Contacts of the helix formed by residues 92 - 119 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F PHE* 3.6 19.1 - - - -
44F LEU* 3.8 8.3 - - - +
47F VAL* 4.1 17.9 - - + +
91F ASN* 1.3 73.2 - - - +
93F LEU* 1.3 57.2 + - - +
95F ALA* 3.6 1.2 + - - +
96F MET* 3.0 38.4 + - + +
151F LEU* 4.1 7.6 - - + -
156F LEU* 4.0 6.7 - - - -
163F GLU* 2.8 30.5 + - - +
166F PHE* 3.8 35.0 - - + -
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Residues in contact with LEU 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ASN* 2.9 10.3 + - - +
92F THR* 1.3 75.6 - - - +
94F GLU* 1.3 62.4 + - - +
96F MET* 3.3 1.4 + - - +
97F GLN* 2.9 52.6 + - - +
148F ILE* 3.9 30.3 - - + +
151F LEU* 3.9 24.0 - - + -
152F LYS* 4.3 15.7 - - + -
156F LEU* 3.4 18.9 - - + +
157F PRO* 3.7 35.2 - - + -
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Residues in contact with GLU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F ARG* 3.0 39.5 + - - +
89F TRP 3.4 11.7 - - - +
90F GLY* 3.7 8.1 - - - -
91F ASN* 3.1 27.9 + - - +
93F LEU* 1.3 80.0 - - - +
95F ALA* 1.3 57.3 + - - +
97F GLN* 3.5 14.7 + - - +
98F ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F MET* 3.8 9.7 - - - +
37F PHE* 3.7 27.4 - - + -
51F PHE* 4.1 11.7 - - + -
89F TRP* 3.7 16.1 + - + -
91F ASN 3.0 17.3 + - - +
92F THR 3.9 2.5 - - - +
94F GLU* 1.3 76.5 - - - +
96F MET* 1.3 60.7 + - - +
98F ALA* 3.4 7.3 + - - +
99F ALA* 2.9 27.5 + - - +
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Residues in contact with MET 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F VAL* 4.6 3.8 - - + -
50F PHE* 4.0 16.8 - - + -
51F PHE* 3.7 30.3 - - + -
92F THR* 3.0 26.1 + - + +
93F LEU 3.3 4.0 + - - +
95F ALA* 1.3 74.2 - - - +
97F GLN* 1.3 61.3 + - - +
99F ALA* 3.3 2.8 + - - +
100F LEU* 2.8 24.6 + - - +
144F ILE* 3.4 19.9 - - + +
147F PHE* 3.9 31.4 - - + -
148F ILE* 3.8 18.2 - - + -
151F LEU* 3.8 16.6 - - + -
166F PHE* 4.3 16.8 - - + -
171F VAL* 5.3 1.3 - - + -
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Residues in contact with GLN 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F LEU* 2.9 42.6 + - + +
94F GLU* 3.8 14.5 - - - +
95F ALA 3.3 0.2 - - - -
96F MET* 1.3 72.3 - - - +
98F ALA* 1.3 65.3 + - - +
100F LEU* 3.3 3.8 + - + +
101F GLN* 3.1 25.3 + - - +
148F ILE* 4.0 21.1 - - + +
152F LYS* 4.1 21.1 + - - -
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Residues in contact with ALA 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F MET* 4.0 4.8 - - + +
85F GLU* 5.4 4.3 - - - +
86F ARG* 5.6 2.7 - - - +
89F TRP* 3.8 32.1 - - + -
94F GLU 3.0 15.3 + - - +
95F ALA 3.5 8.3 - - - +
97F GLN* 1.3 75.3 - - - +
99F ALA* 1.3 58.3 + - - +
101F GLN* 3.4 7.0 + - - +
102F LEU* 3.0 28.1 + - - +
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Residues in contact with ALA 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR* 3.9 27.1 + - + +
33F MET* 4.2 5.4 - - + +
51F PHE* 4.2 8.3 - - + -
95F ALA 2.9 17.5 + - - +
96F MET* 3.5 10.3 - - - +
98F ALA* 1.3 75.3 - - - +
100F LEU* 1.3 60.6 + - - +
102F LEU* 3.2 6.2 + - - +
103F GLU* 2.9 34.6 + - - +
144F ILE* 4.1 12.3 - - + -
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Residues in contact with LEU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F MET 2.8 20.2 + - - +
97F GLN* 3.3 6.0 + - + +
99F ALA* 1.3 72.2 - - - +
101F GLN* 1.3 58.1 + - + +
103F GLU* 3.4 3.5 + - - +
104F LYS* 3.0 41.2 + - + +
141F ILE* 3.9 42.4 - - + +
144F ILE* 3.9 11.6 - - + +
145F GLY* 4.5 2.9 - - - +
148F ILE* 3.7 21.8 - - + -
3O GLN* 3.8 38.1 - - + +
4O VAL* 4.9 0.9 - - + -
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Residues in contact with GLN 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F GLN 3.1 13.3 + - - +
98F ALA* 3.7 8.5 - - - +
99F ALA 3.3 0.2 - - - -
100F LEU* 1.3 76.5 - - + +
102F LEU* 1.3 60.2 + - - +
104F LYS* 3.2 11.4 + - - +
105F THR* 2.9 33.8 + - - +
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Residues in contact with LEU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F LEU* 5.4 2.2 - - + -
25F TYR* 4.1 27.4 - - + -
26F ALA* 3.9 25.1 - - + +
29F THR* 3.7 28.5 - - + -
30F TYR* 3.9 33.4 - - + +
98F ALA 3.0 17.4 + - - +
99F ALA* 3.2 5.8 + - - +
101F GLN* 1.3 76.3 - - - +
103F GLU* 1.3 58.8 + - + +
105F THR* 3.4 11.0 + - + -
106F VAL* 3.1 36.3 + - + +
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Residues in contact with GLU 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F ALA* 6.5 0.4 - - - -
30F TYR* 2.8 28.9 + - - +
54F HIS* 3.6 14.0 + - - -
58F GLU* 3.4 12.3 - - - +
99F ALA 2.9 14.7 + - - +
100F LEU* 3.8 4.9 - - - +
102F LEU* 1.3 76.3 - - - +
104F LYS* 1.3 59.0 + - - +
106F VAL* 3.3 6.3 + - - +
107F ASN* 2.8 26.2 + - - +
137F GLN* 3.0 28.6 + - - +
140F ASP* 4.4 8.1 - - + -
141F ILE* 3.9 14.6 - - + -
144F ILE* 3.9 14.3 - - + +
177F MG 2.9 27.3 - - - -
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Residues in contact with LYS 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F LEU* 3.0 28.0 + - + +
101F GLN* 3.7 9.9 - - - +
103F GLU* 1.3 76.3 - - - +
105F THR* 1.3 57.7 + - - +
107F ASN* 4.1 0.4 - - - -
108F GLN* 2.9 26.0 + - - +
141F ILE* 4.2 12.3 - - + -
2O SER 4.9 0.8 + - - -
3O GLN* 2.8 30.8 + - - +
4O VAL 4.4 9.0 - - - +
5O ARG 3.5 16.8 + - - -
6O GLN* 3.1 39.3 + - + +
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Residues in contact with THR 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F LEU* 4.6 19.3 - - + -
25F TYR* 6.5 0.9 - - + -
101F GLN* 2.9 20.9 + - - +
102F LEU* 3.5 12.1 - - + +
103F GLU 3.2 0.2 - - - -
104F LYS* 1.3 76.4 - - - +
106F VAL* 1.3 62.7 + - - +
108F GLN* 3.4 7.1 + - - +
109F ALA* 3.1 22.2 + - - +
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Residues in contact with VAL 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F MET* 5.1 1.8 - - - -
22F LEU* 3.9 30.1 - - + +
23F GLU* 4.0 10.5 - - - +
26F ALA* 4.2 24.2 - - + -
58F GLU* 4.9 0.7 - - - +
102F LEU* 3.1 20.8 + - + +
103F GLU* 3.7 9.4 - - - +
105F THR* 1.3 71.8 - - - +
107F ASN* 1.3 65.9 + - - +
109F ALA* 3.2 3.3 + - - +
110F LEU* 3.0 31.4 + - + +
137F GLN* 3.9 11.9 - - - +
176F MG 3.8 21.8 - - - -
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Residues in contact with ASN 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F GLU 2.8 22.3 + - - +
104F LYS 3.6 0.2 - - - +
106F VAL* 1.3 72.4 - - - +
108F GLN* 1.3 57.7 + - - +
110F LEU* 3.1 9.6 + - - +
111F LEU* 2.9 42.8 + - - +
134F LEU* 4.8 9.2 - - - +
137F GLN* 3.6 22.8 - - - +
138F VAL* 5.0 9.5 - - - +
141F ILE* 3.9 16.0 - - + +
6O GLN* 3.1 40.1 + - - +
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Residues in contact with GLN 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F LYS 2.9 18.1 + - - +
105F THR* 3.6 6.7 - - - +
107F ASN* 1.3 78.7 - - - +
109F ALA* 1.3 56.8 + - - +
111F LEU* 3.4 15.8 + - - +
112F ASP* 2.9 63.7 + - - +
6O GLN* 3.5 20.2 + - - +
7O ASN* 5.8 2.6 - - - +
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Residues in contact with ALA 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F MET* 3.1 21.0 - - + +
22F LEU* 3.7 22.0 - - + -
105F THR 3.1 13.3 + - - +
106F VAL 3.2 8.7 + - - +
108F GLN* 1.3 77.5 - - - +
110F LEU* 1.3 58.4 + - - +
112F ASP* 3.4 10.1 + - - +
113F LEU* 2.9 22.5 + - - +
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Residues in contact with LEU 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F MET* 3.7 23.8 - - + -
23F GLU* 4.9 1.6 - - - +
65F PHE* 4.0 22.0 - - + -
106F VAL* 3.0 24.9 + - + +
107F ASN* 3.1 7.2 + - - +
109F ALA* 1.3 75.6 - - - +
111F LEU* 1.3 59.9 + - - +
113F LEU* 3.4 3.0 + - - +
114F HIS* 2.9 26.9 + - - +
129F LEU* 4.2 15.1 - - + +
133F TYR* 3.9 32.1 - - + -
134F LEU* 3.9 16.6 - - + +
137F GLN* 3.7 30.7 - - + +
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Residues in contact with LEU 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F ASN* 2.9 43.2 + - - +
108F GLN* 3.7 20.4 - - - +
110F LEU* 1.3 75.5 - - - +
112F ASP* 1.3 59.2 + - - +
114F HIS* 3.2 6.7 + - - +
115F LYS* 3.0 27.2 + - - +
134F LEU* 4.6 16.4 - - + -
6O GLN* 4.5 3.6 - - + -
7O ASN* 3.8 33.0 - - + +
123O PRO* 3.7 33.9 - - + +
124O HIS* 5.3 4.3 - - + +
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Residues in contact with ASP 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F GLN* 2.9 48.4 + - - +
109F ALA* 3.4 10.3 - - - +
111F LEU* 1.3 75.9 - - - +
113F LEU* 1.3 61.0 - - - +
115F LYS* 3.3 8.2 + - - +
116F LEU* 3.0 26.9 + - - +
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Residues in contact with LEU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F CYS 4.3 8.1 - - - +
15F ALA* 3.5 31.0 - - + +
16F VAL* 4.3 17.5 - - + -
19F MET* 3.7 35.0 - - + -
65F PHE* 4.5 2.2 - - + -
109F ALA 2.9 16.5 + - - +
110F LEU 3.7 4.7 - - - +
111F LEU 3.3 0.2 - - - -
112F ASP* 1.3 76.3 - - - +
114F HIS* 1.3 58.5 + - - +
116F LEU* 3.4 9.3 + - + +
117F ALA* 3.0 27.1 + - - +
125F LEU* 4.4 10.8 - - + -
129F LEU* 3.9 26.2 - - + +
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Residues in contact with HIS 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F LEU 2.9 14.3 + - - +
111F LEU* 3.3 13.0 - - - +
112F ASP 3.1 0.2 - - - -
113F LEU* 1.3 74.7 - - - +
115F LYS* 1.3 61.7 + - - +
117F ALA* 3.3 4.0 + - - +
118F THR* 2.9 43.2 + - - -
126F CYS* 3.6 30.4 + - + +
129F LEU* 3.8 18.3 - - + +
130F GLU* 2.9 25.4 + - - -
134F LEU* 4.2 7.2 - - + -
121O VAL* 6.1 1.2 - - - +
123O PRO* 3.5 36.6 - - + +
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Residues in contact with LYS 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F LEU 3.0 13.4 + - - +
112F ASP* 3.3 11.9 + - - +
114F HIS* 1.3 74.1 + - - +
116F LEU* 1.3 60.6 + - - +
118F THR* 3.2 9.5 + - + +
119F ASP* 2.9 29.3 + - - +
121O VAL* 4.3 25.1 - - + -
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Residues in contact with LEU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ASP* 3.6 39.9 - - + +
12F CYS* 4.0 11.4 - - - -
15F ALA* 3.7 19.7 - - + -
18F ARG* 5.4 2.0 - - - +
112F ASP 3.0 13.8 + - - +
113F LEU* 3.6 10.8 - - + +
114F HIS 3.3 0.2 - - - -
115F LYS* 1.3 76.7 - - - +
117F ALA* 1.3 56.3 + - - +
119F ASP* 3.3 5.4 + - + +
120F LYS* 2.9 50.7 + - + +
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Residues in contact with ALA 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F CYS* 4.3 10.5 - - - -
113F LEU 3.0 14.1 + - - +
114F HIS* 3.3 10.5 + - - +
116F LEU* 1.3 73.1 - - - +
118F THR* 1.3 64.2 + - - +
120F LYS 3.5 0.5 + - - -
121F VAL 3.1 4.0 + - - -
122F ASP* 2.9 34.4 + - + +
125F LEU* 3.9 28.3 - - + -
126F CYS* 3.6 17.0 - - - +
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Residues in contact with THR 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F HIS* 2.9 30.6 + - - -
115F LYS* 3.5 9.9 - - + +
117F ALA* 1.3 77.3 - - - +
119F ASP* 1.3 63.0 + - - +
121F VAL* 3.1 17.8 + - - +
126F CYS* 3.5 15.0 - - - -
121O VAL* 6.4 2.2 - - + -
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Residues in contact with ASP 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F LYS* 2.9 16.4 + - + +
116F LEU* 3.6 9.4 - - + +
118F THR* 1.3 77.6 - - - +
120F LYS* 1.3 72.4 + - + +
121F 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