Contacts of the helix formed by residues 45 - 71 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 5.1 4.1 + - - -
37G PHE 4.6 1.6 - - - -
38G ASP* 3.4 45.1 + - - -
43G ALA* 3.3 15.3 + - + -
44G LEU* 1.3 69.0 - - - +
46G ASN* 1.3 65.2 + - - +
48G ALA* 3.5 6.1 - - - +
49G GLU* 3.1 30.4 + - + +
167G ASP* 3.6 3.4 + - - +
142H LYS* 4.0 2.9 - - - -
146H ASP* 3.0 34.3 + - + -
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Residues in contact with ASN 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G HIS* 1.3 77.7 - - - +
47G VAL* 1.3 65.4 + - - +
49G GLU* 3.3 9.1 + - - +
50G PHE 3.0 17.5 + - - -
167G ASP* 3.0 46.2 + - - +
168G LYS* 4.4 10.7 - - - +
171G VAL* 3.2 27.6 - - + +
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Residues in contact with VAL 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G PHE* 3.9 20.6 - - + -
44G LEU* 3.5 18.4 - - + +
46G ASN* 1.3 76.4 - - - +
48G ALA* 1.3 62.6 + - - +
50G PHE* 3.2 8.7 + - - +
51G PHE* 3.2 44.8 + - + -
92G THR* 4.1 26.2 - - + +
96G MET* 4.6 4.7 - - + -
163G GLU 5.8 0.2 - - - +
166G PHE* 4.3 13.0 - - + -
167G ASP* 3.1 22.3 + - + +
171G VAL* 4.6 4.7 - - + -
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Residues in contact with ALA 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G TYR* 3.2 39.9 - - + +
37G PHE* 3.7 24.7 - - + +
38G ASP* 4.1 4.3 - - + +
44G LEU 3.0 14.0 + - - +
45G HIS* 3.5 15.3 - - - +
46G ASN 3.2 0.2 - - - -
47G VAL* 1.3 77.7 - - - +
49G GLU* 1.3 57.1 + - - +
51G PHE* 3.4 1.8 + - - -
52G LYS 3.0 20.8 + - - -
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Residues in contact with GLU 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 5.8 1.4 - - - -
34G TYR* 3.6 24.1 + - - -
45G HIS* 3.1 18.6 + - + +
46G ASN* 3.3 10.7 + - - +
48G ALA* 1.3 74.9 - - - +
50G PHE* 1.3 61.8 + - - +
52G LYS* 3.3 24.0 + - - +
53G GLU* 2.9 39.3 + - - +
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Residues in contact with PHE 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G TYR* 5.9 0.4 - + - -
46G ASN 3.0 13.6 + - - +
47G VAL* 3.2 10.5 + - - +
49G GLU* 1.3 77.0 - - - +
51G PHE* 1.3 92.2 + + - +
53G GLU* 3.5 8.4 + - + +
54G HIS* 3.2 55.5 + + - -
96G MET* 4.0 21.5 - - + -
143G ARG* 3.9 18.2 - - - -
144G ILE* 4.5 12.1 - - + -
147G PHE* 3.7 28.3 - + - -
171G VAL* 3.7 19.9 - - + +
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Residues in contact with PHE 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G TYR* 3.6 49.3 - + - +
33G MET* 3.8 29.4 - - + -
34G TYR 4.0 4.0 - - - +
37G PHE* 3.7 23.1 - + - -
47G VAL* 3.2 36.8 + - + -
48G ALA* 3.9 5.8 - - - +
49G GLU 3.2 0.2 - - - -
50G PHE* 1.3 97.9 - + - +
52G LYS* 1.3 59.4 + - - +
54G HIS* 3.2 5.0 + - + +
55G SER* 2.9 24.8 + - - -
95G ALA* 4.1 12.3 - - + -
96G MET* 3.7 23.6 - - + -
99G ALA* 4.2 8.3 - - + -
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Residues in contact with LYS 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 3.7 25.2 + - - +
34G TYR* 3.7 38.1 + - + +
48G ALA 3.0 17.4 + - - +
49G GLU* 3.6 33.1 + - - +
50G PHE 3.3 0.2 - - - -
51G PHE* 1.3 76.9 - - - +
53G GLU* 1.3 62.1 + - + +
55G SER* 3.2 20.6 + - - +
56G HIS* 3.3 28.5 + - + +
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Residues in contact with GLU 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLU* 2.9 27.4 + - + +
50G PHE* 3.6 9.2 - - + +
52G LYS* 1.3 78.5 - - + +
54G HIS* 1.3 63.5 + - + +
56G HIS* 3.3 10.7 + - - +
57G GLU* 3.1 35.4 + - - +
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Residues in contact with HIS 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G TYR* 3.9 23.4 - + + -
50G PHE* 3.2 41.0 + + - +
51G PHE* 3.2 11.0 + - + +
53G GLU* 1.3 80.8 - - + +
55G SER* 1.3 63.3 + - - +
57G GLU* 3.4 16.9 + - - +
58G GLU* 3.2 32.1 + - - +
103G GLU* 3.6 18.0 + - - -
140G ASP* 3.7 26.2 - - + -
143G ARG* 3.1 28.0 + - - -
144G ILE* 4.9 4.9 - - + -
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Residues in contact with SER 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 4.4 5.0 + - - -
27G SER* 2.9 48.5 + - - +
30G TYR* 3.7 14.3 - - - +
31G SER* 3.8 15.2 - - - -
51G PHE 2.9 9.6 + - - -
52G LYS* 3.2 16.5 + - - +
53G GLU 3.3 0.2 - - - -
54G HIS* 1.3 74.6 - - - +
56G HIS* 1.3 76.4 + - - +
57G GLU 3.3 0.2 + - - -
58G GLU 3.4 1.0 + - - -
59G ARG* 3.1 11.7 + - - +
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Residues in contact with HIS 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 6.1 3.1 - - + +
63A GLU* 3.1 28.8 + - - -
52G LYS* 3.3 35.6 + - + +
53G GLU* 3.3 12.7 + - - +
54G HIS 3.2 0.4 - - - -
55G SER* 1.3 90.5 + - - +
57G GLU* 1.3 56.3 + - - +
59G ARG* 3.5 8.4 + - + +
60G GLU* 3.1 25.8 + - - +
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Residues in contact with GLU 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G GLU* 3.1 21.5 + - - +
54G HIS* 3.6 26.5 + - - +
55G SER 3.2 0.2 - - - -
56G HIS* 1.3 75.4 - - - +
58G GLU* 1.3 63.9 + - + +
60G GLU* 3.2 7.4 + - + +
61G HIS* 3.0 45.6 + - + +
140G ASP* 4.1 17.8 - - - +
143G ARG* 5.8 1.6 + - - -
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Residues in contact with GLU 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G GLU* 2.7 30.5 - - - +
26G ALA* 4.2 9.0 - - + -
27G SER* 3.8 12.3 - - - -
30G TYR* 4.0 17.3 - - + -
54G HIS* 3.2 21.5 + - - +
57G GLU* 1.3 80.1 - - - +
59G ARG* 1.3 58.6 + - - +
61G HIS* 3.1 10.3 + - - +
62G ALA* 3.0 25.8 + - - +
103G GLU* 3.4 15.0 - - - +
106G VAL* 4.9 0.8 - - - +
140G ASP* 4.4 0.2 - - - +
176G MG 2.0 32.4 - - - -
177G MG 2.6 24.9 - - - -
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Residues in contact with ARG 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 6.0 2.9 - - + +
59A ARG* 5.7 9.4 - - + -
24G LEU* 4.9 11.4 - - + -
27G SER* 3.6 14.5 + - - +
55G SER 3.1 17.1 + - - +
56G HIS* 3.6 10.5 - - + +
58G GLU* 1.3 74.1 - - - +
60G GLU* 1.3 65.0 + - - +
62G ALA* 3.2 8.9 + - - +
63G GLU* 3.1 35.8 + - + +
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Residues in contact with GLU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G HIS 3.1 15.3 + - - +
57G GLU* 3.6 10.3 - - - +
59G ARG* 1.3 76.5 - - - +
61G HIS* 1.3 59.5 + - + +
63G GLU* 3.5 12.6 + - - +
64G LYS* 3.1 32.4 + - - +
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Residues in contact with HIS 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G GLU* 3.4 16.4 + - - +
57G GLU* 3.0 30.3 + - + +
58G GLU* 3.1 18.4 + - - +
59G ARG 3.2 0.2 - - - -
60G GLU* 1.3 78.8 - - + +
62G ALA* 1.3 64.5 + - - +
64G LYS* 3.4 18.4 + - - -
65G PHE* 3.3 12.9 + - - -
132G GLU 4.6 7.0 + - - -
133G TYR* 3.0 39.7 + + + -
136G GLU* 5.1 13.9 - - + +
137G GLN* 5.1 1.1 - - - -
140G ASP* 5.6 0.2 - - - -
176G MG 2.7 24.0 - - - -
177G MG 4.3 10.3 - - - -
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Residues in contact with ALA 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G LEU* 3.7 16.2 - - + +
23G GLU* 3.8 10.3 - - + +
24G LEU* 3.7 35.9 - - + -
58G GLU 3.0 12.9 + - - +
59G ARG 3.2 8.7 + - - +
61G HIS* 1.3 76.3 - - - +
63G GLU* 1.3 64.7 + - + +
65G PHE* 3.3 8.7 + - - +
66G MET* 3.1 26.8 + - + +
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Residues in contact with GLU 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 4.9 5.0 + - - +
34A TYR* 5.1 10.7 + - + -
52A LYS* 3.6 21.7 + - - +
55A SER* 4.4 5.4 + - - -
56A HIS* 3.0 35.1 + - - -
24G LEU* 6.4 0.2 - - + -
59G ARG* 3.1 24.5 + - + +
60G GLU* 3.8 11.8 - - - +
61G HIS 3.3 0.2 - - - -
62G ALA* 1.3 76.3 - - + +
64G LYS* 1.3 63.8 + - - +
66G MET* 3.2 25.8 + - + +
67G LYS* 3.1 24.6 + - - +
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Residues in contact with LYS 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G GLU* 3.1 20.1 + - - +
61G HIS* 3.6 17.5 + - - +
62G ALA 3.3 0.4 - - - -
63G GLU* 1.3 76.5 - - - +
65G PHE* 1.3 57.6 + - - +
67G LYS* 3.5 7.7 + - - +
68G TYR* 2.9 27.0 + - - +
128G PHE* 3.7 9.9 - - + -
132G GLU* 2.9 52.7 + - + +
133G TYR* 3.2 22.2 - - + +
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Residues in contact with PHE 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G VAL* 3.9 29.0 - - + +
19G MET* 3.4 31.9 - - + -
20G LEU* 4.2 18.2 - - + -
23G GLU* 4.1 15.5 - - + -
61G HIS 3.3 16.7 + - - -
62G ALA 3.3 8.6 + - - +
63G GLU 3.2 0.6 - - - -
64G LYS* 1.3 78.2 - - - +
66G MET* 1.3 64.6 + - - +
68G TYR* 3.5 3.9 - + + +
69G GLN* 3.0 24.8 + - - +
110G LEU* 4.0 11.7 - - + -
113G LEU* 4.5 7.9 - - + -
125G LEU* 5.3 0.2 - - + -
128G PHE* 3.5 25.6 - + - -
129G LEU* 4.0 11.9 - - + -
133G TYR* 3.4 30.5 - + - -
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Residues in contact with MET 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 5.6 0.4 - - + -
31A SER* 3.3 40.6 - - - +
34A TYR* 4.5 15.7 - - + -
35A ALA* 4.3 13.0 - - + -
20G LEU* 3.8 29.6 - - + +
24G LEU* 5.1 7.4 - - + -
62G ALA* 3.1 21.8 + - + +
63G GLU* 3.2 23.5 + - + +
65G PHE* 1.3 76.1 - - - +
67G LYS* 1.3 61.3 + - - +
69G GLN* 3.4 5.1 - - - +
70G ASN* 3.3 26.8 + - - -
76G VAL* 3.9 21.2 - - + +
78G LEU* 4.7 7.9 - - + -
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Residues in contact with LYS 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.3 29.8 - - - +
38A ASP* 3.2 32.5 + - - +
45A HIS* 5.1 5.1 + - - -
49A GLU* 5.8 1.8 - - - -
63G GLU 3.1 8.9 + - - +
64G LYS* 3.6 11.7 - - - +
66G MET* 1.3 79.6 - - - +
68G TYR* 1.3 59.3 + - - +
70G ASN* 3.5 3.3 + - - +
71G LYS* 3.0 44.3 + - + +
142O LYS* 6.0 0.4 - - - +
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Residues in contact with TYR 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G TYR* 3.9 18.6 - + - -
16G VAL* 4.6 7.6 - - + -
64G LYS 2.9 17.9 + - - +
65G PHE* 3.5 6.5 - - - +
66G MET 3.2 0.2 - - - -
67G LYS* 1.3 72.8 - - - +
69G GLN* 1.3 68.5 - - - +
71G LYS* 3.1 17.3 + - + +
72G ARG* 2.8 52.5 + - + +
124G HIS* 2.8 41.6 + + - -
125G LEU* 3.2 36.0 - - + -
128G PHE* 3.6 44.0 - + + -
135O GLU* 5.6 0.2 - - - -
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Residues in contact with GLN 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G TYR* 3.0 36.4 + - - -
13G GLU* 3.2 27.7 + - - +
16G VAL* 3.5 14.5 - - + +
17G ASN* 3.4 18.4 + - - -
20G LEU* 5.8 1.1 - - + +
65G PHE 3.0 14.1 + - - +
66G MET 3.4 6.5 - - - +
68G TYR* 1.3 83.1 - - - +
70G ASN* 1.3 60.4 + - - +
72G ARG* 3.2 5.2 + - - +
73G GLY 3.1 3.5 + - - -
74G GLY* 2.9 44.2 + - - +
75G ARG 4.0 6.5 - - - -
76G VAL* 3.7 24.5 - - + +
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Residues in contact with ASN 70 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 6.3 0.4 - - - -
35A ALA* 3.1 30.2 + - - +
38A ASP* 3.1 39.7 + - - +
39A ARG* 3.3 27.3 - - - +
40A ASP* 4.9 3.3 + - - +
4G VAL* 4.5 0.7 - - - +
66G MET 3.3 12.5 + - - -
67G LYS 3.9 3.1 - - - +
69G GLN* 1.3 76.1 - - - +
71G LYS* 1.3 65.3 + - - +
73G GLY* 3.2 10.4 + - - -
74G GLY 3.9 11.6 - - - +
75G ARG* 4.0 1.9 + - - +
76G VAL* 4.6 9.5 + - - +
142O LYS* 3.2 17.4 - - - +
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Residues in contact with LYS 71 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G VAL* 3.4 17.3 - - - +
67G LYS* 3.0 29.4 + - + +
68G TYR* 3.1 22.8 + - + +
70G ASN* 1.3 76.6 - - - +
72G ARG* 1.3 62.6 + - + +
128G PHE* 6.2 2.2 - - - -
135O GLU* 2.8 36.0 + - - +
138O VAL* 4.3 24.4 - - + +
139O LYS* 4.5 11.6 - - - +
142O LYS* 4.1 27.4 - - + +
----------------------------------------------------------
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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