Contacts of the helix formed by residues 92 - 119 (chain N) 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 N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N PHE* 3.6 19.8 - - - -
44N LEU* 3.8 8.0 - - - +
47N VAL* 4.1 16.9 - - + +
91N ASN* 1.3 72.4 - - - +
93N LEU* 1.3 57.4 + - - +
95N ALA* 3.9 0.9 - - - +
96N MET* 3.0 39.7 + - + +
151N LEU* 4.1 7.4 - - + -
156N LEU* 4.0 7.2 - - - -
163N GLU* 2.8 30.3 + - - +
166N PHE* 3.8 35.2 - - + -
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Residues in contact with LEU 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91N ASN* 2.9 10.7 + - - +
92N THR* 1.3 75.4 - - - +
94N GLU* 1.3 62.6 + - - +
96N MET* 3.3 1.2 + - - +
97N GLN* 2.9 51.5 + - - +
148N ILE* 3.9 29.8 - - + +
151N LEU* 3.9 24.0 - - + -
152N LYS* 4.3 16.8 - - + -
156N LEU* 3.4 18.2 - - + +
157N PRO* 3.7 35.9 - - + -
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Residues in contact with GLU 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86N ARG* 3.0 39.0 + - - +
89N TRP 3.4 12.1 - - - +
90N GLY* 3.7 8.6 - - - -
91N ASN* 3.1 25.6 + - - +
92N THR 3.4 0.2 - - - -
93N LEU* 1.3 79.6 - - - +
95N ALA* 1.3 58.2 + - - +
97N GLN* 3.5 15.4 + - - +
98N ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N MET* 3.8 10.0 - - - +
37N PHE* 3.7 26.9 - - + -
51N PHE* 4.1 12.1 - - + -
89N TRP* 3.7 16.7 + - + -
91N ASN 3.0 18.0 + - - +
92N THR 3.9 2.5 - - - +
94N GLU* 1.3 76.1 - - - +
96N MET* 1.3 58.3 + - - +
98N ALA* 3.4 7.8 + - - +
99N ALA* 2.9 27.2 + - - +
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Residues in contact with MET 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47N VAL* 4.6 4.0 - - + -
50N PHE* 4.0 16.8 - - + -
51N PHE* 3.7 30.5 - - + -
92N THR* 3.0 25.9 + - + +
93N LEU 3.3 4.5 + - - +
95N ALA* 1.3 73.9 - - - +
97N GLN* 1.3 60.8 + - - +
99N ALA* 3.3 2.4 + - - -
100N LEU* 2.8 24.3 + - - +
144N ILE* 3.4 21.3 - - + +
147N PHE* 3.9 32.5 - - + -
148N ILE* 3.7 17.8 - - + +
151N LEU* 3.8 17.0 - - + -
166N PHE* 4.3 16.8 - - + -
171N VAL* 5.3 1.3 - - + -
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Residues in contact with GLN 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93N LEU* 2.9 42.6 + - + +
94N GLU* 3.8 14.5 - - - +
96N MET* 1.3 73.6 - - - +
98N ALA* 1.3 65.9 + - - +
100N LEU* 3.3 3.6 + - - +
101N GLN* 3.1 25.8 + - - +
148N ILE* 4.0 20.7 - - + +
152N LYS* 4.1 21.5 + - - -
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Residues in contact with ALA 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N MET* 4.0 4.5 - - + -
85N GLU* 5.4 4.7 - - - +
86N ARG* 5.6 2.2 - - - +
89N TRP* 3.8 32.1 - - + -
94N GLU 3.0 14.9 + - - +
95N ALA 3.5 8.5 - - - +
97N GLN* 1.3 76.9 - - - +
99N ALA* 1.3 58.5 + - - +
101N GLN* 3.4 6.7 + - - +
102N LEU* 3.0 27.5 + - - +
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Residues in contact with ALA 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N TYR* 3.9 27.8 - - + +
33N MET* 4.2 5.1 - - + +
51N PHE* 4.2 8.3 - - + -
95N ALA 2.9 17.5 + - - +
96N MET* 3.5 10.3 - - - +
97N GLN 3.2 0.2 - - - -
98N ALA* 1.3 74.7 - - - +
100N LEU* 1.3 59.5 + - - +
102N LEU* 3.2 5.6 + - - +
103N GLU* 2.9 34.7 + - - +
144N ILE* 4.1 12.3 - - + -
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Residues in contact with LEU 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96N MET 2.8 19.8 + - - +
97N GLN* 3.3 6.5 + - - +
99N ALA* 1.3 73.2 - - - +
101N GLN* 1.3 59.5 + - + +
103N GLU* 3.4 3.1 + - - +
104N LYS* 3.0 41.9 + - + +
141N ILE* 3.9 41.5 - - + +
144N ILE* 3.9 12.3 - - + +
145N GLY* 4.5 3.4 - - - +
148N ILE* 3.7 22.2 - - + -
3Q GLN* 3.8 38.6 - - + +
4Q VAL* 4.9 0.4 - - + -
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Residues in contact with GLN 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97N GLN 3.1 12.5 + - - +
98N ALA* 3.7 8.7 - - - +
100N LEU* 1.3 76.7 - - + +
102N LEU* 1.3 61.1 + - - +
104N LYS* 3.2 10.2 + - - +
105N THR* 2.9 34.8 + - - +
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Residues in contact with LEU 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N LEU* 5.4 1.8 - - + -
25N TYR* 4.1 28.0 - - + -
26N ALA* 3.9 24.9 - - + +
29N THR* 3.7 28.5 - - + -
30N TYR* 3.9 33.2 - - + +
98N ALA 3.0 17.2 + - - +
99N ALA* 3.2 5.8 + - - +
101N GLN* 1.3 76.2 - - - +
103N GLU* 1.3 59.1 + - + +
105N THR* 3.4 9.9 + - + -
106N VAL* 3.1 36.2 + - + +
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Residues in contact with GLU 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N ALA* 6.2 0.6 - - - +
30N TYR* 2.8 28.9 + - - +
54N HIS* 3.6 14.6 + - - -
58N GLU* 3.4 11.7 - - - +
99N ALA 2.9 13.6 + - - +
100N LEU* 3.8 5.2 - - - +
102N LEU* 1.3 76.4 - - - +
104N LYS* 1.3 59.9 + - - +
106N VAL* 3.3 6.1 + - - +
107N ASN* 2.8 25.6 + - - +
137N GLN* 3.0 28.5 + - - +
140N ASP* 4.4 6.7 - - + -
141N ILE* 3.9 14.4 - - + -
144N ILE* 3.9 15.0 - - + -
177N MG 2.9 27.7 - - - -
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Residues in contact with LYS 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100N LEU* 3.0 29.0 + - + +
101N GLN* 3.7 9.9 - - - +
103N GLU* 1.3 75.1 - - - +
105N THR* 1.3 58.4 + - - +
107N ASN* 4.1 0.7 - - - -
108N GLN* 2.9 26.2 + - - +
141N ILE* 4.2 10.5 - - + -
2Q SER 4.9 0.6 + - - -
3Q GLN* 2.9 31.0 + - - +
4Q VAL 4.4 5.8 - - - +
5Q ARG 3.5 16.8 + - - -
6Q GLN* 3.1 44.2 + - + +
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Residues in contact with THR 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N LEU* 4.6 20.0 - - + -
25N TYR* 6.5 0.7 - - + -
101N GLN* 2.9 20.5 + - - +
102N LEU* 3.5 12.6 - - + +
104N LYS* 1.3 78.1 - - - +
106N VAL* 1.3 62.2 + - - +
108N GLN* 3.4 6.4 + - - +
109N ALA* 3.1 22.5 + - - +
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Residues in contact with VAL 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N MET* 5.1 1.8 - - - -
22N LEU* 3.9 28.9 - - + +
23N GLU* 4.0 10.1 - - - +
26N ALA* 4.2 24.7 - - + -
58N GLU* 4.9 0.4 - - - +
102N LEU* 3.1 18.6 + - + +
103N GLU* 3.7 10.3 - - - +
105N THR* 1.3 72.4 - - - +
107N ASN* 1.3 65.6 + - - +
109N ALA* 3.2 3.3 + - - +
110N LEU* 3.0 31.0 + - + +
137N GLN* 3.9 11.7 - - - +
176N MG 3.8 22.2 - - - -
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Residues in contact with ASN 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103N GLU 2.8 21.7 + - - +
104N LYS 3.6 0.2 - - - +
105N THR 3.3 0.2 - - - -
106N VAL* 1.3 73.2 - - - +
108N GLN* 1.3 58.1 + - - +
110N LEU* 3.1 9.7 + - - +
111N LEU* 2.9 43.6 + - - +
134N LEU* 4.8 8.8 - - - +
137N GLN* 3.6 22.9 - - - +
138N VAL* 5.0 9.9 - - - +
141N ILE* 3.9 16.8 - - + +
6Q GLN* 3.1 39.0 + - - +
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Residues in contact with GLN 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104N LYS 2.9 18.6 + - - +
105N THR* 3.6 6.7 - - - +
107N ASN* 1.3 77.9 - - - +
109N ALA* 1.3 57.3 + - - +
111N LEU* 3.4 16.8 + - - +
112N ASP* 2.9 64.1 + - - +
6Q GLN* 3.6 20.7 + - - +
7Q ASN* 5.8 2.0 - - - +
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Residues in contact with ALA 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N MET* 3.1 21.0 - - + +
22N LEU* 3.7 22.2 - - + -
105N THR* 3.1 14.3 + - + +
106N VAL 3.2 8.5 + - - +
108N GLN* 1.3 77.6 - - - +
110N LEU* 1.3 58.3 + - - +
112N ASP* 3.4 9.5 + - - +
113N LEU* 2.9 22.3 + - - +
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Residues in contact with LEU 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N MET* 3.7 23.8 - - + -
23N GLU* 4.9 1.8 - - - +
65N PHE* 4.0 21.3 - - + -
106N VAL* 3.0 24.7 + - + +
107N ASN* 3.4 6.5 - - - +
109N ALA* 1.3 76.1 - - - +
111N LEU* 1.3 60.1 + - - +
113N LEU* 3.4 3.0 + - - +
114N HIS* 2.9 27.0 + - - +
129N LEU* 4.2 14.5 - - + +
133N TYR* 3.9 31.9 - - + -
134N LEU* 3.9 15.1 - - + +
137N GLN* 3.7 31.2 - - + +
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Residues in contact with LEU 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107N ASN* 2.9 43.2 + - - +
108N GLN* 3.7 19.7 - - - +
110N LEU* 1.3 74.8 - - - +
112N ASP* 1.3 59.8 + - - +
114N HIS* 3.2 6.4 + - - +
115N LYS* 3.0 27.9 + - - +
134N LEU* 4.6 16.2 - - + -
6Q GLN* 4.5 3.8 - - + -
7Q ASN* 3.8 33.0 - - + +
123Q PRO* 3.7 34.6 - - + +
124Q HIS* 5.3 3.8 - - + +
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Residues in contact with ASP 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108N GLN* 2.9 48.2 + - - +
109N ALA* 3.4 9.8 - - - +
111N LEU* 1.3 76.7 - - - +
113N LEU* 1.3 59.6 + - - +
115N LYS* 3.3 8.5 + - - +
116N LEU* 3.0 26.5 + - - +
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Residues in contact with LEU 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N CYS* 4.3 9.2 - - - +
15N ALA* 3.5 31.6 - - + +
16N VAL* 4.3 16.8 - - + -
19N MET* 3.7 34.3 - - + -
65N PHE* 4.5 2.2 - - + -
109N ALA 2.9 17.2 + - - +
110N LEU* 3.7 5.2 - - + +
111N LEU 3.3 0.2 - - - -
112N ASP* 1.3 74.6 - - - +
114N HIS* 1.3 59.5 + - - +
116N LEU* 3.4 10.2 + - + +
117N ALA* 3.0 26.2 + - - +
125N LEU* 4.4 9.9 - - + -
129N LEU* 3.9 26.2 - - + -
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Residues in contact with HIS 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110N LEU 2.9 15.6 + - - +
111N LEU* 3.3 12.8 - - - +
112N ASP 3.1 0.2 - - - -
113N LEU* 1.3 75.2 - - - +
115N LYS* 1.3 60.1 + - - +
117N ALA* 3.3 5.2 + - - +
118N THR* 2.9 43.7 + - - -
126N CYS* 3.6 31.7 + - + +
129N LEU* 3.8 16.8 - - + +
130N GLU* 2.9 24.7 + - - -
134N LEU* 4.2 8.1 - - + -
121Q VAL* 6.1 1.6 - - - +
123Q PRO* 3.5 36.4 - - + +
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Residues in contact with LYS 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111N LEU 3.0 13.6 + - - +
112N ASP* 3.3 10.7 + - - +
114N HIS* 1.3 75.1 + - - +
116N LEU* 1.3 60.8 + - - +
118N THR* 3.2 9.7 + - + +
119N ASP* 2.9 29.7 + - - +
121Q VAL* 4.3 24.0 - - + -
123Q PRO* 5.9 0.2 - - - +
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Residues in contact with LEU 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N ASP* 3.6 39.7 - - + +
12N CYS* 4.0 11.9 - - - -
15N ALA* 3.7 19.7 - - + -
18N ARG* 5.4 2.5 - - - +
112N ASP 3.0 13.6 + - - +
113N LEU* 3.6 11.0 - - + +
114N HIS 3.3 0.2 - - - -
115N LYS* 1.3 76.6 - - - +
117N ALA* 1.3 56.8 + - - +
119N ASP* 3.3 6.0 + - + +
120N LYS* 2.9 50.2 + - + +
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Residues in contact with ALA 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N CYS* 4.3 10.5 - - - -
113N LEU 3.0 13.4 + - - +
114N HIS* 3.5 10.3 - - - +
116N LEU* 1.3 74.0 - - - +
118N THR* 1.3 64.3 + - - +
120N LYS 3.5 0.5 + - - -
121N VAL 3.1 3.6 + - - -
122N ASP* 2.9 34.7 + - + +
125N LEU* 3.9 28.3 - - + -
126N CYS* 3.6 17.7 - - - +
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Residues in contact with THR 118 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114N HIS* 2.9 31.5 + - - -
115N LYS* 3.2 10.7 + - + +
117N ALA* 1.3 76.8 - - - +
119N ASP* 1.3 64.7 + - - +
121N VAL* 3.1 18.3 + - - +
126N CYS* 3.5 15.2 - - - -
121Q VAL* 6.4 2.0 - - + -
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Residues in contact with ASP 119 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115N LYS* 2.9 16.9 + - + +
116N LEU* 3.6 8.7 - - + +
118N THR* 1.3 79.2 - - - +
120N LYS* 1.3 72.8 + - + +
121N VAL* 3.2 8.9 + - - +
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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