Contacts of the helix formed by residues 92 - 119 (chain R) 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 R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R PHE* 3.6 19.3 - - - -
44R LEU* 3.8 8.1 - - - +
47R VAL* 4.1 17.4 - - + +
91R ASN* 1.3 72.1 - - - +
93R LEU* 1.3 58.6 + - - +
95R ALA* 3.6 1.2 + - - +
96R MET* 3.0 39.1 + - + +
151R LEU* 4.1 7.9 - - + -
156R LEU* 4.0 7.0 - - - -
163R GLU* 2.8 31.0 + - - +
166R PHE* 3.8 34.8 - - + -
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Residues in contact with LEU 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91R ASN* 2.9 11.2 + - - +
92R THR* 1.3 75.0 - - - +
94R GLU* 1.3 62.2 + - - +
96R MET* 3.3 1.6 + - - +
97R GLN* 2.9 51.9 + - + +
148R ILE* 3.9 30.5 - - + +
151R LEU* 3.9 23.6 - - + -
152R LYS* 4.3 16.2 - - + -
156R LEU* 3.4 19.5 - - + +
157R PRO* 3.7 34.8 - - + -
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Residues in contact with GLU 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R ARG* 3.0 40.1 + - - +
89R TRP 3.4 11.7 - - - +
90R GLY* 3.7 8.6 - - - -
91R ASN* 3.1 26.9 + - - +
93R LEU* 1.3 80.6 - - - +
95R ALA* 1.3 57.4 + - - +
97R GLN* 3.5 15.4 + - - +
98R ALA* 3.0 26.5 + - - +
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Residues in contact with ALA 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R MET* 3.8 9.7 - - - +
37R PHE* 3.7 26.9 - - + -
51R PHE* 4.1 11.2 - - + -
89R TRP* 3.7 16.5 + - + -
91R ASN 3.0 18.4 + - - +
92R THR 3.9 2.2 - - - +
94R GLU* 1.3 75.6 - - - +
96R MET* 1.3 59.6 + - - +
98R ALA* 3.4 8.1 + - - +
99R ALA* 2.9 27.4 + - - +
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Residues in contact with MET 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R VAL* 4.6 3.6 - - + -
50R PHE* 4.0 16.8 - - + -
51R PHE* 3.7 30.5 - - + -
92R THR* 3.0 26.2 + - + +
93R LEU 3.7 3.4 - - - +
95R ALA* 1.3 74.0 - - - +
97R GLN* 1.3 62.2 + - - +
99R ALA* 3.3 2.6 + - - +
100R LEU* 2.8 23.7 + - - +
144R ILE* 3.4 20.3 - - + +
147R PHE* 3.9 31.2 - - + -
148R ILE* 3.8 17.9 - - + -
151R LEU* 3.8 17.5 - - + -
166R PHE* 4.3 16.2 - - + -
171R VAL* 5.3 1.3 - - + -
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Residues in contact with GLN 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R LEU* 2.9 43.2 + - + +
94R GLU* 3.8 14.3 - - - +
96R MET* 1.3 71.9 - - - +
98R ALA* 1.3 65.5 + - - +
100R LEU* 3.3 3.4 + - + +
101R GLN* 3.1 25.6 + - - +
148R ILE* 4.0 20.9 - - + +
152R LYS* 4.1 21.3 + - - -
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Residues in contact with ALA 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R MET* 4.0 5.1 - - + +
85R GLU* 5.4 4.0 - - - +
86R ARG* 5.6 2.2 - - - +
89R TRP* 3.8 32.3 - - + -
94R GLU 3.0 14.9 + - - +
95R ALA 3.5 8.5 - - - +
96R MET 3.3 0.2 - - - -
97R GLN* 1.3 76.0 - - - +
99R ALA* 1.3 57.6 + - - +
101R GLN* 3.4 6.8 + - - +
102R LEU* 3.0 27.8 + - - +
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Residues in contact with ALA 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30R TYR* 3.9 27.1 + - + +
33R MET* 4.2 5.1 - - + +
51R PHE* 4.2 8.5 - - + -
95R ALA 2.9 17.1 + - - +
96R MET* 3.5 9.4 - - - +
98R ALA* 1.3 74.9 - - - +
100R LEU* 1.3 60.4 + - - +
102R LEU* 3.2 5.4 + - - +
103R GLU* 2.9 34.7 + - - +
144R ILE* 4.1 12.1 - - + -
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Residues in contact with LEU 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLN* 3.8 38.6 - - + +
4C VAL* 5.0 0.7 - - + -
96R MET 2.8 20.1 + - - +
97R GLN* 3.3 6.5 + - - +
99R ALA* 1.3 72.6 - - - +
101R GLN* 1.3 58.8 + - + +
103R GLU* 3.4 3.7 + - + +
104R LYS* 3.0 42.2 + - + +
141R ILE* 3.9 41.1 - - + +
144R ILE* 3.9 11.8 - - + +
145R GLY* 4.5 3.6 - - - +
148R ILE* 3.7 22.7 - - + -
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Residues in contact with GLN 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R GLN 3.1 12.7 + - - +
98R ALA* 3.7 8.7 - - - +
99R ALA 3.3 0.2 - - - -
100R LEU* 1.3 76.0 - - + +
102R LEU* 1.3 59.6 + - - +
104R LYS* 3.2 10.3 + - - +
105R THR* 2.9 34.4 + - - +
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Residues in contact with LEU 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22R LEU* 5.4 1.8 - - + -
25R TYR* 4.1 27.1 - - + -
26R ALA* 3.9 26.0 - - + +
29R THR* 3.7 28.5 - - + -
30R TYR* 3.9 33.7 - - + +
98R ALA 3.0 17.8 + - - +
99R ALA* 3.2 5.1 + - - +
101R GLN* 1.3 76.1 - - - +
103R GLU* 1.3 60.1 + - + +
105R THR* 3.4 9.9 + - + -
106R VAL* 3.1 35.9 + - + +
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Residues in contact with GLU 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26R ALA* 6.5 0.4 - - - -
30R TYR* 2.8 28.6 + - - +
54R HIS* 3.6 14.2 + - - -
58R GLU* 3.4 12.1 - - - +
99R ALA 2.9 14.5 + - - +
100R LEU* 3.8 5.2 - - - +
102R LEU* 1.3 76.1 - - - +
104R LYS* 1.3 60.4 + - - +
106R VAL* 3.3 5.4 + - - +
107R ASN* 2.8 26.0 + - - +
137R GLN* 3.0 29.0 + - - +
140R ASP* 4.4 6.5 - - + -
141R ILE* 3.9 14.8 - - + -
144R ILE* 3.9 14.1 - - + -
177R MG 2.9 27.7 - - - -
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Residues in contact with LYS 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER 5.0 0.6 + - - -
3C GLN* 3.0 29.8 + - - +
4C VAL 4.5 5.4 - - - +
5C ARG 3.5 16.6 + - - -
6C GLN* 3.1 43.7 + - + +
100R LEU* 3.0 28.4 + - + +
101R GLN* 3.7 9.4 - - - +
103R GLU* 1.3 76.6 - - - +
105R THR* 1.3 57.8 + - - +
107R ASN* 4.1 0.2 - - - -
108R GLN* 2.9 26.2 + - - +
141R ILE* 4.2 11.7 - - + -
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Residues in contact with THR 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22R LEU* 4.6 19.1 - - + -
25R TYR* 6.5 0.9 - - + -
101R GLN* 2.9 21.3 + - - +
102R LEU* 3.5 12.3 - - + +
103R GLU 3.2 0.2 - - - -
104R LYS* 1.3 76.4 - - - +
106R VAL* 1.3 63.6 + - + +
108R GLN* 3.4 6.4 + - - +
109R ALA* 3.1 21.8 + - - +
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Residues in contact with VAL 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R MET* 5.1 1.6 - - - -
22R LEU* 3.9 29.8 - - + +
23R GLU* 4.0 9.9 - - - +
26R ALA* 4.2 24.9 - - + -
58R GLU* 4.9 0.7 - - - +
102R LEU* 3.1 19.9 + - + +
103R GLU* 3.7 9.2 - - - +
105R THR* 1.3 71.3 - - - +
107R ASN* 1.3 66.0 + - - +
109R ALA* 3.2 3.1 + - - +
110R LEU* 3.0 31.6 + - + +
137R GLN* 3.9 11.9 - - - +
176R MG 3.8 21.8 - - - -
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Residues in contact with ASN 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLN* 3.1 40.7 + - - +
103R GLU 2.8 21.9 + - - +
104R LYS 3.6 0.2 - - - +
105R THR 3.3 0.2 - - - -
106R VAL* 1.3 71.5 - - - +
108R GLN* 1.3 57.3 + - - +
110R LEU* 3.1 10.1 + - - +
111R LEU* 2.9 41.7 + - - +
134R LEU* 4.8 9.2 - - - +
137R GLN* 3.6 23.6 - - - +
138R VAL* 5.0 9.2 - - - +
141R ILE* 3.9 16.6 - - + +
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Residues in contact with GLN 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLN* 3.6 20.9 + - - +
7C ASN* 5.9 1.8 - - - +
104R LYS 2.9 19.0 + - - +
105R THR* 3.6 6.5 - - - +
107R ASN* 1.3 78.5 - - - +
109R ALA* 1.3 58.0 + - - +
111R LEU* 3.4 16.1 + - - +
112R ASP* 2.9 63.3 + - - +
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Residues in contact with ALA 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R MET* 3.1 20.6 - - + +
22R LEU* 3.7 22.4 - - + -
105R THR 3.1 13.2 + - - +
106R VAL 3.2 8.7 + - - +
108R GLN* 1.3 77.7 - - - +
110R LEU* 1.3 58.6 + - - +
112R ASP* 3.4 9.9 + - - +
113R LEU* 2.9 22.0 + - - +
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Residues in contact with LEU 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19R MET* 3.7 23.8 - - + -
23R GLU* 4.9 1.8 - - - +
65R PHE* 4.0 21.5 - - + -
106R VAL* 3.0 24.9 + - + +
107R ASN* 3.4 7.2 - - - +
109R ALA* 1.3 75.4 - - - +
111R LEU* 1.3 59.4 + - - +
113R LEU* 3.4 2.9 + - + +
114R HIS* 2.9 26.7 + - - +
129R LEU* 4.2 14.4 - - + +
133R TYR* 3.9 32.1 - - + -
134R LEU* 3.9 15.4 - - + +
137R GLN* 3.7 30.7 - - + +
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Residues in contact with LEU 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLN* 4.6 4.3 - - + +
7C ASN* 3.8 33.0 - - + +
123C PRO* 3.7 34.3 - - + +
124C HIS* 5.4 4.3 - - + +
107R ASN* 2.9 41.9 + - - +
108R GLN* 3.7 20.6 - - - +
110R LEU* 1.3 74.8 - - - +
112R ASP* 1.3 60.0 + - - +
114R HIS* 3.2 6.7 + - - +
115R LYS* 3.0 26.7 + - - +
134R LEU* 4.6 16.4 - - + -
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Residues in contact with ASP 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108R GLN* 2.9 48.5 + - - +
109R ALA* 3.4 9.7 - - - +
111R LEU* 1.3 75.3 - - - +
113R LEU* 1.3 60.7 + - - +
115R LYS* 3.3 8.8 + - - +
116R LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R CYS* 4.3 9.6 - - - +
15R ALA* 3.5 31.4 - - + +
16R VAL* 4.3 17.3 - - + -
19R MET* 3.7 34.8 - - + -
65R PHE* 4.5 2.5 - - + -
109R ALA 2.9 17.0 + - - +
110R LEU* 3.7 5.4 - - + +
111R LEU 3.3 0.2 - - - -
112R ASP* 1.3 75.2 - - - +
114R HIS* 1.3 59.3 + - - +
116R LEU* 3.4 9.5 + - + +
117R ALA* 3.0 26.3 + - - +
125R LEU* 4.4 9.9 - - + -
129R LEU* 3.9 25.6 - - + -
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Residues in contact with HIS 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C VAL* 6.1 1.4 - - - +
123C PRO* 3.6 37.1 - - + +
110R LEU 2.9 13.7 + - - +
111R LEU* 3.3 12.6 - - - +
112R ASP 3.1 0.2 - - - -
113R LEU* 1.3 76.0 - - - +
115R LYS* 1.3 61.2 + - - +
117R ALA* 3.3 4.1 + - - +
118R THR* 2.9 43.1 + - - -
126R CYS* 3.6 30.6 + - + +
129R LEU* 3.8 18.1 - - + +
130R GLU* 2.9 25.8 + - - -
134R LEU* 4.2 7.4 - - + -
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Residues in contact with LYS 115 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C VAL* 4.3 24.2 - - + -
111R LEU 3.0 12.8 + - - +
112R ASP* 3.3 11.9 + - - +
114R HIS* 1.3 74.6 + - - +
116R LEU* 1.3 59.6 + - - +
118R THR* 3.2 9.2 + - + +
119R ASP* 2.9 29.8 + - - +
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Residues in contact with LEU 116 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R ASP* 3.6 39.0 - - + +
12R CYS* 4.0 12.1 - - - -
15R ALA* 3.7 20.0 - - + -
18R ARG* 5.4 2.2 - - - +
112R ASP 3.0 13.8 + - - +
113R LEU* 3.6 10.5 - - + +
114R HIS 3.3 0.2 - - - -
115R LYS* 1.3 77.2 - - - +
117R ALA* 1.3 56.3 + - - +
119R ASP* 3.3 5.6 + - + +
120R LYS* 2.9 50.5 + - + +
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Residues in contact with ALA 117 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R CYS* 4.3 10.7 - - - -
113R LEU 3.0 14.3 + - - +
114R HIS* 3.5 10.3 - - - +
116R LEU* 1.3 73.8 - - - +
118R THR* 1.3 62.9 + - - +
120R LYS 3.5 0.5 + - - -
121R VAL 3.1 3.5 + - - -
122R ASP* 2.9 34.3 + - + +
125R LEU* 3.9 28.5 - - + -
126R CYS* 3.6 17.9 - - - +
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Residues in contact with THR 118 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C VAL* 6.4 1.8 - - + -
114R HIS* 2.9 30.9 + - - -
115R LYS* 3.2 10.7 + - + +
117R ALA* 1.3 77.8 - - - +
119R ASP* 1.3 61.4 + - - +
121R VAL* 3.1 18.2 + - - +
126R CYS* 3.5 14.8 - - - -
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Residues in contact with ASP 119 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115R LYS* 2.9 16.7 + - + +
116R LEU* 3.6 9.4 - - + +
118R THR* 1.3 79.4 - - - +
120R LYS* 1.3 72.6 + - + +
121R VAL* 3.2 9.6 + - - +
----------------------------------------------------------
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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