Contacts of the helix formed by residues 92 - 119 (chain W) 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 W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W PHE* 3.6 19.1 - - - -
44W LEU* 3.8 8.3 - - - +
47W VAL* 4.1 17.5 - - + +
91W ASN* 1.3 72.1 - - - +
93W LEU* 1.3 57.9 + - - +
95W ALA* 3.9 1.3 - - - +
96W MET* 3.0 38.1 + - + +
151W LEU* 4.1 7.6 - - + -
156W LEU* 4.0 6.5 - - - -
163W GLU* 2.8 30.8 + - - +
166W PHE* 3.8 35.0 - - + -
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Residues in contact with LEU 93 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91W ASN* 2.9 10.1 + - - +
92W THR* 1.3 75.4 - - - +
94W GLU* 1.3 61.5 + - - +
96W MET* 3.3 1.0 + - - +
97W GLN* 2.9 53.0 + - - +
148W ILE* 3.9 29.4 - - + +
151W LEU* 3.9 23.6 - - + -
152W LYS* 4.3 15.9 - - + -
156W LEU* 3.4 18.7 - - + +
157W PRO* 3.7 35.2 - - + -
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Residues in contact with GLU 94 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86W ARG* 3.0 40.4 + - - +
89W TRP 3.4 12.6 - - - +
90W GLY* 3.7 7.1 - - - -
91W ASN* 3.1 27.1 + - - +
92W THR 3.4 0.2 - - - -
93W LEU* 1.3 79.2 - - - +
95W ALA* 1.3 57.3 + - - +
97W GLN* 3.5 13.8 + - - +
98W ALA* 3.0 26.5 + - - +
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Residues in contact with ALA 95 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W MET* 3.8 9.6 - - - +
37W PHE* 3.7 26.9 - - + -
51W PHE* 4.1 11.4 - - + -
89W TRP* 3.7 16.5 + - + -
91W ASN 3.0 18.8 + - - +
92W THR 3.9 2.7 - - - +
94W GLU* 1.3 75.9 - - - +
96W MET* 1.3 59.3 + - - +
98W ALA* 3.4 7.6 + - - +
99W ALA* 2.9 27.2 + - - +
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Residues in contact with MET 96 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47W VAL* 4.6 4.5 - - + -
50W PHE* 4.0 16.2 - - + -
51W PHE* 3.7 31.0 - - + -
92W THR* 3.0 25.5 + - + +
93W LEU 3.3 3.8 + - - +
95W ALA* 1.3 73.4 - - - +
97W GLN* 1.3 61.7 + - - +
99W ALA* 4.1 1.8 - - - -
100W LEU* 2.8 24.3 + - - +
144W ILE* 3.4 20.0 - - + +
147W PHE* 3.9 32.8 - - + -
148W ILE* 3.8 17.7 - - + -
151W LEU* 3.8 17.3 - - + -
166W PHE* 4.3 16.8 - - + -
171W VAL* 5.3 1.3 - - + -
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Residues in contact with GLN 97 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93W LEU* 2.9 43.2 + - + +
94W GLU* 3.8 14.8 - - - +
95W ALA 3.3 0.2 - - - -
96W MET* 1.3 71.3 - - - +
98W ALA* 1.3 66.4 + - - +
100W LEU* 3.3 4.0 + - - +
101W GLN* 3.1 24.9 + - - +
148W ILE* 4.0 20.7 - - + +
152W LYS* 4.1 21.8 + - - -
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Residues in contact with ALA 98 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W MET* 4.0 4.5 - - + -
85W GLU* 5.4 4.3 - - - +
86W ARG* 5.6 2.5 - - - +
89W TRP* 3.8 32.3 - - + -
94W GLU 3.0 15.1 + - - +
95W ALA 3.5 8.7 - - - +
97W GLN* 1.3 76.9 - - - +
99W ALA* 1.3 58.6 + - - +
101W GLN* 3.4 6.2 + - - +
102W LEU* 3.0 27.8 + - - +
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Residues in contact with ALA 99 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30W TYR* 3.9 26.9 - - + +
33W MET* 4.2 5.1 - - + +
51W PHE* 4.2 8.7 - - + -
95W ALA 2.9 17.7 + - - +
96W MET* 3.5 9.4 - - - +
97W GLN 3.2 0.2 - - - -
98W ALA* 1.3 75.1 - - - +
100W LEU* 1.3 60.3 + - - +
102W LEU* 3.2 6.2 + - - +
103W GLU* 2.9 34.8 + - - +
144W ILE* 4.1 12.3 - - + -
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Residues in contact with LEU 100 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I GLN* 3.9 38.6 - - + +
4I VAL* 4.9 0.7 - - + -
96W MET 2.8 20.0 + - - +
97W GLN* 3.3 6.3 + - - +
99W ALA* 1.3 72.7 - - - +
101W GLN* 1.3 59.7 + - + +
103W GLU* 3.4 3.1 + - - +
104W LYS* 3.0 41.7 + - + +
141W ILE* 3.9 41.7 - - + +
144W ILE* 3.9 11.8 - - + +
145W GLY* 4.5 3.4 - - - +
148W ILE* 3.7 22.0 - - + -
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Residues in contact with GLN 101 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97W GLN 3.1 12.9 + - - +
98W ALA* 3.7 9.2 - - - +
100W LEU* 1.3 76.9 - - + +
102W LEU* 1.3 60.4 + - - +
104W LYS* 3.2 10.2 + - - +
105W THR* 2.9 35.0 + - - +
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Residues in contact with LEU 102 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22W LEU* 5.4 1.8 - - + -
25W TYR* 4.1 28.0 - - + -
26W ALA* 3.9 24.9 - - + +
29W THR* 3.7 27.6 - - + -
30W TYR* 3.9 33.0 - - + +
98W ALA 3.0 17.6 + - - +
99W ALA* 3.5 5.8 - - - +
101W GLN* 1.3 76.0 - - - +
103W GLU* 1.3 58.5 + - - +
105W THR* 3.4 10.0 + - + -
106W VAL* 3.1 36.4 + - + +
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Residues in contact with GLU 103 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W ALA* 6.5 0.2 - - - -
30W TYR* 2.8 28.2 + - - +
54W HIS* 3.6 14.2 + - - -
58W GLU* 3.4 12.9 - - - +
99W ALA 2.9 14.3 + - - +
100W LEU* 3.8 4.9 - - - +
102W LEU* 1.3 76.4 - - - +
104W LYS* 1.3 59.5 + - - +
106W VAL* 3.3 5.6 + - - +
107W ASN* 2.8 26.0 + - - +
137W GLN* 3.0 28.7 + - - +
140W ASP* 4.4 6.7 - - + -
141W ILE* 3.9 14.6 - - + -
144W ILE* 3.9 15.0 - - + -
177W MG 2.9 28.3 - - - -
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Residues in contact with LYS 104 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I SER 5.0 0.8 + - - -
3I GLN* 2.8 30.3 + - - +
4I VAL 4.4 9.6 - - - +
5I ARG 3.6 16.4 + - - -
6I GLN* 3.2 38.7 + - + +
100W LEU* 3.0 30.6 + - + +
101W GLN* 3.7 9.0 - - - +
103W GLU* 1.3 74.7 - - - +
105W THR* 1.3 57.3 + - - +
107W ASN* 4.1 0.4 - - - -
108W GLN* 2.9 26.5 + - - +
141W ILE* 4.2 12.3 - - + -
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Residues in contact with THR 105 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22W LEU* 4.6 19.5 - - + -
25W TYR* 6.5 0.7 - - + -
101W GLN* 2.9 20.7 + - - +
102W LEU* 3.5 12.1 - - + +
104W LYS* 1.3 77.3 - - - +
106W VAL* 1.3 63.0 + - - +
108W GLN* 3.4 6.2 + - - +
109W ALA* 3.1 22.2 + - - +
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Residues in contact with VAL 106 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19W MET* 5.1 1.6 - - - -
22W LEU* 3.9 29.4 - - + +
23W GLU* 4.0 10.5 - - - +
26W ALA* 4.2 24.2 - - + -
58W GLU* 4.9 0.9 - - - +
102W LEU* 3.1 19.7 + - + +
103W GLU* 3.7 9.9 - - - +
105W THR* 1.3 72.1 - - - +
107W ASN* 1.3 66.6 + - - +
109W ALA* 3.2 3.1 + - - +
110W LEU* 3.0 31.3 + - + +
137W GLN* 3.9 10.8 - - - +
176W MG 3.8 22.4 - - - -
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Residues in contact with ASN 107 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLN* 3.1 39.0 + - - +
103W GLU 2.8 22.3 + - - +
104W LYS 3.6 0.2 - - - +
106W VAL* 1.3 71.8 - - - +
108W GLN* 1.3 58.1 + - - +
110W LEU* 3.1 10.5 + - - +
111W LEU* 2.9 42.4 + - - +
134W LEU* 4.8 9.0 - - - +
137W GLN* 3.6 22.4 - - - +
138W VAL* 5.0 9.3 - - - +
141W ILE* 3.9 17.6 - - + +
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Residues in contact with GLN 108 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLN* 3.4 21.3 + - - +
7I ASN* 5.9 1.9 - - - +
104W LYS 2.9 17.3 + - - +
105W THR* 3.6 7.6 - - - +
107W ASN* 1.3 79.7 - - - +
109W ALA* 1.3 56.9 + - - +
111W LEU* 4.2 15.8 - - - +
112W ASP* 2.9 63.3 + - - +
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Residues in contact with ALA 109 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19W MET* 3.1 19.8 - - + +
22W LEU* 3.7 22.0 - - + -
105W THR* 3.1 13.9 + - + +
106W VAL 3.4 9.0 - - - +
108W GLN* 1.3 77.9 - - - +
110W LEU* 1.3 57.6 + - - +
112W ASP* 3.4 9.7 + - - +
113W LEU* 2.9 22.3 + - - +
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Residues in contact with LEU 110 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19W MET* 3.7 24.7 - - + -
23W GLU* 4.9 1.3 - - - +
65W PHE* 4.0 21.1 - - + -
106W VAL* 3.0 25.1 + - + +
107W ASN* 3.1 7.4 + - - +
109W ALA* 1.3 76.1 - - - +
111W LEU* 1.3 60.5 + - - +
113W LEU* 3.4 2.8 + - - +
114W HIS* 2.9 26.9 + - - +
129W LEU* 4.2 14.3 - - + +
133W TYR* 3.9 32.3 - - + -
134W LEU* 3.9 15.6 - - + +
137W GLN* 3.7 30.1 - - + +
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Residues in contact with LEU 111 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLN* 4.5 4.7 - - + +
7I ASN* 3.9 30.7 - - + +
123I PRO* 3.8 33.4 - - + +
124I HIS* 5.4 4.5 - - + +
107W ASN* 2.9 42.6 + - - +
108W GLN* 3.7 20.0 - - - +
109W ALA 3.3 0.2 - - - -
110W LEU* 1.3 75.8 - - - +
112W ASP* 1.3 59.3 - - - +
114W HIS* 3.2 5.9 + - - +
115W LYS* 3.0 27.5 + - - +
134W LEU* 4.6 16.8 - - + -
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Residues in contact with ASP 112 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108W GLN* 2.9 48.5 + - - +
109W ALA* 3.4 9.3 - - - +
111W LEU* 1.3 75.4 - - - +
113W LEU* 1.3 60.8 + - - +
115W LYS* 3.3 8.2 + - - +
116W LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 113 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12W CYS* 4.3 8.5 - - - +
15W ALA* 3.5 31.9 - - + +
16W VAL* 4.3 17.5 - - + -
19W MET* 3.7 34.3 - - + -
65W PHE* 4.5 2.2 - - + -
109W ALA 2.9 17.2 + - - +
110W LEU* 3.7 4.9 - - + +
111W LEU 3.3 0.2 - - - -
112W ASP* 1.3 75.5 - - - +
114W HIS* 1.3 58.8 + - - +
116W LEU* 3.4 10.0 + - + +
117W ALA* 3.0 26.6 + - - +
125W LEU* 4.4 9.6 - - + -
129W LEU* 3.9 26.5 - - + -
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Residues in contact with HIS 114 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I VAL* 6.2 0.4 - - - +
123I PRO* 3.5 36.8 - - + +
110W LEU 2.9 14.5 + - - +
111W LEU* 3.3 12.8 - - - +
112W ASP 3.1 0.2 - - - -
113W LEU* 1.3 75.3 - - - +
115W LYS* 1.3 60.6 + - - +
117W ALA* 3.3 4.2 + - - +
118W THR* 2.9 43.8 + - - -
126W CYS* 3.6 30.2 + - - +
129W LEU* 3.8 18.1 - - + +
130W GLU* 2.9 25.5 + - - -
134W LEU* 4.2 7.4 - - + -
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Residues in contact with LYS 115 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I VAL* 4.4 23.8 - - + -
111W LEU 3.0 13.0 + - - +
112W ASP* 3.3 10.3 + - - +
114W HIS* 1.3 74.6 + - - +
116W LEU* 1.3 61.1 + - - +
118W THR* 3.2 10.1 + - + -
119W ASP* 2.9 29.2 + - - +
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Residues in contact with LEU 116 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W ASP* 3.6 40.8 - - + +
12W CYS* 4.0 11.0 - - - -
15W ALA* 3.7 19.7 - - + -
18W ARG* 5.4 1.8 - - - +
112W ASP 3.0 14.0 + - - +
113W LEU* 3.6 11.0 - - + +
114W HIS 3.3 0.2 - - - -
115W LYS* 1.3 76.1 - - - +
117W ALA* 1.3 57.1 + - - +
119W ASP* 3.3 5.6 + - + +
120W LYS* 2.9 50.2 + - + +
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Residues in contact with ALA 117 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12W CYS* 4.3 11.2 - - - -
113W LEU 3.0 13.5 + - - +
114W HIS* 3.5 10.5 - - - +
116W LEU* 1.3 73.9 - - - +
118W THR* 1.3 64.6 + - - +
120W LYS 3.5 0.5 + - - -
121W VAL 3.1 3.6 + - - -
122W ASP* 2.9 34.3 + - + +
125W LEU* 3.9 27.8 - - + -
126W CYS* 3.6 17.7 - - - +
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Residues in contact with THR 118 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I VAL* 6.4 2.2 - - + -
114W HIS* 2.9 30.8 + - - -
115W LYS* 3.5 10.3 - - + +
117W ALA* 1.3 77.4 - - - +
119W ASP* 1.3 62.7 + - - +
121W VAL* 3.1 18.2 + - - +
126W CYS* 3.5 15.9 - - - -
----------------------------------------------------------
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Residues in contact with ASP 119 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115W LYS* 2.9 16.5 + - + +
116W LEU* 3.6 9.0 - - + +
118W THR* 1.3 78.8 - - - +
120W LYS* 1.3 72.4 + - + +
121W VAL* 3.2 10.1 + - - +
----------------------------------------------------------
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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