Contacts of the helix formed by residues 45 - 71 (chain U) 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 U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142N LYS* 4.0 2.9 - - - -
146N ASP* 3.1 34.1 + - + -
67Q LYS* 5.0 5.1 + - - -
37U PHE 4.6 1.6 - - - -
38U ASP* 3.4 43.8 + - - -
43U ALA* 3.3 15.5 + - + -
44U LEU* 1.3 69.0 - - - +
46U ASN* 1.3 64.1 + - - +
48U ALA* 3.5 6.9 + - - +
49U GLU* 3.1 30.2 + - + +
167U ASP* 3.6 3.8 + - - +
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Residues in contact with ASN 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45U HIS* 1.3 78.1 - - - +
47U VAL* 1.3 65.8 + - - +
49U GLU* 3.3 8.6 + - - +
50U PHE 3.0 17.7 + - - -
167U ASP* 3.0 45.8 + - - +
168U LYS* 4.4 11.1 - - - +
171U VAL* 3.2 27.4 - - + +
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Residues in contact with VAL 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37U PHE* 3.9 20.4 - - + -
44U LEU* 3.5 17.9 - - + +
46U ASN* 1.3 77.4 - - - +
48U ALA* 1.3 62.0 + - - +
50U PHE* 3.2 9.0 + - - +
51U PHE* 3.2 45.1 + - + -
92U THR* 4.1 25.4 - - + +
96U MET* 4.6 4.9 - - + -
163U GLU 5.8 0.4 - - - +
166U PHE* 4.3 13.2 - - + -
167U ASP* 3.1 22.5 + - + +
171U VAL* 4.6 4.5 - - + -
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Residues in contact with ALA 48 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34U TYR* 3.2 40.3 - - + +
37U PHE* 3.7 24.7 - - + +
38U ASP* 4.1 4.3 - - + +
44U LEU 3.0 14.3 + - - +
45U HIS* 3.5 15.0 - - - +
47U VAL* 1.3 77.2 - - - +
49U GLU* 1.3 58.0 + - - +
51U PHE* 3.4 1.9 + - - -
52U LYS 3.0 21.5 + - - -
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Residues in contact with GLU 49 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67Q LYS* 5.8 1.6 - - - -
34U TYR* 3.6 23.7 + - - -
45U HIS* 3.1 18.8 + - + +
46U ASN* 3.3 11.0 + - - +
48U ALA* 1.3 74.7 - - - +
50U PHE* 1.3 60.1 + - - +
51U PHE 3.2 0.2 - - - -
52U LYS* 3.6 24.5 + - - +
53U GLU* 2.9 40.3 + - - +
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Residues in contact with PHE 50 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U TYR* 5.9 0.2 - + - -
46U ASN 3.0 13.0 + - - +
47U VAL* 3.2 10.7 + - - +
49U GLU* 1.3 78.0 - - - +
51U PHE* 1.3 91.9 + + - +
53U GLU* 3.5 8.6 + - + +
54U HIS* 3.2 55.8 + + - -
96U MET* 4.0 20.2 - - + -
143U ARG* 3.9 17.0 - - - -
144U ILE* 4.5 12.6 - - + -
147U PHE* 3.7 29.4 - + - -
171U VAL* 3.7 20.2 - - + -
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Residues in contact with PHE 51 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U TYR* 3.6 49.2 - + + +
33U MET* 3.8 30.3 - - + -
34U TYR 4.0 4.7 - - - +
37U PHE* 3.7 22.7 - + - -
47U VAL* 3.2 37.0 + - + -
48U ALA* 3.9 5.4 - - - +
50U PHE* 1.3 99.4 - + - +
52U LYS* 1.3 59.2 + - - +
54U HIS* 3.2 5.4 + - + +
55U SER* 2.9 23.7 + - - -
92U THR 5.7 0.2 - - - -
95U ALA* 4.1 11.7 - - + -
96U MET* 3.7 23.8 - - + -
99U ALA* 4.2 8.5 - - + -
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Residues in contact with LYS 52 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q GLU* 3.6 24.8 + - - +
34U TYR* 3.7 38.4 + - + +
48U ALA 3.0 17.1 + - - +
49U GLU* 3.6 34.6 + - - +
51U PHE* 1.3 76.6 - - - +
53U GLU* 1.3 63.0 + - + +
55U SER* 3.2 21.3 + - - +
56U HIS* 3.3 29.3 + - + +
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Residues in contact with GLU 53 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49U GLU* 2.9 26.3 + - + +
50U PHE* 3.6 9.2 - - + +
51U PHE 3.2 0.2 - - - -
52U LYS* 1.3 77.9 - - + +
54U HIS* 1.3 63.4 + - + +
56U HIS* 3.3 10.0 + - - +
57U GLU* 3.1 35.5 + - - +
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Residues in contact with HIS 54 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U TYR* 3.9 22.7 - + + -
50U PHE* 3.2 40.4 + + - +
51U PHE* 3.4 11.0 - - + +
53U GLU* 1.3 82.3 - - + +
55U SER* 1.3 63.9 + - - +
57U GLU* 3.4 18.4 + - - +
58U GLU* 3.2 32.1 + - - +
103U GLU* 3.6 18.1 + - - -
140U ASP* 3.7 26.0 - - + -
143U ARG* 3.1 27.6 + - - -
144U ILE* 4.9 4.9 - - + -
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Residues in contact with SER 55 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q GLU* 4.4 5.2 + - - -
27U SER* 2.9 48.0 + - - +
30U TYR* 3.7 14.5 - - - +
31U SER* 3.8 14.3 + - - -
51U PHE 2.9 8.7 + - - -
52U LYS* 3.2 16.6 + - - +
53U GLU 3.3 0.2 - - - -
54U HIS* 1.3 74.9 - - - +
56U HIS* 1.3 76.4 + - - +
58U GLU 3.4 1.2 + - - -
59U ARG* 3.1 11.8 + - - +
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Residues in contact with HIS 56 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59Q ARG* 6.0 3.5 - - + +
63Q GLU* 3.0 34.4 + - - -
52U LYS* 3.4 28.5 + - + +
53U GLU* 3.3 11.7 + - - +
54U HIS 3.2 0.4 - - - -
55U SER* 1.3 90.6 + - - +
57U GLU* 1.3 55.5 + - - +
59U ARG* 3.5 7.8 + - + +
60U GLU* 3.1 26.5 + - - +
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Residues in contact with GLU 57 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53U GLU* 3.1 21.3 + - - +
54U HIS* 3.6 25.0 + - - +
55U SER 3.2 0.2 - - - -
56U HIS* 1.3 74.1 - - - +
58U GLU* 1.3 63.6 + - + +
60U GLU* 3.2 7.7 + - + +
61U HIS* 2.9 45.7 + - + +
140U ASP* 4.1 17.5 - - - +
143U ARG* 5.8 1.6 + - - -
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Residues in contact with GLU 58 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U GLU* 2.7 30.1 - - - +
26U ALA* 4.2 9.4 - - + -
27U SER* 3.8 13.2 - - - +
30U TYR* 4.0 15.9 - - + -
54U HIS* 3.2 21.4 + - - +
55U SER 3.4 0.2 + - - -
57U GLU* 1.3 81.1 - - - +
59U ARG* 1.3 57.7 + - - +
61U HIS* 3.1 11.1 + - - +
62U ALA* 3.0 25.5 + - - +
103U GLU* 3.4 15.0 - - - +
106U VAL* 4.9 1.1 - - - +
176U MG 2.0 32.3 - - - -
177U MG 2.6 24.8 - - - -
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Residues in contact with ARG 59 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56Q HIS* 6.0 3.1 - - + +
24U LEU* 4.9 12.3 - - + +
27U SER* 3.6 13.8 + - - +
55U SER 3.1 17.7 + - - +
56U HIS* 3.6 10.1 - - + +
58U GLU* 1.3 75.8 - - - +
60U GLU* 1.3 62.4 + - - +
62U ALA* 3.2 8.4 + - - +
63U GLU* 3.1 36.3 + - + +
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Residues in contact with GLU 60 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56U HIS 3.1 14.3 + - - +
57U GLU* 3.2 10.7 + - + +
59U ARG* 1.3 75.5 - - - +
61U HIS* 1.3 59.9 + - + +
63U GLU* 3.5 12.7 + - - +
64U LYS* 3.1 32.8 + - - +
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Residues in contact with HIS 61 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U GLU* 3.4 15.5 - - - +
57U GLU* 2.9 30.9 + - + +
58U GLU* 3.1 18.1 + - - +
59U ARG 3.2 0.4 - - - -
60U GLU* 1.3 77.8 - - + +
62U ALA* 1.3 63.4 + - - +
64U LYS* 3.4 17.7 + - - -
65U PHE* 3.3 13.0 + - - -
132U GLU 4.6 6.7 + - - -
133U TYR* 3.0 40.4 + + + -
136U GLU* 5.1 12.9 - - + +
137U GLN* 5.1 1.3 - - - -
140U ASP* 5.6 0.4 - - - -
176U MG 2.7 23.8 - - - -
177U MG 4.3 10.5 - - - -
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Residues in contact with ALA 62 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U LEU* 3.7 16.6 - - + +
23U GLU* 3.8 9.6 - - + +
24U LEU* 3.7 34.3 - - + -
58U GLU 3.0 12.5 + - - +
59U ARG 3.5 8.5 - - - +
61U HIS* 1.3 75.4 - - - +
63U GLU* 1.3 64.3 + - + +
65U PHE* 3.3 8.7 + - - +
66U MET* 3.1 27.2 + - + +
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Residues in contact with GLU 63 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q SER* 4.8 5.1 + - - +
34Q TYR* 5.1 11.0 - - + -
52Q LYS* 3.6 20.5 + - - +
55Q SER* 4.4 5.7 + - - -
56Q HIS* 3.1 33.4 + - - -
24U LEU* 6.4 0.2 - - + -
59U ARG* 3.1 25.3 + - + +
60U GLU* 3.8 11.6 - - - +
62U ALA* 1.3 75.3 - - + +
64U LYS* 1.3 64.4 + - - +
66U MET* 3.2 25.1 + - + +
67U LYS* 3.1 23.7 + - - +
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Residues in contact with LYS 64 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60U GLU* 3.1 20.4 + - - +
61U HIS* 3.6 17.8 + - - +
62U ALA 3.3 0.6 - - - -
63U GLU* 1.3 76.4 - - - +
65U PHE* 1.3 57.4 + - - +
67U LYS* 3.5 8.1 + - - +
68U TYR* 2.9 27.0 + - - +
128U PHE* 3.7 9.5 - - + -
132U GLU* 2.9 52.4 + - + +
133U TYR* 3.2 22.0 - - + +
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Residues in contact with PHE 65 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U VAL* 3.9 30.3 - - + +
19U MET* 3.4 33.0 - - + -
20U LEU* 4.2 18.3 - - + +
23U GLU* 4.1 14.8 - - + -
61U HIS 3.3 17.1 + - - -
62U ALA 3.3 8.8 + - - +
63U GLU 3.2 0.4 - - - -
64U LYS* 1.3 77.4 - - - +
66U MET* 1.3 63.1 + - - +
68U TYR* 3.5 3.2 - - + +
69U GLN* 3.0 24.8 + - - +
110U LEU* 4.0 11.2 - - + -
113U LEU* 4.5 7.4 - - + -
125U LEU* 5.3 0.2 - - + -
128U PHE* 3.5 25.4 - + - -
129U LEU* 4.0 12.1 - - + -
133U TYR* 3.4 30.7 - + - -
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Residues in contact with MET 66 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q TYR* 5.5 0.4 - - + -
31Q SER* 3.3 39.9 - - - +
34Q TYR* 4.5 14.8 - - + -
35Q ALA* 4.3 14.1 - - + -
20U LEU* 3.8 29.1 - - + +
24U LEU* 5.1 7.9 - - + -
62U ALA* 3.1 21.1 + - + +
63U GLU* 3.2 22.4 + - + +
65U PHE* 1.3 75.3 - - - +
67U LYS* 1.3 62.2 + - - +
69U GLN* 3.4 4.7 - - - +
70U ASN* 3.3 27.0 + - - -
76U VAL* 3.9 21.0 - - + +
78U LEU* 4.7 8.1 - - + -
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Residues in contact with LYS 67 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142K LYS* 6.0 0.6 - - - +
34Q TYR* 3.3 29.6 - - - +
38Q ASP* 3.1 33.4 + - - +
45Q HIS* 5.0 5.3 + - - -
49Q GLU* 5.8 1.1 - - - -
63U GLU 3.1 9.5 + - - +
64U LYS* 3.6 11.7 - - - +
66U MET* 1.3 78.4 - - - +
68U TYR* 1.3 57.3 + - - +
70U ASN* 3.5 3.5 + - - +
71U LYS* 3.0 44.5 + - + +
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Residues in contact with TYR 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135K GLU* 5.7 0.2 - - - -
8U TYR* 3.9 18.4 - + - -
16U VAL* 4.6 8.1 - - + -
64U LYS 2.9 18.3 + - - +
65U PHE* 3.5 6.5 - - - +
67U LYS* 1.3 75.3 - - - +
69U GLN* 1.3 67.5 + - - +
71U LYS* 3.1 17.2 + - + +
72U ARG* 2.8 51.3 + - + +
124U HIS* 2.8 42.4 + + - -
125U LEU* 3.2 35.9 - - + -
128U PHE* 3.6 43.1 - + + -
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Residues in contact with GLN 69 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8U TYR* 3.0 36.1 + - - -
13U GLU* 3.2 27.7 + - - +
16U VAL* 3.5 14.4 - - + +
17U ASN* 3.4 18.6 + - - -
20U LEU* 5.8 1.1 - - + +
65U PHE 3.0 14.8 + - - +
66U MET 3.4 7.0 - - - +
68U TYR* 1.3 82.3 - - - +
70U ASN* 1.3 61.1 + - - +
72U ARG* 3.2 5.0 + - - +
73U GLY 3.1 3.6 + - - -
74U GLY* 2.9 42.5 + - - -
75U ARG 4.0 7.0 - - - -
76U VAL* 3.7 23.6 - - + +
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Residues in contact with ASN 70 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142K LYS* 3.3 17.6 - - - +
35Q ALA* 3.0 30.3 + - - +
38Q ASP* 3.2 39.2 + - - +
39Q ARG* 3.2 28.2 - - - +
40Q ASP* 4.8 3.6 + - - +
4U VAL* 4.5 0.9 - - - +
66U MET 3.3 12.9 + - - -
67U LYS 3.9 3.4 - - - +
69U GLN* 1.3 77.2 - - - +
71U LYS* 1.3 65.7 + - - +
73U GLY* 3.2 10.0 + - - -
74U GLY 3.9 12.4 - - - +
75U ARG* 4.0 1.9 + - - +
76U VAL* 4.6 9.2 + - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135K GLU* 2.8 36.8 + - - +
138K VAL* 4.3 24.2 - - + +
139K LYS* 4.6 12.0 - - - +
142K LYS* 4.2 28.4 - - + +
4U VAL* 3.4 17.5 - - - +
67U LYS* 3.0 28.0 + - + +
68U TYR* 3.1 22.7 + - + +
70U ASN* 1.3 75.8 - - - +
72U ARG* 1.3 62.4 + - + +
124U HIS* 5.4 0.2 - - + -
128U PHE* 6.2 2.4 - - - -
----------------------------------------------------------
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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