLN* 3.2 15.6 + - + +
110M LEU* 1.3 79.8 - - - +
112M VAL* 1.3 54.6 + - + +
114M LYS* 3.3 14.4 + - + +
115M GLU* 2.8 53.5 + - + +
----------------------------------------------------------
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Residues in contact with VAL 112 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M LYS* 4.2 14.8 - - + +
12M VAL* 4.9 0.4 - - + -
15M VAL* 4.2 28.9 - - + -
108M GLN 3.2 13.7 + - - +
109M PHE* 3.0 9.5 + - + +
111M LYS* 1.3 75.8 - - + +
113M CYS* 1.3 60.2 + - - +
115M GLU* 3.1 17.1 + - - +
116M GLN* 2.9 51.0 + - + +
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Residues in contact with CYS 113 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M VAL* 3.7 22.4 - - - -
15M VAL* 4.4 3.8 - - - -
109M PHE 3.0 16.9 + - - -
110M LEU 2.9 8.1 + - - +
112M VAL* 1.3 76.2 - - - +
114M LYS* 1.3 58.5 + - - +
116M GLN 3.3 1.7 + - - -
117M GLY 3.0 4.7 + - - -
118M ASP* 2.7 47.4 + - + +
121M THR* 3.6 29.8 - - - -
122M ALA* 3.8 9.4 - - + -
125M PHE* 3.9 17.3 - - - -
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Residues in contact with LYS 114 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110M LEU* 3.0 41.2 + - + +
111M LYS* 3.4 13.5 - - + +
113M CYS* 1.3 79.2 - - - +
115M GLU* 1.3 62.2 + - + +
117M GLY* 3.1 13.2 + - - -
118M ASP 4.7 3.4 - - - +
119M ILE* 5.4 11.7 - - + +
122M ALA* 4.2 9.0 - - + -
126M GLU* 4.2 11.3 + - - -
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Residues in contact with GLU 115 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111M LYS* 2.8 41.5 + - + +
112M VAL* 3.1 22.5 + - - +
114M LYS* 1.3 77.3 - - + +
116M GLN* 1.3 73.7 + - - +
117M GLY 3.2 2.2 + - - -
----------------------------------------------------------
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Residues in contact with GLN 116 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M ARG* 2.7 57.6 + - - +
11M LYS* 3.1 40.3 + - + +
12M VAL* 3.6 28.3 - - + -
112M VAL* 2.9 30.8 + - + +
113M CYS 3.9 0.4 - - - +
115M GLU* 1.3 91.6 + - - +
117M GLY* 1.3 57.8 - - - +
118M ASP* 3.3 3.1 + - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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