Contacts of the helix formed by residues 45 - 71 (chain T) 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 T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P LYS* 5.0 4.1 + - - -
37T PHE 4.6 1.6 - - - -
38T ASP* 3.4 44.9 + - - -
43T ALA* 3.3 14.2 + - + -
44T LEU* 1.3 68.4 - - - +
46T ASN* 1.3 65.7 + - - +
48T ALA* 3.5 7.4 - - - +
49T GLU* 3.1 30.5 + - + +
167T ASP* 3.6 3.2 + - - +
142U LYS* 4.0 2.5 - - - -
146U ASP* 3.0 34.4 + - + -
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Residues in contact with ASN 46 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T HIS* 1.3 79.2 - - - +
47T VAL* 1.3 65.7 + - - +
49T GLU* 3.3 8.3 + - - +
50T PHE 3.0 17.2 + - - -
167T ASP* 2.9 46.2 + - - +
168T LYS* 4.4 10.9 - - - +
171T VAL* 3.2 28.4 - - + +
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Residues in contact with VAL 47 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T PHE* 3.9 20.9 - - + -
44T LEU* 3.5 19.3 - - + +
45T HIS 3.3 0.2 - - - -
46T ASN* 1.3 76.6 - - - +
48T ALA* 1.3 62.1 + - - +
50T PHE* 3.2 9.1 + - - +
51T PHE* 3.2 45.5 + - + -
92T THR* 4.1 25.6 - - + +
96T MET* 4.6 4.5 - - + -
163T GLU 5.8 0.4 - - - +
166T PHE* 4.3 13.7 - - + -
167T ASP* 3.1 22.5 + - + +
171T VAL* 4.4 4.5 - - + +
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Residues in contact with ALA 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34T TYR* 3.2 40.1 - - + +
37T PHE* 3.7 24.2 - - + +
38T ASP* 4.1 3.8 - - + +
44T LEU 3.0 13.8 + - - +
45T HIS* 3.5 15.5 - - - +
46T ASN 3.2 0.2 - - - -
47T VAL* 1.3 77.8 - - - +
49T GLU* 1.3 56.6 + - - +
51T PHE* 3.4 2.2 + - - -
52T LYS 3.0 21.1 + - - -
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Residues in contact with GLU 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P LYS* 5.8 1.6 - - - -
34T TYR* 3.6 23.4 + - - -
45T HIS* 3.1 18.4 + - + +
46T ASN* 3.3 11.4 + - - +
48T ALA* 1.3 74.0 - - - +
50T PHE* 1.3 60.8 + - - +
52T LYS* 3.6 25.2 + - - +
53T GLU* 2.9 39.3 + - - +
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Residues in contact with PHE 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30T TYR* 5.9 0.4 - + - -
46T ASN 3.0 12.6 + - - +
47T VAL* 3.2 10.7 + - - +
49T GLU* 1.3 77.1 - - - +
51T PHE* 1.3 94.9 + + - +
53T GLU* 3.5 9.0 + - + +
54T HIS* 3.2 55.0 + + - -
96T MET* 4.0 20.9 - - + -
143T ARG* 3.9 17.3 - - - -
144T ILE* 4.5 11.2 - - + -
147T PHE* 3.7 29.6 - + - -
171T VAL* 3.7 21.1 - - + +
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Residues in contact with PHE 51 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30T TYR* 3.6 48.9 - + - +
33T MET* 3.8 28.5 - - + -
34T TYR 4.0 4.7 - - - +
37T PHE* 3.7 22.4 - + - -
47T VAL* 3.2 37.9 + - + -
48T ALA 3.9 5.4 - - - +
50T PHE* 1.3 98.9 - + - +
52T LYS* 1.3 58.1 + - - +
54T HIS* 3.2 5.1 + - + +
55T SER* 2.9 24.4 + - - -
92T THR 5.7 0.2 - - - -
95T ALA* 4.1 12.6 - - + -
96T MET* 3.7 23.8 - - + -
99T ALA* 4.2 8.5 - - + -
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Residues in contact with LYS 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63P GLU* 3.6 24.8 + - - +
34T TYR* 3.7 37.7 + - + +
48T ALA 3.0 16.8 + - - +
49T GLU* 3.6 34.4 + - - +
50T PHE 3.3 0.2 - - - -
51T PHE* 1.3 78.2 - - - +
53T GLU* 1.3 62.9 + - + +
55T SER* 3.2 21.1 + - - +
56T HIS* 3.3 30.3 + - + +
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Residues in contact with GLU 53 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49T GLU* 2.9 25.0 + - + +
50T PHE* 3.6 9.7 - - + +
51T PHE 3.2 0.2 - - - -
52T LYS* 1.3 79.2 - - + +
54T HIS* 1.3 62.8 - - + +
56T HIS* 3.3 10.9 + - - +
57T GLU* 3.1 36.2 + - - +
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Residues in contact with HIS 54 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30T TYR* 3.9 23.0 - + + -
50T PHE* 3.2 41.5 + + - +
51T PHE* 3.2 11.0 + - - +
53T GLU* 1.3 82.9 - - + +
55T SER* 1.3 63.1 + - - +
57T GLU* 3.6 18.3 + - - +
58T GLU* 3.2 32.6 + - - +
103T GLU* 3.6 17.9 + - - -
140T ASP* 3.7 26.2 - - + -
143T ARG* 3.1 28.2 + - - -
144T ILE* 4.9 4.5 - - + -
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Residues in contact with SER 55 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63P GLU* 4.4 5.4 + - - -
27T SER* 2.9 46.2 + - - +
30T TYR* 3.7 14.8 - - - +
31T SER* 3.8 14.3 - - - -
34T TYR* 5.8 0.2 - - - +
51T PHE 2.9 9.2 + - - -
52T LYS* 3.2 16.3 + - - +
53T GLU 3.3 0.4 - - - -
54T HIS* 1.3 74.2 - - - +
56T HIS* 1.3 77.0 + - - +
58T GLU 3.4 1.4 + - - -
59T ARG* 3.1 12.5 + - - +
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Residues in contact with HIS 56 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59P ARG* 6.0 3.3 - - + +
63P GLU* 3.0 34.8 + - - -
52T LYS* 3.3 28.3 + - + +
53T GLU* 3.3 12.9 + - - +
54T HIS 3.2 0.2 - - - -
55T SER* 1.3 90.4 + - - +
57T GLU* 1.3 55.7 - - - +
59T ARG* 3.5 7.8 + - + +
60T GLU* 3.1 26.2 + - - +
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Residues in contact with GLU 57 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53T GLU* 3.1 21.9 + - - +
54T HIS* 3.6 25.2 + - - +
55T SER 3.2 0.2 - - - -
56T HIS* 1.3 76.0 - - + +
58T GLU* 1.3 64.1 + - + +
60T GLU* 3.2 6.9 + - - +
61T HIS* 2.9 45.2 + - + +
140T ASP* 4.1 17.7 - - - +
143T ARG* 5.8 1.6 + - - -
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Residues in contact with GLU 58 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23T GLU* 2.7 31.2 - - - +
26T ALA* 4.2 8.9 - - + +
27T SER* 3.8 13.0 - - - +
30T TYR* 4.0 16.8 - - + -
54T HIS* 3.2 20.8 + - - +
57T GLU* 1.3 80.0 - - - +
59T ARG* 1.3 58.1 + - - +
61T HIS* 3.1 11.2 + - - +
62T ALA* 3.0 26.5 + - - +
103T GLU* 3.4 15.2 - - - +
106T VAL* 4.9 0.8 - - - +
176T MG 2.0 32.5 - - - -
177T MG 2.6 25.0 - - - -
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Residues in contact with ARG 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P HIS* 6.0 3.4 - - + +
24T LEU* 4.9 11.7 - - + -
27T SER* 3.6 13.2 + - - +
55T SER 3.1 17.7 + - - +
56T HIS* 3.6 9.6 - - + +
58T GLU* 1.3 74.2 - - - +
60T GLU* 1.3 64.1 + - - +
62T ALA* 3.2 8.6 + - - +
63T GLU* 3.1 36.3 + - + +
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Residues in contact with GLU 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56T HIS 3.1 15.7 + - - +
57T GLU* 3.2 9.8 + - - +
59T ARG* 1.3 75.5 - - - +
61T HIS* 1.3 59.2 + - + +
63T GLU* 3.5 12.0 + - - +
64T LYS* 3.1 32.1 + - - +
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Residues in contact with HIS 61 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23T GLU* 3.4 15.9 - - - +
57T GLU* 2.9 30.6 + - + +
58T GLU* 3.1 18.1 + - - +
59T ARG 3.2 0.2 - - - -
60T GLU* 1.3 78.6 - - + +
62T ALA* 1.3 63.7 + - - +
64T LYS* 3.4 18.8 + - - +
65T PHE* 3.3 13.0 + - - -
132T GLU 4.6 7.2 + - - -
133T TYR* 3.0 39.9 + + + -
136T GLU* 5.1 13.9 - - + +
137T GLN* 5.1 0.9 - - - -
140T ASP* 5.6 0.2 - - - -
176T MG 2.7 23.4 - - - -
177T MG 4.3 10.3 - - - -
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Residues in contact with ALA 62 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T LEU* 3.7 16.2 - - + +
23T GLU* 3.8 9.8 - - + +
24T LEU* 3.7 35.0 - - + -
58T GLU 3.0 12.1 + - - +
59T ARG 3.2 8.5 + - - +
61T HIS* 1.3 76.4 - - - +
63T GLU* 1.3 63.3 + - + +
65T PHE* 3.3 8.8 + - - +
66T MET* 3.1 27.0 + - + +
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Residues in contact with GLU 63 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P SER* 4.8 5.7 + - - +
34P TYR* 5.1 10.3 + - + -
52P LYS* 3.6 21.4 - - - +
55P SER* 4.4 5.2 + - - -
56P HIS* 3.1 34.3 + - - -
24T LEU* 6.4 0.2 - - + -
59T ARG* 3.1 24.7 + - + +
60T GLU* 3.8 11.9 - - - +
62T ALA* 1.3 75.5 - - + +
64T LYS* 1.3 64.8 + - - +
66T MET* 3.2 24.9 + - + +
67T LYS* 3.1 24.3 + - - +
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Residues in contact with LYS 64 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60T GLU* 3.1 21.1 + - - +
61T HIS* 3.6 17.5 + - - +
62T ALA 3.3 0.2 - - - -
63T GLU* 1.3 76.3 - - - +
65T PHE* 1.3 57.2 - - - +
67T LYS* 3.5 7.8 + - - +
68T TYR* 2.9 27.0 + - - +
128T PHE* 3.7 10.4 - - + -
132T GLU* 2.9 54.0 + - + +
133T TYR* 3.2 21.1 - - + +
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Residues in contact with PHE 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16T VAL* 3.9 29.1 - - + +
19T MET* 3.4 32.8 - - + -
20T LEU* 4.2 18.1 - - + +
23T GLU* 4.1 14.8 - - + -
61T HIS 3.3 16.7 + - - -
62T ALA 3.3 8.0 + - - +
63T GLU 3.2 0.6 - - - -
64T LYS* 1.3 78.2 - - - +
66T MET* 1.3 63.8 + - - +
68T TYR* 3.5 3.6 - + + +
69T GLN* 3.0 24.3 + - - +
110T LEU* 4.0 11.9 - - + -
113T LEU* 4.5 7.9 - - + -
125T LEU* 5.3 0.4 - - + -
128T PHE* 3.5 25.8 - + - -
129T LEU* 4.0 11.2 - - + -
133T TYR* 3.4 30.1 - + - -
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Residues in contact with MET 66 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P TYR* 5.5 0.2 - - + -
31P SER* 3.3 39.9 - - - +
34P TYR* 4.5 15.5 - - + -
35P ALA* 4.3 13.0 - - + -
20T LEU* 3.8 29.1 - - + +
24T LEU* 5.1 7.6 - - + -
62T ALA* 3.1 20.9 + - + +
63T GLU* 3.2 23.1 + - + +
65T PHE* 1.3 75.8 - - - +
67T LYS* 1.3 62.2 + - - +
69T GLN* 3.4 4.7 - - - +
70T ASN* 3.3 27.2 + - - -
76T VAL* 3.9 21.4 - - + +
78T LEU* 4.7 8.1 - - + -
----------------------------------------------------------
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Residues in contact with LYS 67 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142L LYS* 5.9 0.8 - - - +
34P TYR* 3.3 30.0 - - - +
38P ASP* 3.1 32.5 + - - +
45P HIS* 5.0 5.1 + - - -
49P GLU* 5.8 1.8 - - - -
63T GLU 3.1 9.7 + - - +
64T LYS* 3.6 11.4 - - - +
66T MET* 1.3 78.9 - - - +
68T TYR* 1.3 57.5 + - - +
70T ASN* 3.5 3.3 + - - +
71T LYS* 3.0 44.8 + - + +
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Residues in contact with TYR 68 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L GLU* 5.7 0.2 - - - -
8T TYR* 3.9 18.6 - + - -
16T VAL* 4.6 7.6 - - + -
64T LYS 2.9 18.6 + - - +
65T PHE* 3.5 6.3 - - - +
67T LYS* 1.3 74.1 - - - +
69T GLN* 1.3 66.4 + - - +
71T LYS* 3.1 17.8 + - + +
72T ARG* 2.8 52.6 + - + +
124T HIS* 2.8 41.6 + + - -
125T LEU* 3.2 35.9 - - + -
128T PHE* 3.6 42.4 - + + -
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Residues in contact with GLN 69 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8T TYR* 3.0 35.4 + - - -
13T GLU* 3.2 27.5 + - - +
16T VAL* 3.5 15.2 - - + +
17T ASN* 3.4 18.8 + - - -
20T LEU* 5.8 1.0 - - + +
65T PHE 3.0 13.9 + - - +
66T MET 3.4 6.7 - - - +
68T TYR* 1.3 82.9 - - - +
70T ASN* 1.3 61.0 + - - +
72T ARG* 3.2 5.1 + - - +
73T GLY 3.1 3.5 + - - -
74T GLY* 2.9 42.8 + - - -
75T ARG 4.0 6.7 - - - -
76T VAL* 3.7 24.2 - - + +
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Residues in contact with ASN 70 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142L LYS* 3.3 17.4 - - - +
35P ALA* 3.0 30.9 + - - +
38P ASP* 3.2 38.8 + - - +
39P ARG* 3.3 28.7 - - - +
40P ASP* 4.9 3.5 + - - +
4T VAL* 4.5 0.9 - - - +
66T MET 3.3 13.3 + - - +
67T LYS 3.9 3.4 - - - +
69T GLN* 1.3 77.1 - - - +
71T LYS* 1.3 65.1 + - - +
73T GLY* 3.2 10.2 + - - -
74T GLY 3.9 11.9 - - - +
75T ARG* 4.0 1.9 + - - +
76T VAL* 4.6 9.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L GLU* 2.8 36.1 + - - +
138L VAL* 4.3 23.6 - - + +
139L LYS* 4.6 11.6 - - - +
142L LYS* 4.1 28.5 - - + +
4T VAL* 3.4 17.7 - - - +
67T LYS* 3.0 30.0 + - + +
68T TYR* 3.3 22.8 - - + +
70T ASN* 1.3 75.5 - - - +
72T ARG* 1.3 63.8 + - + +
128T 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