Contacts of the helix formed by residues 45 - 71 (chain B) 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 HIS 45 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE 4.6 2.0 - - - -
38B ASP* 3.4 37.1 + - - -
43B ALA* 3.3 14.6 + - - -
44B LEU* 1.3 68.8 - - - +
46B ASN* 1.3 64.4 + - - +
48B ALA* 3.5 6.4 - - - +
49B GLU* 3.1 30.4 + - + +
167B ASP* 3.6 3.4 + - - +
67F LYS* 5.0 5.1 + - - -
142G LYS* 4.0 9.2 - - - -
146G ASP* 3.0 35.6 + - + -
150G ASN* 5.9 0.2 - - - -
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Residues in contact with ASN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B HIS* 1.3 76.3 - - - +
47B VAL* 1.3 66.2 + - - +
49B GLU* 3.3 9.4 + - - +
50B PHE 3.0 17.3 + - - -
167B ASP* 2.9 46.2 + - - +
168B LYS* 4.4 10.9 - - - +
171B VAL* 3.2 27.8 - - + +
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.9 20.6 - - + -
44B LEU* 3.5 18.8 - - + +
46B ASN* 1.3 77.4 - - - +
48B ALA* 1.3 61.5 + - - +
50B PHE* 3.2 8.5 + - - +
51B PHE* 3.2 45.5 + - + -
92B THR* 4.1 25.4 - - + +
96B MET* 4.6 4.5 - - + -
163B GLU 5.8 0.2 - - - +
166B PHE* 4.3 13.5 - - + -
167B ASP* 3.1 22.9 + - + +
171B VAL* 4.6 4.9 - - + -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 3.2 40.5 - - + +
37B PHE* 3.7 24.4 - - + +
38B ASP* 4.1 4.3 - - + +
44B LEU 3.0 14.3 + - - +
45B HIS* 3.5 15.0 - - - +
47B VAL* 1.3 77.4 - - - +
49B GLU* 1.3 57.2 + - - +
51B PHE* 3.4 2.1 + - - -
52B LYS 3.0 21.1 + - - -
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 3.6 23.2 + - - -
45B HIS* 3.1 18.4 + - + +
46B ASN* 3.3 12.1 + - - +
48B ALA* 1.3 74.2 - - - +
50B PHE* 1.3 61.2 + - - +
52B LYS* 3.6 24.9 + - - +
53B GLU* 2.9 38.8 + - - +
67F LYS* 5.7 1.6 - - - -
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 5.9 0.4 - + - -
46B ASN 3.0 13.6 + - - +
47B VAL* 3.2 11.2 + - - +
49B GLU* 1.3 75.7 - - - +
51B PHE* 1.3 92.7 + + - +
53B GLU* 3.5 7.7 + - + +
54B HIS* 3.2 53.5 + + - -
96B MET* 4.0 20.2 - - + -
143B ARG* 3.9 18.2 - - - -
144B ILE* 4.5 12.3 - - + -
147B PHE* 3.7 28.7 - + - -
171B VAL* 3.7 20.6 - - + -
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 3.6 49.9 - + + +
33B MET* 3.8 28.9 - - + -
34B TYR 4.0 4.9 - - - +
37B PHE* 3.7 22.2 - + - -
47B VAL* 3.2 37.0 + - + -
48B ALA* 3.9 4.9 - - - +
49B GLU 3.2 0.2 - - - -
50B PHE* 1.3 98.5 - + - +
52B LYS* 1.3 59.4 + - - +
54B HIS* 3.2 5.4 + - + +
55B SER* 2.9 23.6 + - - -
92B THR 5.7 0.2 - - - -
95B ALA* 4.1 12.3 - - + -
96B MET* 3.7 23.3 - - + -
99B ALA* 4.2 9.0 - - + -
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 3.7 37.6 + - + +
48B ALA 3.0 17.6 + - - +
49B GLU* 3.6 33.8 + - - +
50B PHE 3.3 0.4 - - - -
51B PHE* 1.3 76.8 - - - +
53B GLU* 1.3 63.6 + - + +
55B SER* 3.2 21.1 + - - +
56B HIS* 3.3 29.3 + - + +
63F GLU* 3.6 25.5 + - - +
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 2.9 26.0 + - + +
50B PHE* 3.6 9.7 - - + +
52B LYS* 1.3 78.3 - - + +
54B HIS* 1.3 63.1 - - + +
56B HIS* 3.3 10.5 + - - +
57B GLU* 3.1 36.0 + - - +
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Residues in contact with HIS 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 3.9 23.7 - + + -
50B PHE* 3.2 42.7 + + - +
51B PHE* 3.2 10.5 + - - +
53B GLU* 1.3 81.4 - - + +
55B SER* 1.3 64.8 + - - +
57B GLU* 3.4 17.9 + - - +
58B GLU* 3.2 32.2 + - - +
103B GLU* 3.6 17.8 + - - -
140B ASP* 3.7 25.6 - - + -
143B ARG* 3.1 26.9 + - - -
144B ILE* 4.9 4.5 - - + -
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Residues in contact with SER 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER* 2.9 47.2 + - - +
30B TYR* 3.7 14.5 - - - +
31B SER* 3.8 14.6 + - - -
51B PHE 2.9 9.8 + - - -
52B LYS* 3.2 15.8 + - - +
53B GLU 3.3 0.2 - - - -
54B HIS* 1.3 73.6 - - - +
56B HIS* 1.3 76.0 + - - +
58B GLU 3.4 0.9 + - - -
59B ARG* 3.1 12.5 + - - +
63F GLU* 4.4 5.2 + - - -
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Residues in contact with HIS 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LYS* 3.4 28.3 + - + +
53B GLU* 3.3 12.8 + - - +
54B HIS 3.2 0.6 - - - -
55B SER* 1.3 90.3 + - - +
57B GLU* 1.3 56.2 + - - +
59B ARG* 3.5 8.8 + - + +
60B GLU* 3.1 25.6 + - - +
59F ARG* 6.0 3.3 - - + +
63F GLU* 3.0 35.4 + - - -
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLU* 3.1 21.9 + - - +
54B HIS* 3.6 25.0 + - - +
55B SER 3.2 0.2 - - - -
56B HIS* 1.3 75.9 - - - +
58B GLU* 1.3 64.6 + - + +
60B GLU* 3.2 6.4 + - - +
61B HIS* 3.0 45.5 + - + +
140B ASP* 4.1 18.2 - - - +
143B ARG* 5.8 1.4 + - - -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU* 2.7 30.7 - - - +
26B ALA* 4.2 8.9 - - + +
27B SER* 3.8 12.6 - - - -
30B TYR* 4.0 17.0 - - + -
54B HIS* 3.2 21.1 + - - +
57B GLU* 1.3 79.9 - - - +
59B ARG* 1.3 58.4 + - - +
61B HIS* 3.1 11.2 + - - +
62B ALA* 3.0 25.8 + - - +
103B GLU* 3.4 15.0 - - - +
106B VAL* 4.9 0.8 - - - +
176B MG 2.0 32.6 - - - -
177B MG 2.6 25.2 - - - -
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.9 12.1 - - + -
27B SER* 3.6 13.8 + - - +
55B SER 3.1 17.6 + - - +
56B HIS* 3.6 9.2 - - + +
57B GLU 3.1 0.2 - - - -
58B GLU* 1.3 74.8 - - - +
60B GLU* 1.3 64.7 + - - +
62B ALA* 3.2 8.8 + - - +
63B GLU* 3.1 36.1 + - + +
56F HIS* 6.0 2.9 - - + +
59F ARG* 5.7 9.9 - - + -
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B HIS 3.1 14.9 + - - +
57B GLU* 3.2 10.9 + - - +
59B ARG* 1.3 77.2 - - - +
61B HIS* 1.3 60.5 + - + +
63B GLU* 3.5 11.6 + - - +
64B LYS* 3.1 32.2 + - - +
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Residues in contact with HIS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU* 3.4 16.2 - - - +
57B GLU* 3.0 31.8 + - + +
58B GLU* 3.1 17.7 + - - +
59B ARG 3.2 0.2 - - - -
60B GLU* 1.3 77.3 - - + +
62B ALA* 1.3 64.3 + - - +
64B LYS* 3.4 18.3 + - - +
65B PHE* 3.3 13.2 + - - -
132B GLU 4.6 6.5 + - - -
133B TYR* 3.0 39.4 + + + -
136B GLU* 5.1 13.9 - - + +
137B GLN* 5.1 0.9 - - - -
140B ASP* 5.6 0.4 - - - -
176B MG 2.7 24.4 - - - -
177B MG 4.3 10.5 - - - -
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.7 16.9 - - + +
23B GLU* 3.8 9.8 - - + +
24B LEU* 3.7 34.8 - - + -
58B GLU 3.0 11.9 + - - +
59B ARG 3.5 9.2 - - - +
61B HIS* 1.3 76.8 - - - +
63B GLU* 1.3 62.9 + - + +
65B PHE* 3.3 8.5 + - - +
66B MET* 3.1 26.5 + - + +
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 6.4 0.4 - - + -
59B ARG* 3.1 26.0 + - + +
60B GLU* 3.8 11.9 - - - +
61B HIS 3.3 0.2 - - - -
62B ALA* 1.3 75.5 - - + +
64B LYS* 1.3 63.8 + - - +
66B MET* 3.2 23.8 + - + +
67B LYS* 3.1 25.1 + - - +
31F SER* 4.8 5.1 + - - +
34F TYR* 5.1 11.1 - - + -
52F LYS* 3.6 20.9 + - - +
55F SER* 4.4 5.5 + - - -
56F HIS* 3.0 35.0 + - - -
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Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU* 3.1 20.1 + - - +
61B HIS* 3.6 18.4 - - - +
62B ALA 3.3 0.4 - - - -
63B GLU* 1.3 76.5 - - - +
65B PHE* 1.3 58.0 + - - +
67B LYS* 3.5 7.1 + - - +
68B TYR* 2.9 27.4 + - - +
128B PHE* 3.7 10.5 - - + -
132B GLU* 2.9 52.3 + - + +
133B TYR* 3.2 22.2 - - + +
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 3.9 29.6 - - + +
19B MET* 3.4 32.3 - - + -
20B LEU* 4.2 19.0 - - + +
23B GLU* 4.1 14.8 - - + -
61B HIS 3.3 16.7 + - - -
62B ALA 3.3 7.5 + - - +
63B GLU 3.2 0.6 - - - -
64B LYS* 1.3 78.0 - - - +
66B MET* 1.3 64.6 + - - +
68B TYR* 3.5 3.2 - + + +
69B GLN* 3.0 24.8 + - - +
110B LEU* 4.0 11.2 - - + -
113B LEU* 4.5 8.3 - - + -
125B LEU* 5.3 0.2 - - + -
128B PHE* 3.5 24.9 - + - -
129B LEU* 4.0 12.8 - - + -
133B TYR* 3.4 31.4 - + - -
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Residues in contact with MET 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.8 30.5 - - + +
24B LEU* 5.1 7.2 - - + -
62B ALA* 3.1 20.9 + - + +
63B GLU* 3.2 22.9 + - + +
65B PHE* 1.3 76.4 - - - +
67B LYS* 1.3 61.4 + - - +
69B GLN* 3.4 5.0 - - - +
70B ASN* 3.3 27.2 + - - +
76B VAL* 3.9 20.7 - - + +
78B LEU* 4.7 7.4 - - + -
28F TYR* 5.5 0.4 - - + -
31F SER* 3.3 39.9 - - - +
34F TYR* 4.5 15.5 - - + -
35F ALA* 4.3 13.0 - - + -
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU 3.1 9.6 + - - +
64B LYS* 3.6 11.0 - - - +
66B MET* 1.3 79.0 - - - +
68B TYR* 1.3 59.2 + - - +
70B ASN* 3.5 3.3 + - - +
71B LYS* 3.0 43.7 + - + +
34F TYR* 3.3 28.9 + - - +
38F ASP* 3.1 33.3 + - - +
45F HIS* 5.0 4.9 + - - -
49F GLU* 5.7 2.2 - - - -
142V LYS* 6.0 0.6 - - - +
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Residues in contact with TYR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TYR* 3.9 18.6 - + - -
16B VAL* 4.6 8.1 - - + -
64B LYS 2.9 18.6 + - - +
65B PHE* 3.5 6.3 - - - +
67B LYS* 1.3 75.0 - - - +
69B GLN* 1.3 69.3 + - - +
71B LYS* 3.1 17.4 + - + +
72B ARG* 2.8 52.1 + - + +
124B HIS* 2.8 41.8 + + - -
125B LEU* 3.2 36.0 - - + -
128B PHE* 3.6 42.8 - + + -
135V GLU* 5.4 0.4 - - - -
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TYR* 3.0 36.2 + - - -
13B GLU* 3.2 28.6 + - - +
16B VAL* 3.5 13.8 - - + +
17B ASN* 3.4 19.6 + - - -
20B LEU* 6.0 0.7 - - + -
65B PHE 3.0 14.4 + - - +
66B MET 3.4 6.7 - - - +
68B TYR* 1.3 82.5 - - - +
70B ASN* 1.3 60.9 + - - +
72B ARG* 3.2 4.5 + - - +
73B GLY 3.1 3.8 + - - -
74B GLY* 2.9 43.4 + - - -
75B ARG 4.0 6.3 - - - -
76B VAL* 3.7 23.6 - - + +
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Residues in contact with ASN 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 4.5 0.9 - - - +
66B MET 3.3 12.3 + - - -
67B LYS 3.9 3.1 - - - +
69B GLN* 1.3 76.5 - - - +
71B LYS* 1.3 65.7 + - - +
73B GLY* 3.2 10.7 + - - -
74B GLY 3.9 12.0 - - - +
75B ARG* 4.8 1.7 + - - +
76B VAL* 4.6 9.3 + - - +
34F TYR* 6.3 0.2 - - - -
35F ALA* 3.0 30.3 + - - +
38F ASP* 3.2 39.2 + - - +
39F ARG* 3.3 28.6 - - - +
40F ASP* 4.9 3.5 + - - +
142V LYS* 3.3 16.9 - - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 3.4 17.3 - - - +
67B LYS* 3.0 29.3 + - + +
68B TYR* 3.1 23.0 + - + +
70B ASN* 1.3 75.7 - - - +
72B ARG* 1.3 64.2 + - + +
124B HIS* 5.4 0.2 - - + -
128B PHE* 6.2 3.0 - - - -
135V GLU* 2.8 35.5 + - - +
138V VAL* 4.3 24.8 - - + +
139V LYS* 4.6 12.0 - - - +
141V ILE* 5.9 0.2 - - - +
142V LYS* 4.1 27.9 - - + +
----------------------------------------------------------
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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