Contacts of the helix formed by residues 92 - 119 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE* 3.6 20.5 - - - -
44E LEU* 3.8 8.1 - - - +
47E VAL* 4.1 17.2 - - + +
91E ASN* 1.3 71.9 - - - +
93E LEU* 1.3 57.0 + - - +
95E ALA* 3.9 0.9 - - - +
96E MET* 3.0 39.0 + - + +
151E LEU* 4.1 7.4 - - + -
156E LEU* 4.0 6.7 - - - -
163E GLU* 2.8 31.2 + - + +
166E PHE* 3.8 34.5 - - + -
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Residues in contact with LEU 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E ASN* 2.9 10.5 + - - +
92E THR* 1.3 75.6 - - - +
94E GLU* 1.3 61.8 + - - +
96E MET* 3.3 1.8 + - - +
97E GLN* 2.9 53.3 + - - +
148E ILE* 3.9 29.2 - - + +
151E LEU* 3.9 23.6 - - + -
152E LYS* 4.3 16.8 - - + -
156E LEU* 3.4 18.9 - - + +
157E PRO* 3.7 35.0 - - + -
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Residues in contact with GLU 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E ARG* 3.0 39.9 + - - +
89E TRP 3.4 11.4 - - - +
90E GLY* 3.7 7.6 - - - -
91E ASN* 3.1 27.0 + - - +
93E LEU* 1.3 79.4 - - - +
95E ALA* 1.3 58.2 + - - +
97E GLN* 3.5 13.9 + - - +
98E ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E MET* 3.8 9.9 - - - +
37E PHE* 3.7 27.6 - - + -
51E PHE* 4.1 11.7 - - + -
89E TRP* 3.7 17.2 + - + -
91E ASN 3.0 17.5 + - - +
92E THR 3.9 2.0 - - - +
94E GLU* 1.3 75.7 - - - +
96E MET* 1.3 60.2 + - - +
98E ALA* 3.4 7.4 + - - +
99E ALA* 2.9 27.7 + - - +
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Residues in contact with MET 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E VAL* 4.6 3.8 - - + -
50E PHE* 4.0 16.8 - - + -
51E PHE* 3.7 31.2 - - + -
92E THR* 3.0 26.8 + - + +
93E LEU 3.7 4.0 - - - +
95E ALA* 1.3 73.8 - - - +
97E GLN* 1.3 62.1 + - - +
99E ALA* 3.3 2.5 + - - +
100E LEU* 2.8 23.6 + - - +
144E ILE* 3.4 20.7 - - + +
147E PHE* 3.9 33.9 - - + -
148E ILE* 3.7 17.9 - - + +
151E LEU* 3.8 17.7 - - + -
166E PHE* 4.3 16.6 - - + -
171E VAL* 5.3 0.9 - - + -
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Residues in contact with GLN 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E LEU* 2.9 41.8 + - + +
94E GLU* 3.8 14.5 - - - +
96E MET* 1.3 73.9 - - - +
98E ALA* 1.3 66.6 - - - +
100E LEU* 3.3 3.7 + - - +
101E GLN* 3.1 25.5 + - - +
148E ILE* 4.0 20.9 - - + +
152E LYS* 4.1 21.5 + - - -
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Residues in contact with ALA 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E MET* 4.0 4.6 - - + +
85E GLU* 5.4 3.4 - - - +
86E ARG* 5.6 2.5 - - - +
89E TRP* 3.8 33.0 - - + -
94E GLU 3.0 15.7 + - - +
95E ALA 3.5 8.1 - - - +
97E GLN* 1.3 76.1 - - - +
99E ALA* 1.3 57.8 + - - +
101E GLN* 3.4 7.2 + - - +
102E LEU* 3.0 27.4 + - - +
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Residues in contact with ALA 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E TYR* 3.9 27.1 - - + +
33E MET* 4.2 5.6 - - + +
51E PHE* 4.2 8.5 - - + -
95E ALA 2.9 17.7 + - - +
96E MET* 3.5 9.4 - - - +
98E ALA* 1.3 74.2 - - - +
100E LEU* 1.3 59.0 + - - +
102E LEU* 3.2 6.0 + - - +
103E GLU* 2.9 35.5 + - - +
144E ILE* 4.1 12.6 - - + -
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E MET 2.8 19.6 + - - +
97E GLN* 3.3 6.3 + - + +
99E ALA* 1.3 72.4 - - - +
101E GLN* 1.3 60.3 + - + +
103E GLU* 3.4 4.1 + - + +
104E LYS* 3.0 42.3 + - + +
141E ILE* 3.9 41.7 - - + +
144E ILE* 3.9 12.0 - - + +
145E GLY* 4.5 3.4 - - - +
148E ILE* 3.7 21.8 - - + -
3V GLN* 3.7 37.0 - - + +
4V VAL* 4.9 0.7 - - + -
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Residues in contact with GLN 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E GLN 3.1 13.7 + - - +
98E ALA* 3.7 9.2 - - - +
100E LEU* 1.3 75.7 - - + +
102E LEU* 1.3 61.2 + - - +
104E LYS* 3.2 10.8 + - - +
105E THR* 2.9 34.0 + - - +
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E LEU* 5.4 1.8 - - + -
25E TYR* 4.1 27.8 - - + -
26E ALA* 3.9 24.7 - - + +
29E THR* 3.7 28.9 - - + -
30E TYR* 3.9 32.5 - - + +
33E MET* 5.2 0.2 - - + -
98E ALA 3.0 18.3 + - - +
99E ALA* 3.5 5.4 - - - +
101E GLN* 1.3 75.6 - - - +
103E GLU* 1.3 59.3 + - - +
105E THR* 3.4 10.4 + - + -
106E VAL* 3.1 35.9 + - + +
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Residues in contact with GLU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E ALA* 6.5 0.2 - - - -
30E TYR* 2.8 29.0 + - - +
54E HIS* 3.6 14.6 + - - -
58E GLU* 3.4 13.0 - - - +
99E ALA 2.9 14.7 + - - +
100E LEU* 3.8 5.6 - - - +
102E LEU* 1.3 76.4 - - - +
104E LYS* 1.3 59.7 + - - +
106E VAL* 3.3 6.0 + - - +
107E ASN* 2.8 25.8 + - - +
137E GLN* 3.0 30.1 + - - +
140E ASP* 4.4 7.0 - - + -
141E ILE* 3.9 13.7 - - + -
144E ILE* 3.9 14.4 - - + -
177E MG 2.9 27.7 - - - -
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Residues in contact with LYS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E LEU* 3.0 29.7 + - + +
101E GLN* 3.7 9.2 - - - +
103E GLU* 1.3 75.3 - - - +
105E THR* 1.3 57.7 + - - +
107E ASN* 4.1 0.2 - - - -
108E GLN* 2.9 26.3 + - - +
141E ILE* 4.2 11.9 - - + -
2V SER 4.9 0.6 + - - -
3V GLN* 2.9 30.5 + - - +
4V VAL 4.4 5.6 - - - +
5V ARG 3.5 17.4 + - - -
6V GLN* 3.0 44.6 + - + +
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Residues in contact with THR 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E LEU* 4.6 20.0 - - + -
25E TYR* 6.5 0.4 - - + -
101E GLN 2.9 21.3 + - - -
102E LEU* 3.5 12.2 - - + +
103E GLU 3.2 0.2 - - - -
104E LYS* 1.3 76.3 - - - +
106E VAL* 1.3 62.7 + - - +
108E GLN* 3.4 6.7 + - - +
109E ALA* 3.1 22.5 + - - +
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Residues in contact with VAL 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E MET* 5.1 2.0 - - - -
22E LEU* 3.9 29.2 - - + +
23E GLU* 4.0 10.3 - - - +
26E ALA* 4.2 24.2 - - + -
58E GLU* 4.9 0.7 - - - +
102E LEU* 3.1 20.6 + - + +
103E GLU* 3.3 10.5 + - - +
105E THR* 1.3 72.2 - - - +
107E ASN* 1.3 65.7 + - - +
109E ALA* 3.2 3.5 + - - +
110E LEU* 3.0 31.1 + - + +
137E GLN* 3.9 11.9 - - - +
176E MG 3.8 22.2 - - - -
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Residues in contact with ASN 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E GLU 2.8 20.6 + - - +
106E VAL* 1.3 72.4 - - - +
108E GLN* 1.3 58.1 + - - +
110E LEU* 3.1 9.8 + - - +
111E LEU* 2.9 42.3 + - - +
134E LEU* 4.8 8.7 - - - +
137E GLN* 3.6 22.7 - - - +
138E VAL* 5.0 9.9 - - - +
141E ILE* 3.9 16.4 - - + +
6V GLN* 3.1 40.5 + - - +
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Residues in contact with GLN 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E LYS 2.9 18.3 + - - +
105E THR* 3.6 7.2 - - - +
107E ASN* 1.3 78.1 - - - +
109E ALA* 1.3 56.8 + - - +
111E LEU* 3.4 16.0 + - - +
112E ASP* 2.9 63.8 + - - +
6V GLN* 3.6 20.5 + - - +
7V ASN* 5.8 2.4 + - - +
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Residues in contact with ALA 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E MET* 3.1 20.6 - - + +
22E LEU* 3.7 22.0 - - + -
105E THR* 3.1 13.2 + - + +
106E VAL 3.4 9.2 - - - +
108E GLN* 1.3 77.5 - - - +
110E LEU* 1.3 57.6 + - - +
112E ASP* 3.4 10.5 + - - +
113E LEU* 2.9 22.2 + - - +
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Residues in contact with LEU 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E MET* 3.7 24.7 - - + -
23E GLU* 4.9 1.6 - - - +
65E PHE* 4.0 20.6 - - + -
106E VAL* 3.0 26.4 + - + +
107E ASN* 3.4 7.2 - - - +
109E ALA* 1.3 75.6 - - - +
111E LEU* 1.3 59.7 + - - +
113E LEU* 3.4 3.0 + - - +
114E HIS* 2.9 27.0 + - - +
129E LEU* 4.2 14.4 - - + +
133E TYR* 3.9 32.8 - - + -
134E LEU* 3.9 15.3 - - + +
137E GLN* 3.7 30.5 - - + +
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Residues in contact with LEU 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E ASN* 2.9 43.2 + - - +
108E GLN* 3.7 20.0 - - - +
110E LEU* 1.3 74.6 - - - +
112E ASP* 1.3 59.9 + - - +
114E HIS* 3.2 6.7 + - - +
115E LYS* 3.0 26.7 + - - +
134E LEU* 4.6 15.9 - - + -
6V GLN* 4.5 4.0 - - + -
7V ASN* 3.8 32.1 - - + +
121V VAL* 6.1 0.3 - - - +
123V PRO* 3.7 35.2 - - + +
124V HIS* 5.3 4.7 - - + +
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Residues in contact with ASP 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E GLN* 2.9 49.9 + - - +
109E ALA* 3.4 9.4 - - - +
110E LEU 3.2 0.2 - - - -
111E LEU* 1.3 76.7 - - - +
113E LEU* 1.3 60.5 + - - +
115E LYS* 3.3 8.8 + - - +
116E LEU* 3.0 25.8 + - - +
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Residues in contact with LEU 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E CYS* 4.3 9.0 - - - +
15E ALA* 3.5 31.9 - - + +
16E VAL* 4.3 17.5 - - + -
19E MET* 3.7 35.4 - - + -
65E PHE* 4.5 1.8 - - + -
109E ALA 2.9 17.4 + - - +
110E LEU* 3.7 5.2 - - + +
112E ASP* 1.3 76.2 - - - +
114E HIS* 1.3 58.9 + - - +
116E LEU* 3.4 9.9 + - + +
117E ALA* 3.0 25.8 + - - +
125E LEU* 4.4 10.1 - - + -
129E LEU* 3.9 25.4 - - + -
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Residues in contact with HIS 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E LEU 2.9 14.7 + - - +
111E LEU* 3.3 13.2 - - - +
112E ASP 3.1 0.2 - - - -
113E LEU* 1.3 74.5 - - - +
115E LYS* 1.3 61.3 + - - +
117E ALA* 3.3 4.2 + - - +
118E THR* 2.9 43.1 + - - -
126E CYS* 3.6 31.1 + - - +
129E LEU* 3.8 18.1 - - + +
130E GLU* 2.9 25.3 + - - -
134E LEU* 4.2 7.2 - - + -
121V VAL* 6.1 1.6 - - - +
123V PRO* 3.5 35.4 - - + +
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Residues in contact with LYS 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E LEU 3.0 13.2 + - - +
112E ASP* 3.5 11.2 - - - +
114E HIS* 1.3 75.3 + - - +
116E LEU* 1.3 60.1 + - - +
118E THR* 3.2 8.9 + - + -
119E ASP* 2.9 29.3 + - - +
121V VAL* 4.2 25.8 - - + -
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Residues in contact with LEU 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASP* 3.6 40.8 - - + +
12E CYS* 4.0 11.2 - - - -
15E ALA* 3.7 20.2 - - + -
18E ARG* 5.4 1.8 - - - +
112E ASP 3.0 13.6 + - - +
113E LEU* 3.6 11.4 - - + +
114E HIS 3.3 0.2 - - - -
115E LYS* 1.3 76.5 - - - +
117E ALA* 1.3 57.4 + - - +
119E ASP* 3.3 5.5 + - + +
120E LYS* 2.9 50.4 + - + +
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Residues in contact with ALA 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E CYS* 4.3 11.2 - - - -
113E LEU 3.0 14.7 + - - +
114E HIS* 3.5 10.5 - - - +
116E LEU* 1.3 72.7 - - - +
118E THR* 1.3 64.0 + - - +
120E LYS 3.5 0.9 + - - -
121E VAL 3.1 3.5 + - - -
122E ASP* 2.9 34.2 + - + +
125E LEU* 3.9 27.6 - - + -
126E CYS* 3.6 17.9 - - - +
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Residues in contact with THR 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E HIS* 2.9 31.2 + - - -
115E LYS* 3.2 10.5 + - + +
117E ALA* 1.3 76.5 - - - +
119E ASP* 1.3 62.4 + - - +
121E VAL* 3.1 17.9 + - - +
126E CYS* 3.5 14.9 - - - -
121V VAL* 6.4 2.0 - - + -
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Residues in contact with ASP 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E LYS 2.9 16.0 + - - +
116E LEU* 3.6 9.0 - - + +
118E THR* 1.3 79.4 - - - +
120E LYS* 1.3 74.2 + - + +
121E VAL* 3.2 9.1 + - - +
----------------------------------------------------------
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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