Contacts of the helix formed by residues 92 - 119 (chain M) in PDB entry 1MFR
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 THR 92 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M PHE* 3.6 20.0 - - - -
44M LEU* 3.8 7.8 - - - +
47M VAL* 4.1 17.4 - - + +
91M ASN* 1.3 73.2 - - - +
93M LEU* 1.3 58.0 + - - +
95M ALA* 3.9 1.2 - - - +
96M MET* 3.0 38.0 + - + +
151M LEU* 4.1 8.3 - - + -
156M LEU* 4.0 7.0 - - - -
163M GLU* 2.8 31.0 + - + +
166M PHE* 3.8 33.7 - - + -
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Residues in contact with LEU 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91M ASN* 2.9 10.7 + - - +
92M THR* 1.3 75.0 - - - +
94M GLU* 1.3 62.0 + - - +
96M MET* 3.3 1.4 + - - +
97M GLN* 2.9 52.9 + - - +
148M ILE* 3.9 29.8 - - + +
151M LEU* 3.9 23.8 - - + -
152M LYS* 4.3 16.2 - - + -
156M LEU* 3.4 18.6 - - + +
157M PRO* 3.7 35.4 - - + -
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Residues in contact with GLU 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M ARG* 3.0 39.3 + - - +
89M TRP 3.4 11.9 - - - +
90M GLY* 3.7 8.3 - - - -
91M ASN* 3.1 27.0 + - - +
92M THR 3.4 0.2 - - - -
93M LEU* 1.3 79.1 - - - +
95M ALA* 1.3 57.3 + - - +
97M GLN* 3.5 14.8 + - - +
98M ALA* 3.0 26.3 + - - +
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Residues in contact with ALA 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M MET* 3.8 10.1 - - - +
37M PHE* 3.7 26.7 - - + -
51M PHE* 4.1 10.8 - - + -
89M TRP* 3.7 16.3 + - + -
91M ASN 3.0 18.4 + - - +
92M THR 3.9 2.9 - - - +
94M GLU* 1.3 76.0 - - - +
96M MET* 1.3 60.5 + - - +
98M ALA* 3.4 7.7 + - - +
99M ALA* 2.9 27.4 + - - +
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Residues in contact with MET 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M VAL* 4.6 4.5 - - + -
50M PHE* 4.0 16.2 - - + -
51M PHE* 3.7 31.2 - - + -
92M THR* 3.0 26.6 + - + +
93M LEU 3.7 3.1 - - - +
95M ALA* 1.3 73.9 - - - +
97M GLN* 1.3 61.6 + - - +
99M ALA* 3.5 2.0 - - - +
100M LEU* 2.8 24.3 + - - +
144M ILE* 3.4 19.7 - - + +
147M PHE* 3.9 34.1 - - + -
148M ILE* 3.8 18.6 - - + -
151M LEU* 3.8 17.3 - - + -
166M PHE* 4.3 15.9 - - + -
171M VAL* 5.3 1.1 - - + -
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Residues in contact with GLN 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93M LEU* 2.9 43.9 + - + +
94M GLU* 3.8 14.1 - - - +
96M MET* 1.3 71.9 - - - +
98M ALA* 1.3 65.5 + - - +
100M LEU* 3.3 3.7 + - - +
101M GLN* 3.1 25.6 + - - +
148M ILE* 4.0 20.7 - - + +
152M LYS* 4.1 21.5 + - - -
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Residues in contact with ALA 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M MET* 4.0 4.7 - - + +
85M GLU* 5.4 4.3 - - - +
86M ARG* 5.6 2.5 - - - +
89M TRP* 3.8 32.3 - - + -
94M GLU 3.0 16.2 + - - +
95M ALA 3.5 8.5 - - - +
97M GLN* 1.3 76.1 - - - +
99M ALA* 1.3 58.5 - - - +
101M GLN* 3.4 7.1 + - - +
102M LEU* 3.0 27.0 + - - +
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Residues in contact with ALA 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M TYR* 3.9 26.9 - - + +
33M MET* 4.2 5.3 - - + +
51M PHE* 4.2 8.5 - - + -
95M ALA 2.9 17.3 + - - +
96M MET* 3.5 10.3 - - - +
98M ALA* 1.3 74.3 - - - +
100M LEU* 1.3 59.8 + - - +
102M LEU* 3.2 6.3 + - - +
103M GLU* 2.9 34.6 + - - +
144M ILE* 4.1 12.8 - - + -
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Residues in contact with LEU 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L GLN* 3.8 37.9 - - + +
4L VAL* 4.9 0.7 - - + -
96M MET 2.8 19.7 + - - +
97M GLN* 3.3 6.0 + - - +
99M ALA* 1.3 72.2 - - - +
101M GLN* 1.3 59.3 + - + +
103M GLU* 3.4 3.7 + - - +
104M LYS* 3.0 41.9 + - + +
141M ILE* 3.9 42.0 - - + +
144M ILE* 3.9 11.6 - - + +
145M GLY* 4.5 3.4 - - - +
148M ILE* 3.7 23.1 - - + -
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Residues in contact with GLN 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97M GLN 3.1 11.6 + - - +
98M ALA* 3.7 9.4 - - - +
100M LEU* 1.3 76.7 - - + +
102M LEU* 1.3 61.8 + - - +
104M LYS* 3.2 10.8 + - - +
105M THR* 2.9 33.7 + - - +
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Residues in contact with LEU 102 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M LEU* 5.4 1.6 - - + -
25M TYR* 4.1 27.6 - - + -
26M ALA* 3.9 24.2 - - + +
29M THR* 3.7 28.3 - - + -
30M TYR* 3.9 33.2 - - + +
98M ALA 3.0 17.8 + - - +
99M ALA* 3.2 6.0 + - - +
101M GLN* 1.3 76.1 - - - +
103M GLU* 1.3 60.2 + - + +
105M THR* 3.4 10.6 + - + -
106M VAL* 3.1 35.5 + - + +
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Residues in contact with GLU 103 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M ALA* 6.5 0.4 - - - -
30M TYR* 2.8 28.2 + - - +
54M HIS* 3.6 14.4 + - - -
58M GLU* 3.4 12.5 - - - +
99M ALA 2.9 14.3 + - - +
100M LEU* 3.8 5.4 - - - +
102M LEU* 1.3 76.7 - - - +
104M LYS* 1.3 59.4 + - - +
106M VAL* 3.3 5.2 + - - +
107M ASN* 2.8 25.6 + - - +
137M GLN* 3.0 29.1 + - - +
140M ASP* 4.4 7.4 - - + -
141M ILE* 3.9 15.0 - - + -
144M ILE* 3.9 14.6 - - + -
177M MG 2.9 28.0 - - - -
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Residues in contact with LYS 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2L SER 4.9 0.4 + - - -
3L GLN* 2.8 31.8 + - - +
4L VAL 4.4 9.9 - - - +
5L ARG 3.6 16.6 + - - -
6L GLN* 3.1 38.8 + - + +
100M LEU* 3.0 30.1 + - + +
101M GLN* 3.7 9.0 - - - +
103M GLU* 1.3 73.9 - - - +
105M THR* 1.3 56.8 + - - +
107M ASN* 4.1 0.4 - - - -
108M GLN* 2.9 25.6 + - - +
141M ILE* 4.2 11.7 - - + -
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Residues in contact with THR 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M LEU* 4.6 19.3 - - + -
25M TYR* 6.5 0.4 - - + -
101M GLN* 2.9 20.3 + - - +
102M LEU* 3.5 13.4 - - + +
104M LYS* 1.3 76.6 - - - +
106M VAL* 1.3 61.9 + - - +
108M GLN* 3.4 7.0 + - - +
109M ALA* 3.1 22.5 + - - +
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Residues in contact with VAL 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M MET* 5.1 1.6 - - - -
22M LEU* 3.9 30.5 - - + +
23M GLU* 4.0 9.6 - - - +
26M ALA* 4.2 24.2 - - + -
58M GLU* 4.9 0.7 - - - +
102M LEU* 3.1 19.5 + - + +
103M GLU* 3.7 10.1 - - - +
105M THR* 1.3 71.9 - - - +
107M ASN* 1.3 65.2 + - - +
109M ALA* 3.2 3.3 + - - +
110M LEU* 3.0 30.6 + - + +
137M GLN* 3.9 12.3 - - - +
176M MG 3.8 22.4 - - - -
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Residues in contact with ASN 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L GLN* 3.1 39.0 + - - +
103M GLU 2.8 21.3 + - - +
105M THR 3.3 0.2 - - - -
106M VAL* 1.3 73.0 - - - +
108M GLN* 1.3 57.7 + - - +
110M LEU* 3.1 9.9 + - - +
111M LEU* 2.9 42.1 + - - +
134M LEU* 4.8 8.8 - - - +
137M GLN* 3.6 22.4 - - - +
138M VAL* 5.0 10.3 - - - +
141M ILE* 3.9 17.5 - - + +
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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
----------------------------------------------------------
6L GLN* 3.5 21.0 + - - +
7L ASN* 5.8 2.1 - - - +
104M LYS 2.9 18.6 + - - +
105M THR* 3.6 6.7 - - - +
107M ASN* 1.3 79.2 - - - +
109M ALA* 1.3 57.4 + - - +
111M LEU* 3.4 16.0 + - - +
112M ASP* 2.9 62.7 + - - +
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Residues in contact with ALA 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M MET* 3.1 19.9 - - + +
22M LEU* 3.7 22.7 - - + -
105M THR 3.1 12.8 + - - +
106M VAL 3.2 9.6 + - - +
108M GLN* 1.3 78.6 - - - +
110M LEU* 1.3 57.2 + - - +
112M ASP* 3.4 10.1 + - - +
113M LEU* 2.9 22.7 + - - +
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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
----------------------------------------------------------
19M MET* 3.7 24.7 - - + -
23M GLU* 4.9 2.2 - - - +
65M PHE* 4.0 20.4 - - + -
106M VAL* 3.0 25.5 + - + +
107M ASN* 3.4 6.5 - - - +
109M ALA* 1.3 74.6 - - - +
111M LEU* 1.3 61.2 + - - +
113M LEU* 3.4 3.0 + - - +
114M HIS* 2.9 26.3 + - - +
129M LEU* 4.2 15.0 - - + +
133M TYR* 3.9 32.1 - - + -
134M LEU* 3.9 15.8 - - + +
137M GLN* 3.7 31.2 - - + +
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Residues in contact with LEU 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L GLN* 4.5 4.7 - - + -
7L ASN* 3.8 32.1 - - + +
123L PRO* 3.7 34.8 - - + +
124L HIS* 5.3 4.5 - - + +
107M ASN* 2.9 43.7 + - - +
108M GLN* 3.7 19.3 - - - +
110M LEU* 1.3 75.9 - - - +
112M ASP* 1.3 59.2 + - - +
114M HIS* 3.2 6.1 + - - +
115M LYS* 3.0 27.4 + - - +
134M LEU* 4.6 15.7 - - + -
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Residues in contact with ASP 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108M GLN* 2.9 48.5 + - - +
109M ALA* 3.4 10.1 - - - +
111M LEU* 1.3 76.1 - - - +
113M LEU* 1.3 60.9 + - - +
115M LYS* 3.3 8.0 + - - +
116M LEU* 3.0 26.7 + - - +
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Residues in contact with LEU 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M CYS* 4.3 8.5 - - - +
15M ALA* 3.5 31.0 - - + +
16M VAL* 4.3 17.5 - - + -
19M MET* 3.7 34.1 - - + -
65M PHE* 4.5 2.2 - - + -
109M ALA 2.9 16.8 + - - +
110M LEU* 3.7 5.6 - - + +
112M ASP* 1.3 76.5 - - - +
114M HIS* 1.3 59.3 + - - +
116M LEU* 3.4 10.6 + - + +
117M ALA* 3.0 26.0 + - - +
125M LEU* 4.4 10.1 - - + -
129M LEU* 3.9 25.8 - - + -
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Residues in contact with HIS 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121L VAL* 6.1 1.2 - - - +
123L PRO* 3.5 36.9 - - + +
110M LEU 2.9 14.1 + - - +
111M LEU* 3.3 12.1 - - - +
112M ASP 3.1 0.4 - - - -
113M LEU* 1.3 75.4 - - - +
115M LYS* 1.3 59.7 + - - +
117M ALA* 3.3 3.9 + - - +
118M THR* 2.9 43.0 + - - -
126M CYS* 3.6 31.3 + - - +
129M LEU* 3.8 19.0 - - + +
130M GLU* 2.9 25.6 + - - -
134M LEU* 4.2 7.9 - - + -
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Residues in contact with LYS 115 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121L VAL* 4.3 24.9 - - + -
111M LEU 3.0 12.8 + - - +
112M ASP* 3.3 11.4 + - - +
114M HIS* 1.3 74.8 + - - +
116M LEU* 1.3 60.0 + - - +
118M THR* 3.2 10.0 + - + +
119M ASP* 2.9 29.7 + - - +
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Residues in contact with LEU 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M ASP* 3.6 39.5 - - + +
12M CYS* 4.0 11.7 - - - -
15M ALA* 3.7 20.0 - - + -
18M ARG* 5.4 2.2 - - - +
112M ASP 3.0 15.0 + - - +
113M LEU* 3.6 10.1 - - + +
115M LYS* 1.3 76.6 - - - +
117M ALA* 1.3 57.6 + - - +
119M ASP* 3.3 5.5 + - + +
120M LYS* 2.9 49.5 + - + +
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Residues in contact with ALA 117 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M CYS* 4.3 10.5 - - - -
113M LEU 3.0 13.1 + - - +
114M HIS* 3.3 10.7 + - - +
116M LEU* 1.3 74.1 - - - +
118M THR* 1.3 64.2 + - - +
120M LYS 3.5 0.5 + - - -
121M VAL 3.1 3.8 + - - -
122M ASP* 2.9 34.8 + - + +
125M LEU* 3.9 28.0 - - + -
126M CYS* 3.6 17.7 - - - +
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Residues in contact with THR 118 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121L VAL* 6.4 2.5 - - + -
114M HIS* 2.9 31.3 + - - -
115M LYS* 3.5 10.5 - - + +
117M ALA* 1.3 76.6 - - - +
119M ASP* 1.3 62.5 + - - +
121M VAL* 3.1 17.5 + - - +
126M CYS* 3.5 15.1 - - - -
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Residues in contact with ASP 119 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115M LYS 2.9 16.1 + - - +
116M LEU* 3.6 8.3 - - + +
118M THR* 1.3 79.7 - - - +
120M LYS* 1.3 74.1 + - + +
121M VAL* 3.4 9.4 + - - +
----------------------------------------------------------
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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