Contacts of the helix formed by residues 49 - 70 (chain E) in PDB entry 6DVD
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 SER 49 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990D ASP* 3.4 30.1 - - - -
1267D TYR* 3.4 20.9 + - - -
44E LEU* 4.5 3.1 - - - -
47E VAL* 3.5 14.0 - - - +
48E SER* 1.3 82.3 + - - +
50E LYS* 1.3 64.3 + - - +
51E TYR* 3.6 3.3 + - - +
52E ALA* 3.2 21.2 + - - +
53E LEU* 3.2 17.0 + - - +
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Residues in contact with LYS 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506D ARG* 5.7 2.6 - - - +
557D ILE* 4.3 19.2 + - + +
558D LEU* 3.7 26.2 + - + +
563D ASN* 3.6 28.5 + - - +
564D ASN* 4.8 7.1 - - - +
706D MET* 4.2 26.6 - - - +
984D ALA 5.6 0.8 + - - -
985D THR* 4.6 20.6 + - - +
987D LYS* 5.4 1.3 - - - +
990D ASP* 3.4 14.9 + - - +
40E ILE* 6.0 2.0 - - - -
44E LEU* 4.2 26.4 - - + +
49E SER* 1.3 73.2 - - - +
51E TYR* 1.3 66.1 + - + +
53E LEU* 3.4 12.1 + - - +
54E VAL* 3.4 17.7 + - - +
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Residues in contact with TYR 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078C ALA 4.4 0.3 + - - -
1079C TYR 3.1 30.6 + - - -
1080C GLY* 3.7 2.9 + - - -
506D ARG* 4.9 1.4 + - - -
558D LEU* 3.8 17.9 - - + -
990D ASP* 3.9 28.3 - - + -
991D ILE 4.4 8.1 - - - -
993D GLU* 3.1 54.5 + - + +
1261D GLY* 3.5 31.2 - - - -
1262D THR* 3.5 31.1 - - + +
1267D TYR* 4.0 13.5 - - + +
49E SER* 3.3 2.4 - - - +
50E LYS* 1.3 79.7 - - + +
52E ALA* 1.3 62.1 + - - +
54E VAL* 3.5 7.7 + - - +
55E ILE* 3.7 8.8 + - - +
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Residues in contact with ALA 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1267D TYR* 3.8 21.0 - - + -
1270D ILE* 5.6 0.2 - - - -
47E VAL* 3.7 13.9 - - + -
48E SER* 3.5 19.1 - - - +
49E SER* 3.2 19.7 + - - +
51E TYR* 1.3 75.4 - - - +
53E LEU* 1.3 63.0 + - - +
54E VAL 3.3 0.2 + - - -
55E ILE* 3.3 3.8 + - - +
56E TYR* 3.1 39.4 + - + +
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Residues in contact with LEU 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557D ILE* 3.7 32.3 - - + -
40E ILE* 4.8 2.0 - - + -
43E LEU* 3.9 37.2 - - + +
44E LEU* 4.1 13.5 - - + -
47E VAL* 3.5 17.6 - - + +
49E SER 3.2 12.5 + - - +
50E LYS 3.4 8.2 + - - +
52E ALA* 1.3 76.5 - - - +
54E VAL* 1.3 62.3 + - - +
56E TYR* 4.4 4.0 - - + -
57E ALA* 3.0 22.5 + - - +
96E LEU* 4.5 7.4 - - + -
99E ILE* 4.1 34.1 - - + -
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Residues in contact with VAL 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083C TYR* 5.7 0.2 - - + -
550D GLU* 4.0 5.6 - - + +
553D ALA* 3.6 32.2 - - + +
554D GLU* 3.5 26.0 - - + -
557D ILE* 3.8 13.0 - - + -
558D LEU* 3.8 24.7 - - + -
1262D THR* 4.1 8.5 - - + -
50E LYS 3.4 15.2 + - - +
51E TYR 3.7 8.3 - - - +
52E ALA 3.2 0.8 - - - -
53E LEU* 1.3 78.7 - - - +
55E ILE* 1.3 63.6 + - + +
58E ALA* 2.9 28.8 + - - +
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Residues in contact with ILE 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083C TYR* 3.5 39.3 - - + +
550D GLU* 4.9 7.0 - - + -
1262D THR* 4.2 11.9 - - - +
1267D TYR* 3.3 35.4 - - + +
1268D ARG* 4.2 0.4 - - - +
1270D ILE* 4.2 12.8 - - + -
1272D VAL* 5.2 0.4 - - - +
51E TYR 3.7 12.7 + - - +
52E ALA 3.3 7.0 + - - +
53E LEU 3.3 0.2 - - - -
54E VAL* 1.3 76.9 - - + +
56E TYR* 1.3 67.3 + - + +
58E ALA* 4.5 2.2 - - - +
59E LYS* 3.0 52.8 + - + +
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Residues in contact with TYR 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270D ILE* 3.5 46.6 - - + +
1272D VAL* 4.2 20.0 - - + +
46E ARG 5.0 6.5 - - - -
47E VAL* 3.6 30.7 - - + -
48E SER* 5.2 3.0 + - - -
52E ALA* 3.1 20.2 + - + +
53E LEU* 3.8 7.4 - - + +
54E VAL 3.3 0.2 - - - -
55E ILE* 1.3 78.3 - - - +
57E ALA* 1.3 62.7 + - - +
60E ARG* 3.3 22.9 + - - +
99E ILE* 4.1 19.1 - - + +
104E LEU* 5.5 0.3 - - - +
105E GLU 5.3 2.2 - - - +
106E HIS* 3.6 39.6 + + + +
107E THR 4.7 0.5 + - - -
108E GLU* 4.5 9.4 - - - +
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Residues in contact with ALA 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D ALA* 4.8 4.0 - - + -
557D ILE* 4.8 2.2 - - + -
53E LEU 3.0 17.7 + - - +
54E VAL 4.0 2.9 - - - +
56E TYR* 1.3 75.4 - - - +
58E ALA* 1.3 60.2 + - - +
60E ARG* 3.6 1.4 + - - -
61E ALA* 2.9 30.3 + - - +
92E LEU* 4.0 15.6 - - + +
95E ALA* 3.9 8.2 - - + +
96E LEU* 3.6 29.2 - - + -
99E ILE* 3.9 10.2 - - + +
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Residues in contact with ALA 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549D ALA* 3.7 11.8 - - - +
550D GLU* 3.6 44.2 - - + +
553D ALA* 4.2 2.2 - - + +
54E VAL 2.9 20.0 + - - +
55E ILE* 4.1 3.4 - - - +
57E ALA* 1.3 78.5 - - - +
59E LYS* 1.3 58.7 + - + +
61E ALA* 3.1 7.5 + - - +
62E ARG* 3.0 31.7 + - - +
92E LEU* 5.1 0.7 - - - -
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Residues in contact with LYS 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083C TYR* 5.2 6.5 - - - -
550D GLU* 5.4 9.2 - - + +
1268D ARG* 2.9 28.0 + - - +
1269D ASN* 4.4 3.6 - - - +
1270D ILE* 3.1 29.5 + - + +
1272D VAL* 3.8 17.3 - - + -
55E ILE* 3.0 31.9 + - + +
58E ALA* 1.3 78.4 - - + +
60E ARG* 1.3 61.8 + - - +
62E ARG* 3.3 13.5 + - - +
63E GLN* 3.3 23.2 + - - +
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Residues in contact with ARG 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272D VAL* 4.0 10.8 - - + +
1274D PRO* 3.8 15.5 - - - +
56E TYR 3.3 18.2 + - - +
57E ALA* 4.0 3.1 - - - +
58E ALA 3.3 0.4 - - - -
59E LYS* 1.3 75.2 - - - +
61E ALA* 1.3 65.2 + - - +
63E GLN* 3.0 40.7 + - - +
64E ILE* 3.0 21.9 + - + +
79E VAL* 3.3 16.1 + - - +
80E GLY 2.7 30.7 + - - -
81E PRO* 3.9 2.8 - - - +
82E LEU* 3.7 8.3 - - - +
95E ALA* 3.6 11.0 - - + -
98E GLU* 2.6 41.6 + - - +
99E ILE* 5.5 0.2 - - + -
104E LEU* 3.7 28.6 - - + +
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Residues in contact with ALA 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111C ASN* 4.6 1.7 + - - -
549D ALA* 4.3 11.2 - - + -
57E ALA 2.9 19.8 + - - +
58E ALA* 3.1 8.7 + - - +
60E ARG* 1.3 77.1 - - - +
62E ARG* 1.3 57.3 + - - +
64E ILE* 3.6 1.3 + - - +
65E ASN* 3.0 29.1 + - - +
91E PRO* 3.9 29.4 - - + +
92E LEU* 4.1 17.0 - - + +
95E ALA* 4.2 2.0 - - + -
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Residues in contact with ARG 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111C ASN* 3.2 45.9 - - - +
1112C ILE* 3.0 30.3 + - - +
1113C PRO 4.9 1.8 + - - -
548D SER* 4.0 12.5 - - - -
549D ALA* 4.2 8.7 - - + +
550D GLU* 2.7 44.2 + - - -
58E ALA 3.0 17.2 + - - +
59E LYS* 3.5 14.1 - - - +
60E ARG 3.2 0.2 - - - -
61E ALA* 1.3 75.2 - - - +
63E GLN* 1.3 64.3 + - + +
66E ASP* 3.0 28.7 + - - +
78E TYR* 5.5 0.7 - - - -
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Residues in contact with GLN 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1272D VAL* 2.8 38.2 + - - +
1273D GLN* 5.0 4.9 - - - +
1274D PRO* 4.4 10.0 - - - +
59E LYS 3.3 12.7 + - - +
60E ARG* 3.0 37.6 + - - +
62E ARG* 1.3 78.5 - - + +
64E ILE* 1.3 62.1 + - - +
66E ASP 3.2 1.7 + - - -
67E TYR* 3.0 19.4 + - - +
78E TYR* 3.3 48.4 - - + +
79E VAL* 4.5 8.2 + - - +
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Residues in contact with ILE 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ARG* 3.0 29.9 + - - +
61E ALA 4.1 3.6 - - - +
63E GLN* 1.3 75.1 - - - +
65E ASN* 1.3 61.3 + - - +
67E TYR* 3.2 8.2 + - - +
68E TYR* 3.2 45.3 + - + +
79E VAL 4.6 2.9 - - - +
81E PRO* 4.5 13.0 - - + -
91E PRO* 4.0 13.7 - - + +
94E ILE* 3.8 20.0 - - + -
95E ALA* 3.8 26.7 - - + +
98E GLU* 3.3 24.9 - - - +
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Residues in contact with ASN 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109C GLY 3.3 11.4 + - - +
1110C GLU 4.5 4.2 + - - -
1111C ASN* 3.2 32.1 - - - +
61E ALA 3.0 19.9 + - - +
63E GLN 3.2 0.4 - - - -
64E ILE* 1.3 78.5 - - - +
66E ASP* 1.3 61.5 + - - +
68E TYR* 3.4 8.1 + - - +
69E ASN* 3.1 36.0 + - - -
91E PRO* 4.3 22.6 - - + +
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Residues in contact with ASP 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110C GLU* 5.7 1.2 - - - +
1111C ASN* 3.6 17.5 + - - +
62E ARG* 3.0 22.3 + - - +
63E GLN 3.2 0.6 + - - +
65E ASN* 1.3 75.4 - - - +
67E TYR* 1.3 60.5 + - - +
69E ASN* 3.8 8.6 + - - +
70E GLN* 2.9 47.5 + - - +
78E TYR* 3.4 42.3 + - + -
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Residues in contact with TYR 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281D ALA 5.9 3.1 - - - -
63E GLN 3.0 11.1 + - - +
64E ILE* 3.2 8.7 + - - +
66E ASP* 1.3 77.4 - - - +
68E TYR* 1.3 83.1 + + - +
70E GLN 3.5 0.2 - - - -
71E LEU* 2.9 68.3 + - + +
77E GLU* 4.7 10.5 - - + -
78E TYR* 3.3 30.9 - - - +
79E VAL 4.3 0.4 - - - +
80E GLY* 3.6 18.4 - - - -
81E PRO* 3.7 21.5 - - + -
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Residues in contact with TYR 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ILE* 3.2 17.9 + - + -
65E ASN* 3.9 10.3 - - - +
66E ASP 3.4 0.4 - - - -
67E TYR* 1.3 106.0 - + - +
69E ASN* 1.3 61.4 + - - +
70E GLN 3.5 0.2 - - - -
71E LEU* 4.2 15.0 + - + +
72E GLY 5.5 0.3 + - - -
81E PRO* 3.6 23.3 - - + +
85E PRO* 4.0 11.3 - - - +
89E GLU 5.0 6.5 - - - -
91E PRO* 4.9 11.4 - - + -
94E ILE* 3.7 25.4 - - + +
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Residues in contact with ASN 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108C LYS 3.9 8.6 - - - +
1109C GLY* 2.5 38.9 + - - +
1110C GLU* 3.7 12.9 - - + +
1111C ASN 4.9 0.6 - - - +
458D LYS* 5.7 1.0 + - - -
65E ASN* 3.1 27.9 + - - +
66E ASP* 3.4 9.2 + - - +
67E TYR 3.2 0.4 - - - -
68E TYR* 1.3 81.0 - - - +
70E GLN* 1.3 64.6 + - + +
71E LEU 3.6 0.9 - - - -
72E GLY 5.3 1.4 + - - -
73E GLU* 4.2 15.8 - - - +
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Residues in contact with GLN 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ASP* 2.9 30.7 + - - +
67E TYR 3.5 2.5 - - - -
69E ASN* 1.3 82.4 - - + +
71E LEU* 1.3 62.3 + - - +
72E GLY 3.4 1.6 - - - +
73E GLU* 2.8 32.0 - - + +
74E GLY* 3.8 5.4 - - - +
75E ILE 5.0 3.4 - - - +
76E LEU 4.6 1.7 - - - +
77E GLU* 3.7 37.8 - - + +
78E TYR* 4.2 13.6 - - - -
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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