Contacts of the helix formed by residues 45 - 71 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M LYS* 5.1 5.1 + - - -
37S PHE 4.6 1.8 - - - -
38S ASP* 3.4 44.0 + - - -
43S ALA* 3.3 16.1 + - + -
44S LEU* 1.3 68.7 - - - +
46S ASN* 1.3 65.2 + - - +
48S ALA* 3.5 6.8 - - - +
49S GLU* 3.1 31.0 + - + +
167S ASP* 3.6 3.4 + - - +
142T LYS* 4.0 3.1 - - - -
146T ASP* 3.0 33.5 + - + -
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Residues in contact with ASN 46 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S HIS* 1.3 77.1 - - - +
47S VAL* 1.3 65.6 + - - +
49S GLU* 3.3 8.6 + - - +
50S PHE 3.0 17.8 + - - -
167S ASP* 3.0 46.0 + - - +
168S LYS* 4.4 10.7 - - - +
171S VAL* 3.2 28.7 - - + +
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Residues in contact with VAL 47 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S PHE* 3.9 20.0 - - + -
44S LEU* 3.5 17.9 - - + +
46S ASN* 1.3 76.8 - - - +
48S ALA* 1.3 61.9 + - - +
50S PHE* 3.2 9.5 + - - +
51S PHE* 3.2 45.6 + - + -
92S THR* 4.1 26.5 - - + +
96S MET* 4.6 4.3 - - + -
163S GLU 5.8 0.2 - - - +
166S PHE* 4.3 12.8 - - + -
167S ASP* 3.1 23.2 + - + +
171S VAL* 4.6 4.7 - - + -
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Residues in contact with ALA 48 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34S TYR* 3.2 40.3 - - + +
37S PHE* 3.7 23.5 - - + +
38S ASP* 4.1 4.7 - - + +
44S LEU 3.0 14.2 + - - +
45S HIS* 3.5 15.5 - - - +
46S ASN 3.2 0.2 - - - -
47S VAL* 1.3 77.4 - - - +
49S GLU* 1.3 58.0 + - - +
51S PHE* 3.4 2.1 + - - -
52S LYS 3.0 21.1 + - - -
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Residues in contact with GLU 49 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M LYS* 5.8 1.6 - - - -
34S TYR* 3.6 23.6 + - - -
45S HIS* 3.1 18.9 + - + +
46S ASN* 3.3 11.0 + - - +
48S ALA* 1.3 75.0 - - - +
50S PHE* 1.3 61.3 + - - +
52S LYS* 3.6 23.7 + - - +
53S GLU* 2.9 40.1 + - - +
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Residues in contact with PHE 50 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S TYR* 5.9 0.2 - + - -
46S ASN 3.0 13.2 + - - +
47S VAL* 3.2 10.5 + - - +
49S GLU* 1.3 76.5 - - - +
51S PHE* 1.3 92.6 + + - +
53S GLU* 3.5 9.4 + - + +
54S HIS* 3.2 55.6 + + - -
96S MET* 4.0 20.6 - - + -
143S ARG* 3.9 18.2 - - - -
144S ILE* 4.5 12.3 - - + -
147S PHE* 3.7 28.9 - + - -
171S VAL* 3.7 20.4 - - + +
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Residues in contact with PHE 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S TYR* 3.6 48.9 - + + +
33S MET* 3.8 29.8 - - + -
34S TYR 4.0 4.5 - - - +
37S PHE* 3.7 22.4 - + - -
47S VAL* 3.2 36.4 + - + -
48S ALA* 3.9 5.6 - - - +
49S GLU 3.2 0.2 - - - -
50S PHE* 1.3 98.9 - + - +
52S LYS* 1.3 59.6 + - - +
54S HIS* 3.2 5.1 + - + +
55S SER* 2.9 24.8 + - - -
95S ALA* 4.1 12.6 - - + -
96S MET* 3.7 23.6 - - + -
99S ALA* 4.2 8.5 - - + -
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Residues in contact with LYS 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M GLU* 3.6 25.1 + - - +
34S TYR* 3.7 38.8 + - + +
48S ALA 3.0 17.4 + - - +
49S GLU* 3.6 32.9 + - - +
50S PHE 3.3 0.2 - - - -
51S PHE* 1.3 77.1 - - - +
53S GLU* 1.3 62.5 + - + +
55S SER* 3.2 20.3 + - - +
56S HIS* 3.3 30.4 + - + +
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Residues in contact with GLU 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49S GLU* 2.9 27.0 + - + +
50S PHE* 3.6 10.0 - - + +
52S LYS* 1.3 78.1 - - + +
54S HIS* 1.3 63.7 + - + +
56S HIS* 3.3 9.9 + - - +
57S GLU* 3.1 35.7 + - - +
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Residues in contact with HIS 54 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S TYR* 3.9 23.1 - + + -
50S PHE* 3.2 40.4 + + - +
51S PHE* 3.2 10.3 + - - +
53S GLU* 1.3 81.8 - - + +
55S SER* 1.3 63.7 + - - +
57S GLU* 3.4 18.4 + - - +
58S GLU* 3.2 32.8 + - - +
103S GLU* 3.6 17.7 + - - -
140S ASP* 3.7 26.7 - - + -
143S ARG* 3.1 28.0 + - - -
144S ILE* 4.9 4.0 - - + -
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Residues in contact with SER 55 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M GLU* 4.4 5.0 + - - -
27S SER* 2.9 47.0 + - - +
30S TYR* 3.7 14.3 - - - +
31S SER* 3.8 15.2 + - - -
51S PHE 2.9 9.6 + - - -
52S LYS* 3.2 16.3 + - - +
53S GLU 3.3 0.4 - - - -
54S HIS* 1.3 75.3 - - - +
56S HIS* 1.3 77.9 + - - +
58S GLU 3.4 1.0 + - - -
59S ARG* 3.1 12.3 + - - +
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Residues in contact with HIS 56 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M ARG* 6.0 3.3 - - + +
63M GLU* 3.0 34.4 + - - -
52S LYS* 3.3 29.4 + - + +
53S GLU* 3.3 12.3 + - - +
54S HIS 3.2 0.4 - - - -
55S SER* 1.3 90.4 + - - +
57S GLU* 1.3 56.6 + - - +
59S ARG* 3.5 8.2 + - + +
60S GLU* 3.1 26.3 + - - +
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Residues in contact with GLU 57 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53S GLU* 3.1 21.1 + - - +
54S HIS* 3.6 25.5 + - - +
56S HIS* 1.3 76.2 - - - +
58S GLU* 1.3 64.4 + - + +
60S GLU* 3.2 7.2 + - + +
61S HIS* 3.0 47.2 + - + +
140S ASP* 4.1 17.3 - - - +
143S ARG* 5.8 1.6 + - - -
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Residues in contact with GLU 58 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S GLU* 2.7 31.0 - - - +
26S ALA* 4.2 9.2 - - + -
27S SER* 3.8 12.3 - - - -
30S TYR* 4.0 17.5 - - + -
54S HIS* 3.2 22.1 + - - +
57S GLU* 1.3 79.3 - - - +
59S ARG* 1.3 58.6 + - - +
61S HIS* 3.1 10.8 + - - +
62S ALA* 3.0 26.5 + - - +
103S GLU* 3.4 15.1 - - - +
106S VAL* 4.9 0.8 - - - +
176S MG 2.0 32.4 - - - -
177S MG 2.6 24.5 - - - -
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Residues in contact with ARG 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M HIS* 6.0 3.1 - - + +
59M ARG* 5.7 9.4 - - + -
24S LEU* 4.9 11.7 - - + -
27S SER* 3.6 13.4 + - - +
55S SER 3.1 16.9 + - - +
56S HIS* 3.6 10.5 - - + +
58S GLU* 1.3 74.1 - - - +
60S GLU* 1.3 64.0 + - - +
62S ALA* 3.2 8.5 + - - +
63S GLU* 3.1 35.8 + - + +
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Residues in contact with GLU 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S HIS 3.1 15.5 + - - +
57S GLU* 3.2 10.5 + - - +
59S ARG* 1.3 75.5 - - - +
61S HIS* 1.3 59.9 + - + +
63S GLU* 3.5 12.6 + - - +
64S LYS* 3.1 32.8 + - - +
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Residues in contact with HIS 61 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S GLU* 3.4 15.9 - - - +
57S GLU* 3.0 30.3 + - + +
58S GLU* 3.1 19.2 + - - +
59S ARG 3.2 0.2 - - - -
60S GLU* 1.3 78.5 - - + +
62S ALA* 1.3 64.5 + - - +
64S LYS* 3.4 18.4 + - - +
65S PHE* 3.3 13.0 + - - -
132S GLU 4.6 7.2 + - - -
133S TYR* 3.0 40.3 + + + -
136S GLU* 5.1 14.1 - - + +
137S GLN* 5.1 1.3 - - - -
140S ASP* 5.6 0.4 - - - -
176S MG 2.7 23.2 - - - -
177S MG 4.3 9.9 - - - -
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Residues in contact with ALA 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20S LEU* 3.7 16.8 - - + +
23S GLU* 3.8 9.9 - - + -
24S LEU* 3.7 35.2 - - + -
58S GLU 3.0 12.3 + - - +
59S ARG 3.2 8.7 + - - +
61S HIS* 1.3 76.2 - - - +
63S GLU* 1.3 64.9 + - + +
65S PHE* 3.3 9.1 + - - +
66S MET* 3.1 26.3 + - + +
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Residues in contact with GLU 63 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M SER* 4.8 5.5 + - - +
34M TYR* 5.1 11.8 + - + -
52M LYS* 3.6 21.0 - - - +
55M SER* 4.4 5.5 + - - -
56M HIS* 3.0 35.1 + - - -
24S LEU* 6.4 0.2 - - + -
59S ARG* 3.1 24.9 + - + +
60S GLU* 3.8 12.0 - - - +
61S HIS 3.3 0.2 - - - -
62S ALA* 1.3 75.0 - - + +
64S LYS* 1.3 64.9 + - - +
66S MET* 3.2 24.8 + - + +
67S LYS* 3.1 24.1 + - - +
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Residues in contact with LYS 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60S GLU* 3.1 20.3 + - - +
61S HIS* 3.6 17.8 + - - +
62S ALA 3.3 0.4 - - - -
63S GLU* 1.3 74.8 - - - +
65S PHE* 1.3 57.2 + - - +
67S LYS* 3.5 8.3 + - - +
68S TYR* 2.9 27.2 + - - +
128S PHE* 3.7 10.3 - - + -
132S GLU* 2.9 53.3 + - + +
133S TYR* 3.2 21.1 - - + +
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Residues in contact with PHE 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16S VAL* 3.9 30.0 - - + +
19S MET* 3.4 32.1 - - + -
20S LEU* 4.2 18.8 - - + -
23S GLU* 4.1 15.0 - - + -
61S HIS 3.3 16.7 + - - -
62S ALA 3.3 8.4 + - - +
63S GLU 3.2 0.6 - - - -
64S LYS* 1.3 77.8 - - - +
66S MET* 1.3 65.7 + - - +
68S TYR* 3.5 3.2 - - + +
69S GLN* 3.0 24.6 + - - +
110S LEU* 4.0 11.2 - - + -
113S LEU* 4.5 7.9 - - + -
125S LEU* 5.3 0.2 - - + -
128S PHE* 3.5 26.2 - + - -
129S LEU* 4.0 11.9 - - + -
133S TYR* 3.4 30.5 - + - -
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Residues in contact with MET 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M TYR* 5.5 0.2 - - + -
31M SER* 3.3 41.5 - - - +
34M TYR* 4.5 15.0 - - + -
35M ALA* 4.3 12.8 - - + -
20S LEU* 3.8 30.0 - - + +
24S LEU* 5.1 7.9 - - + -
62S ALA* 3.1 21.1 + - + +
63S GLU* 3.2 23.1 + - + +
65S PHE* 1.3 76.3 - - - +
67S LYS* 1.3 61.4 + - - +
69S GLN* 3.4 4.5 - - - +
70S ASN* 3.3 26.8 + - - -
76S VAL* 3.9 21.1 - - + +
78S LEU* 4.7 7.2 - - + -
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Residues in contact with LYS 67 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LYS* 6.0 0.8 - - - +
34M TYR* 3.3 30.7 - - - +
38M ASP* 3.1 33.5 + - - +
45M HIS* 5.0 5.5 + - - -
49M GLU* 5.7 1.8 - - - -
63S GLU 3.1 9.1 + - - +
64S LYS* 3.6 11.9 - - - +
66S MET* 1.3 78.6 - - - +
68S TYR* 1.3 58.3 + - - +
70S ASN* 3.5 3.5 + - - +
71S LYS* 3.0 44.1 + - + +
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Residues in contact with TYR 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLU* 5.7 0.2 - - - -
8S TYR* 3.9 17.9 - + - -
16S VAL* 4.6 7.6 - - + -
64S LYS 2.9 18.4 + - - +
65S PHE* 3.5 6.5 - - - +
67S LYS* 1.3 75.6 - - - +
69S GLN* 1.3 68.4 + - - +
71S LYS* 3.1 16.3 + - + +
72S ARG* 2.8 51.5 + - + +
124S HIS* 2.8 41.6 + + - -
125S LEU* 3.2 36.9 - - + -
128S PHE* 3.6 43.3 - + + -
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Residues in contact with GLN 69 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S TYR* 3.0 35.7 + - - -
13S GLU* 3.2 27.7 + - - +
16S VAL* 3.5 14.7 - - + +
17S ASN* 3.4 18.4 + - - -
20S LEU* 5.8 1.1 - - + +
65S PHE 3.0 14.2 + - - +
66S MET 3.4 7.0 - - - +
68S TYR* 1.3 83.8 - - - +
70S ASN* 1.3 61.3 + - - +
72S ARG* 3.2 5.2 + - - +
73S GLY 3.1 3.5 + - - -
74S GLY* 2.9 43.1 + - - +
75S ARG 4.0 6.5 - - - -
76S VAL* 3.7 24.7 - - + +
----------------------------------------------------------
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Residues in contact with ASN 70 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LYS* 3.3 17.0 - - - +
34M TYR* 6.3 0.2 - - - -
35M ALA* 3.0 30.8 + - - +
38M ASP* 3.2 39.6 + - - +
39M ARG* 3.2 27.7 - - - +
40M ASP* 4.8 3.8 + - - +
4S VAL* 4.5 0.9 - - - +
66S MET 3.3 12.3 + - - -
67S LYS 3.9 2.9 - - - +
69S GLN* 1.3 77.8 - - - +
71S LYS* 1.3 65.1 + - - +
73S GLY* 3.2 9.9 + - - -
74S GLY 3.9 11.5 - - - +
75S ARG* 4.0 1.3 + - - +
76S VAL* 4.6 9.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLU* 2.9 35.4 + - - +
138C VAL* 4.3 24.7 - - + +
139C LYS* 4.6 11.4 - - - +
142C LYS* 4.1 27.4 - - + +
4S VAL* 3.4 17.7 - - - +
67S LYS* 3.0 29.4 + - + +
68S TYR* 3.1 23.4 + - + +
70S ASN* 1.3 76.9 - - - +
72S ARG* 1.3 62.3 + - + +
124S HIS* 5.4 0.4 - - + -
128S PHE* 6.2 2.6 - - - -
----------------------------------------------------------
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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