Contacts of the helix formed by residues 92 - 119 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O PHE* 3.6 18.7 - - - -
44O LEU* 3.8 8.3 - - - +
47O VAL* 4.1 17.7 - - + +
91O ASN* 1.3 72.5 - - - +
93O LEU* 1.3 57.4 + - - +
95O ALA* 3.6 1.2 + - - +
96O MET* 3.0 38.1 + - + +
151O LEU* 4.1 8.3 - - + -
156O LEU* 4.0 6.7 - - - -
163O GLU* 2.8 30.3 + - - +
166O PHE* 3.8 34.8 - - + -
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Residues in contact with LEU 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91O ASN* 2.9 11.2 + - - +
92O THR* 1.3 75.9 - - - +
94O GLU* 1.3 62.0 + - - +
96O MET* 3.3 1.6 + - - +
97O GLN* 2.9 52.0 + - - +
148O ILE* 3.9 30.1 - - + +
151O LEU* 3.9 23.3 - - + -
152O LYS* 4.3 16.4 - - + -
156O LEU* 3.4 18.9 - - + +
157O PRO* 3.7 34.5 - - + -
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Residues in contact with GLU 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O ARG* 3.0 39.8 + - - +
89O TRP 3.4 12.1 - - - +
90O GLY* 3.7 7.7 - - - -
91O ASN* 3.1 26.9 + - - +
93O LEU* 1.3 80.6 - - - +
95O ALA* 1.3 57.1 + - - +
97O GLN* 3.5 15.1 + - + +
98O ALA* 3.0 27.2 + - - +
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Residues in contact with ALA 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O MET* 3.8 9.5 - - - +
37O PHE* 3.7 27.4 - - + -
51O PHE* 4.1 12.3 - - + -
89O TRP* 3.7 16.3 + - + -
91O ASN 3.0 17.7 + - - +
92O THR 3.9 2.0 - - - +
94O GLU* 1.3 74.6 - - - +
96O MET* 1.3 59.7 + - - +
98O ALA* 3.4 7.5 + - - +
99O ALA* 2.9 27.7 + - - +
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Residues in contact with MET 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O VAL* 4.6 4.3 - - + -
50O PHE* 4.0 16.2 - - + -
51O PHE* 3.7 30.7 - - + -
92O THR* 3.0 26.4 + - + +
93O LEU 3.3 4.2 + - - +
95O ALA* 1.3 74.5 - - - +
97O GLN* 1.3 61.5 + - - +
99O ALA* 3.3 2.8 + - - +
100O LEU* 2.8 24.1 + - - +
144O ILE* 3.4 21.1 - - + +
147O PHE* 3.9 33.0 - - + -
148O ILE* 3.7 18.3 - - + +
151O LEU* 3.8 16.8 - - + -
166O PHE* 4.3 17.3 - - + -
171O VAL* 5.3 1.6 - - + -
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Residues in contact with GLN 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93O LEU* 2.9 42.9 + - + +
94O GLU* 3.8 14.7 - - - +
96O MET* 1.3 72.5 - - - +
98O ALA* 1.3 66.0 + - - +
100O LEU* 3.3 4.5 + - + +
101O GLN* 3.1 25.1 + - - +
148O ILE* 4.0 20.9 - - + +
152O LYS* 4.1 21.7 + - - -
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Residues in contact with ALA 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O MET* 4.0 4.4 - - + +
85O GLU* 5.4 4.3 - - - +
86O ARG* 5.6 2.9 - - - +
89O TRP* 3.8 32.1 - - + -
94O GLU 3.0 14.7 + - - +
95O ALA 3.5 8.5 - - - +
96O MET 3.3 0.2 - - - -
97O GLN* 1.3 76.2 - - - +
99O ALA* 1.3 57.9 + - - +
101O GLN* 3.4 6.6 + - - +
102O LEU* 3.0 27.5 + - - +
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Residues in contact with ALA 99 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O TYR* 3.9 27.1 - - + +
33O MET* 4.2 4.5 - - + +
51O PHE* 4.2 8.5 - - + -
95O ALA 2.9 17.3 + - - +
96O MET* 3.5 9.4 - - - +
97O GLN 3.2 0.2 - - - -
98O ALA* 1.3 75.3 - - - +
100O LEU* 1.3 60.4 + - - +
102O LEU* 3.2 6.3 + - - +
103O GLU* 2.9 34.0 + - - +
144O ILE* 4.1 13.0 - - + -
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Residues in contact with LEU 100 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G GLN* 3.7 38.4 - - + +
4G VAL* 4.9 0.7 - - + -
96O MET 2.8 20.0 + - - +
97O GLN* 3.3 6.5 + - + +
99O ALA* 1.3 73.2 - - - +
101O GLN* 1.3 58.5 - - + +
103O GLU* 3.4 3.7 + - - +
104O LYS* 3.0 42.6 + - + +
141O ILE* 3.9 41.3 - - + +
144O ILE* 3.9 11.8 - - + +
145O GLY* 4.5 3.1 - - - +
148O ILE* 3.7 22.4 - - + -
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Residues in contact with GLN 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97O GLN 3.1 12.3 + - - +
98O ALA* 3.7 9.0 - - - +
99O ALA 3.3 0.2 - - - -
100O LEU* 1.3 76.9 - - + +
102O LEU* 1.3 60.3 + - - +
104O LYS* 3.2 10.9 + - - +
105O THR* 2.9 35.0 + - - +
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Residues in contact with LEU 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O LEU* 5.4 1.3 - - + -
25O TYR* 4.1 27.6 - - + -
26O ALA* 3.9 25.8 - - + +
29O THR* 3.7 27.1 - - + -
30O TYR* 3.9 33.7 - - + +
33O MET* 5.2 0.7 - - + -
98O ALA 3.0 17.8 + - - +
99O ALA* 3.2 5.1 + - - +
101O GLN* 1.3 76.3 - - - +
103O GLU* 1.3 58.7 + - + +
105O THR* 3.4 10.9 + - + -
106O VAL* 3.1 36.0 + - + +
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Residues in contact with GLU 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O ALA* 6.2 0.6 - - - +
30O TYR* 2.8 28.5 + - - +
54O HIS* 3.6 13.9 + - - -
58O GLU* 3.4 12.3 - - - +
99O ALA 2.9 14.3 + - - +
100O LEU* 3.8 5.2 - - - +
102O LEU* 1.3 75.8 - - - +
104O LYS* 1.3 59.7 + - - +
106O VAL* 3.3 5.8 + - - +
107O ASN* 2.8 26.2 + - - +
137O GLN* 3.0 28.8 + - - +
140O ASP* 4.4 7.2 - - + -
141O ILE* 3.9 14.6 - - + -
144O ILE* 3.9 14.8 - - + -
177O MG 2.9 29.0 - - - -
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Residues in contact with LYS 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G SER 5.0 0.8 + - - -
3G GLN* 2.9 31.3 + - - +
4G VAL 4.4 6.1 - - - +
5G ARG 3.5 16.8 + - - -
6G GLN* 3.1 43.4 + - + +
100O LEU* 3.0 28.2 + - + +
101O GLN* 3.2 9.6 + - - +
103O GLU* 1.3 74.2 - - - +
105O THR* 1.3 57.4 + - - +
107O ASN* 4.1 0.4 - - - -
108O GLN* 2.9 26.5 + - - +
141O ILE* 4.2 11.0 - - + -
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Residues in contact with THR 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O LEU* 4.6 19.3 - - + -
25O TYR* 6.5 0.4 - - + -
101O GLN* 2.9 20.4 + - - +
102O LEU* 3.5 12.9 - - + +
104O LYS* 1.3 77.7 - - - +
106O VAL* 1.3 63.1 + - - +
108O GLN* 3.4 6.2 + - - +
109O ALA* 3.1 22.0 + - - +
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Residues in contact with VAL 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O MET* 5.1 1.6 - - - -
22O LEU* 3.9 29.8 - - + +
23O GLU* 4.0 10.3 - - - +
26O ALA* 4.2 24.2 - - + -
58O GLU* 4.9 0.7 - - - +
102O LEU* 3.1 19.2 + - + +
103O GLU* 3.7 9.4 - - - +
105O THR* 1.3 72.6 - - - +
107O ASN* 1.3 66.3 + - - +
109O ALA* 3.2 3.8 + - - +
110O LEU* 3.0 30.7 + - + +
137O GLN* 3.9 12.3 - - - +
176O MG 3.8 22.0 - - - -
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Residues in contact with ASN 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G GLN* 3.1 40.8 + - - +
103O GLU 2.8 22.3 + - - +
104O LYS 3.6 0.2 - - - +
106O VAL* 1.3 72.2 - - - +
108O GLN* 1.3 59.9 + - - +
110O LEU* 3.1 9.9 + - - +
111O LEU* 2.9 42.4 + - - +
134O LEU* 4.8 8.3 - - - +
137O GLN* 3.6 23.1 - - - +
138O VAL* 5.0 9.7 - - - +
141O ILE* 3.9 16.2 - - + +
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Residues in contact with GLN 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN* 3.6 19.5 + - - +
7G ASN* 5.8 2.2 - - - +
104O LYS 2.9 17.7 + - - +
105O THR* 3.6 7.4 - - - +
106O VAL 3.2 0.2 - - - -
107O ASN* 1.3 78.6 - - - +
109O ALA* 1.3 57.1 + - - +
111O LEU* 3.4 17.2 + - - +
112O ASP* 2.9 63.5 + - - +
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Residues in contact with ALA 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19O MET* 3.1 20.7 - - + +
22O LEU* 3.7 22.4 - - + -
105O THR* 3.1 13.5 + - + +
106O VAL 3.4 8.3 - - - +
108O GLN* 1.3 77.9 - - - +
110O LEU* 1.3 57.5 + - - +
112O ASP* 3.4 10.0 + - - +
113O LEU* 2.9 22.9 + - - +
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Residues in contact with LEU 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19O MET* 3.7 24.5 - - + -
23O GLU* 4.9 1.8 - - - +
65O PHE* 4.0 20.4 - - + -
106O VAL* 3.0 24.0 + - + +
107O ASN* 3.4 7.0 - - - +
109O ALA* 1.3 76.0 - - - +
111O LEU* 1.3 60.2 + - - +
113O LEU* 3.4 2.8 + - - +
114O HIS* 2.9 27.0 + - - +
129O LEU* 4.2 14.7 - - + +
133O TYR* 3.9 33.0 - - + -
134O LEU* 3.9 15.0 - - + +
137O GLN* 3.7 31.4 - - + +
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Residues in contact with LEU 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN* 4.5 3.8 - - + -
7G ASN* 3.8 33.0 - - + +
123G PRO* 3.7 35.9 - - + +
124G HIS* 5.3 3.8 - - + +
107O ASN* 2.9 44.1 + - - +
108O GLN* 3.7 20.0 - - - +
110O LEU* 1.3 74.3 - - - +
112O ASP* 1.3 59.3 + - - +
114O HIS* 3.2 6.2 + - - +
115O LYS* 3.0 27.4 + - - +
134O LEU* 4.6 15.5 - - + -
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Residues in contact with ASP 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O GLN* 2.9 48.2 + - - +
109O ALA* 3.4 9.8 - - - +
111O LEU* 1.3 76.5 - - - +
113O LEU* 1.3 61.1 + - - +
115O LYS* 3.3 8.7 + - - +
116O LEU* 3.0 26.3 + - - +
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Residues in contact with LEU 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O CYS* 4.3 9.4 - - - +
15O ALA* 3.5 31.0 - - + +
16O VAL* 4.3 17.3 - - + -
19O MET* 3.7 35.0 - - + -
65O PHE* 4.5 1.8 - - + -
109O ALA 2.9 16.5 + - - +
110O LEU* 3.7 5.4 - - + +
112O ASP* 1.3 76.0 - - - +
114O HIS* 1.3 59.4 + - - +
116O LEU* 3.4 10.3 + - + +
117O ALA* 3.0 26.2 + - - +
125O LEU* 4.4 9.9 - - + -
129O LEU* 3.9 26.0 - - + -
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Residues in contact with HIS 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G VAL* 6.1 1.0 - - - +
123G PRO* 3.5 36.6 - - + +
110O LEU 2.9 14.7 + - - +
111O LEU* 3.3 13.0 - - - +
112O ASP 3.1 0.2 - - - -
113O LEU* 1.3 74.1 - - - +
115O LYS* 1.3 61.5 + - - +
117O ALA* 3.3 4.5 + - - +
118O THR* 2.9 43.8 + - - -
126O CYS* 3.6 30.9 + - - +
129O LEU* 3.8 17.4 - - + +
130O GLU* 2.9 25.6 + - - -
134O LEU* 4.2 7.0 - - + -
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Residues in contact with LYS 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G VAL* 4.3 24.5 - - + -
123G PRO* 5.9 0.2 - - - +
111O LEU 3.0 13.6 + - - +
112O ASP* 3.3 11.4 + - - +
114O HIS* 1.3 74.5 + - - +
116O LEU* 1.3 61.0 + - - +
118O THR* 3.2 9.2 + - + -
119O ASP* 2.9 30.4 + - + +
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Residues in contact with LEU 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O ASP* 3.6 39.7 - - + +
12O CYS* 4.0 12.1 - - - -
15O ALA* 3.7 20.4 - - + -
18O ARG* 5.4 2.0 - - - +
112O ASP 3.0 14.4 + - - +
113O LEU* 3.6 10.5 - - + +
114O HIS 3.3 0.2 - - - -
115O LYS* 1.3 76.8 - - - +
117O ALA* 1.3 56.9 + - - +
119O ASP* 3.3 5.1 + - + +
120O LYS* 2.9 50.2 + - + +
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Residues in contact with ALA 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O CYS* 4.3 10.9 - - - -
113O LEU 3.0 14.3 + - - +
114O HIS* 3.5 10.5 - - - +
116O LEU* 1.3 74.4 - - - +
118O THR* 1.3 63.1 + - - +
120O LYS 3.5 0.7 + - - -
121O VAL 3.1 3.6 + - - -
122O ASP* 2.9 35.1 + - + +
125O LEU* 3.9 27.8 - - + -
126O CYS* 3.6 17.7 - - - +
129O LEU* 5.1 0.2 - - + -
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Residues in contact with THR 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G VAL* 6.4 2.0 - - + -
114O HIS* 2.9 30.7 + - - -
115O LYS* 3.5 10.1 - - + +
117O ALA* 1.3 77.4 - - - +
119O ASP* 1.3 62.5 + - - +
121O VAL* 3.1 17.7 + - - +
126O CYS* 3.5 15.3 - - - -
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Residues in contact with ASP 119 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115O LYS 2.9 16.3 + - - +
116O LEU* 3.6 8.7 - - + +
118O THR* 1.3 78.5 - - - +
120O LYS* 1.3 72.8 + - + +
121O VAL* 3.2 10.2 + - - +
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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