Contacts of the helix formed by residues 46 - 74 (chain H) in PDB entry 2YW7
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 ASN 46 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ASN* 5.2 7.1 - - - +
46E ASN* 3.4 25.1 - - - +
44H GLY 3.4 0.4 - - - -
45H PRO* 1.3 88.8 - - - +
47H PHE* 1.3 58.3 + - - +
48H ILE* 3.3 3.1 - - - +
49H GLY* 2.8 25.5 + - - +
50H VAL* 3.7 2.6 + - - +
102H VAL* 3.9 14.3 - - + +
157H GLU* 4.0 25.7 - - - +
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Residues in contact with PHE 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E TRP* 3.8 19.5 - + - -
151E PHE* 3.3 39.5 - + - -
153E ARG 5.5 0.7 - - - -
154E ALA* 4.1 18.4 - - + -
42H VAL* 3.2 27.1 - - - +
43H VAL* 3.6 7.0 - - + -
44H GLY 3.0 38.1 + - - +
45H PRO 3.3 2.2 + - - -
46H ASN* 1.3 72.5 - - - +
48H ILE* 1.3 80.5 + - + +
49H GLY 2.9 4.3 - - - -
50H VAL* 2.9 17.7 + - - +
51H HIS* 3.2 43.0 + + - -
102H VAL* 3.6 9.6 - - + +
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Residues in contact with ILE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E PHE* 3.1 41.3 - - + -
45H PRO 5.6 2.2 - - - +
46H ASN* 3.3 1.0 - - - -
47H PHE* 1.3 102.6 - - + +
49H GLY* 1.3 57.4 + - - +
51H HIS* 3.1 15.3 + - + +
52H GLU* 2.8 54.8 + - + +
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Residues in contact with GLY 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ASN* 2.8 21.3 + - - +
48H ILE* 1.3 79.9 - - - +
50H VAL* 1.3 60.2 + - - -
52H GLU* 3.3 10.5 + - - +
53H MET* 3.3 20.5 + - - +
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Residues in contact with VAL 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H VAL* 4.8 2.2 - - + -
42H VAL* 3.5 25.8 - - + -
46H ASN 4.5 0.4 - - - +
47H PHE 2.9 6.2 + - - +
49H GLY* 1.3 73.5 - - - +
51H HIS* 1.3 63.8 + - - +
53H MET* 2.9 13.8 + - + +
54H ILE* 2.9 53.1 + - + +
102H VAL* 3.6 42.4 - - + -
106H LEU* 3.9 23.3 - - + -
109H LEU* 5.4 1.8 - - + -
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Residues in contact with HIS 51 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E TRP* 4.6 11.9 - + - -
39H HIS* 3.1 49.5 + + - +
42H VAL* 3.4 23.3 + - + +
47H PHE* 3.2 38.5 + + - -
48H ILE* 3.1 22.2 + - + +
50H VAL* 1.3 77.9 - - - +
52H GLU* 1.3 61.5 + - + +
53H MET 3.3 0.3 + - - -
54H ILE 3.4 0.2 + - - -
55H ASP* 3.4 31.5 + - - +
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Residues in contact with GLU 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H ILE* 2.8 39.9 + - + +
49H GLY* 3.7 9.4 - - - +
50H VAL 3.2 0.4 - - - -
51H HIS* 1.3 74.8 - - + +
53H MET* 1.3 57.5 + - - +
55H ASP* 4.9 2.0 - - - +
56H PRO* 3.2 20.5 - - - +
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Residues in contact with MET 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H GLY 3.3 6.6 + - - +
50H VAL* 2.9 24.2 + - + +
52H GLU* 1.3 80.1 - - - +
54H ILE* 1.3 67.6 + - + +
56H PRO* 3.5 14.6 - - - +
57H GLN* 3.9 1.2 - - - +
106H LEU* 4.5 17.9 - - - -
109H LEU* 6.0 1.1 - - - -
148H PHE* 3.2 48.9 - - + -
151H PHE* 3.3 45.1 - - + +
152H VAL* 3.7 23.1 - - + +
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Residues in contact with ILE 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H LEU* 3.8 22.9 - - + +
38H VAL* 3.7 28.5 - - + -
39H HIS* 3.9 25.1 - - + +
50H VAL* 2.9 42.9 + - + +
51H HIS 4.1 2.7 - - - +
53H MET* 1.3 81.4 - - + +
55H ASP* 1.3 56.7 + - - +
57H GLN* 3.0 6.9 + - - +
58H VAL* 2.6 54.4 + - + -
109H LEU* 4.9 5.8 - - + -
148H PHE* 4.7 8.3 - - + -
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Residues in contact with ASP 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H LYS* 4.5 12.6 - - - -
39H HIS* 3.4 26.7 + - - -
51H HIS* 3.4 17.2 + - - +
52H GLU* 4.9 1.6 - - - +
54H ILE* 1.3 76.9 - - - +
56H PRO* 1.4 66.9 - - + +
58H VAL* 3.7 6.3 - - - +
59H GLU* 3.4 25.6 + - - +
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Residues in contact with PRO 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H GLU 3.2 24.2 - - - +
53H MET* 3.5 11.9 - - - +
54H ILE 3.4 2.7 - - - -
55H ASP* 1.4 90.9 - - + +
57H GLN* 1.3 59.3 + - - +
59H GLU* 4.3 3.5 - - + +
60H LEU* 3.0 26.7 + - - +
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Residues in contact with GLN 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H LEU* 3.9 7.2 - - + -
53H MET 3.9 0.2 - - - +
54H ILE 3.0 7.9 + - - +
56H PRO* 1.3 79.5 - - - +
58H VAL* 1.3 60.3 + - - +
60H LEU* 2.7 21.8 + - - +
61H VAL* 2.5 56.2 + - + +
113H TYR* 3.0 31.3 + - - +
144H GLU 5.2 1.1 + - - +
145H LEU* 3.9 13.9 - - - +
148H PHE* 3.1 48.6 - - + +
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Residues in contact with VAL 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H HIS* 4.2 7.0 - - + +
35H LEU* 3.4 27.3 - - + +
36H LYS* 4.0 21.8 - - + +
54H ILE* 2.6 44.5 + - + +
55H ASP* 3.7 9.6 - - - +
57H GLN* 1.3 71.8 - - - +
59H GLU* 1.3 59.7 + - + +
61H VAL* 3.9 2.3 - - - +
62H ARG* 2.9 67.1 + - + +
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Residues in contact with GLU 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ASP 3.4 14.5 + - - +
56H PRO* 4.3 4.3 - - + +
57H GLN 3.1 0.6 - - - -
58H VAL* 1.3 77.7 - - + +
60H LEU* 1.3 55.7 + - - +
62H ARG* 2.7 50.8 + - - +
63H GLY* 2.8 30.5 + - - -
59J GLU* 5.2 5.2 - - - +
62J ARG* 4.3 2.6 + - - -
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Residues in contact with LEU 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H PRO 3.0 22.1 + - - +
57H GLN* 2.7 32.0 + - - +
59H GLU* 1.3 72.0 - - - +
61H VAL* 1.3 56.2 + - - +
63H GLY* 3.1 15.5 + - - -
64H TYR* 3.2 66.6 - - + +
144H GLU* 4.5 10.8 - - + +
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Residues in contact with VAL 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H TYR* 3.5 23.4 - - + +
31H LEU* 3.6 25.4 - - + -
32H HIS* 3.5 24.9 - - + -
35H LEU* 4.4 1.1 - - + -
57H GLN* 2.5 52.1 + - + +
58H VAL 4.0 2.0 - - - +
60H LEU* 1.3 70.2 - - - +
62H ARG* 1.3 63.1 + - - +
64H TYR* 3.1 12.6 + - + +
65H ALA* 3.1 20.3 + - - +
145H LEU* 3.8 11.9 - - + -
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Residues in contact with ARG 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H HIS* 4.1 28.7 + - + -
36H LYS* 3.6 30.5 - - - +
58H VAL* 2.9 38.3 + - - +
59H GLU* 2.7 48.2 + - - +
61H VAL* 1.3 76.5 - - - +
63H GLY* 1.3 61.5 + - - +
64H TYR 3.1 0.7 + - - -
65H ALA* 3.2 9.9 + - - +
66H ASP* 3.2 23.9 + - - +
32J HIS* 4.8 4.6 - - - -
36J LYS* 5.9 0.2 - - - -
59J GLU* 5.3 1.6 + - - -
62J ARG* 3.5 59.5 - - - +
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Residues in contact with GLY 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H GLU 2.8 14.1 + - - -
60H LEU* 3.1 7.9 + - - -
62H ARG* 1.3 75.3 - - - +
64H TYR* 1.3 62.9 + - - +
66H ASP* 3.8 7.4 - - - +
67H GLU* 3.0 31.4 + - - +
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Residues in contact with TYR 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H TYR* 3.3 20.3 - + + -
60H LEU* 3.2 51.2 - - + +
61H VAL* 3.1 15.0 + - + +
62H ARG 3.1 0.4 - - - -
63H GLY* 1.3 82.2 - - - +
65H ALA* 1.3 64.2 + - - +
66H ASP 3.1 1.6 - - - -
67H GLU* 3.9 9.6 - - - +
68H VAL* 3.2 21.7 + - - +
140H ALA* 6.0 0.7 - - + -
141H HIS* 3.3 50.9 - + + -
144H GLU* 2.8 40.4 - - + +
145H LEU* 4.5 14.8 - - + -
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Residues in contact with ALA 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LEU* 3.9 5.9 - - - +
28H TYR* 3.7 15.0 - - + -
29H ASN* 3.3 26.2 - - - +
32H HIS* 5.1 4.3 - - + -
61H VAL 3.1 12.2 + - - +
62H ARG* 3.5 13.7 - - - +
64H TYR* 1.3 76.3 - - - +
66H ASP* 1.3 59.1 + - - +
68H VAL* 3.6 5.6 - - - +
69H ALA* 3.1 26.0 + - - +
40J TRP* 4.2 9.4 - - + -
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Residues in contact with ASP 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H ARG 3.2 10.1 + - - +
63H GLY* 3.8 11.0 - - - +
64H TYR 3.1 0.2 - - - -
65H ALA* 1.3 75.2 - - - +
67H GLU* 1.3 58.7 + - + +
68H VAL 3.1 2.0 - - - -
69H ALA* 2.7 25.9 + - - +
70H GLU* 3.0 31.5 + - - +
36J LYS* 3.3 27.0 + - - -
39J HIS* 5.6 4.9 + - - -
40J TRP* 2.9 26.4 + - - -
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Residues in contact with GLU 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H GLY 3.0 23.0 + - - +
64H TYR* 3.4 13.7 + - - +
66H ASP* 1.3 75.8 - - + +
68H VAL* 1.3 58.1 + - - +
69H ALA 3.6 1.6 + - - -
70H GLU* 4.0 6.0 + - - +
71H ARG* 3.6 28.2 + - - +
137H LEU* 3.6 21.2 - - + +
140H ALA* 5.6 2.3 - - - +
141H HIS* 2.9 27.1 + - - +
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Residues in contact with VAL 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H LEU* 3.8 13.9 - - + +
24H GLN* 4.0 4.0 - - + +
25H LEU* 3.5 36.0 - - - +
28H TYR* 3.7 14.1 - - + -
64H TYR 3.2 12.0 + - - +
65H ALA 3.8 3.4 - - - +
66H ASP 3.1 0.6 - - - -
67H GLU* 1.3 73.9 - - - +
69H ALA* 1.3 57.8 + - - +
70H GLU 3.8 0.2 - - - -
71H ARG* 4.6 6.7 - - - +
72H ILE* 3.6 22.2 - - - +
137H LEU* 3.5 15.7 - - + -
138H LEU* 4.2 11.2 - - + -
141H HIS* 3.4 31.0 - - + +
----------------------------------------------------------
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Residues in contact with ALA 69 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LEU* 3.4 18.8 - - + -
65H ALA 3.1 17.0 - - - +
66H ASP 2.7 10.5 + - - +
68H VAL* 1.3 73.4 - - - +
70H GLU* 1.3 65.1 + - - +
71H ARG 3.5 0.4 - - - -
72H ILE* 3.7 2.7 - - - +
73H ALA* 3.6 10.9 + - - +
79H PRO* 3.2 23.0 - - + +
40J TRP* 3.4 33.7 - - + +
----------------------------------------------------------
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Residues in contact with GLU 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H ASP* 3.0 32.4 + - - +
67H GLU* 4.5 5.8 - - - +
69H ALA* 1.3 76.3 - - + +
71H ARG* 1.3 53.4 + - + +
72H ILE 2.8 8.8 + - - -
73H ALA* 2.9 8.3 + - + +
74H THR* 2.7 43.1 + - + +
40J TRP* 5.3 6.7 - - + -
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Residues in contact with ARG 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H LEU* 3.6 13.1 - - + +
67H GLU 3.6 17.0 + - - +
68H VAL* 5.0 2.9 - - - -
69H ALA 3.5 0.2 - - - -
70H GLU* 1.3 76.3 - - + +
72H ILE* 1.3 64.3 + - - +
74H THR* 3.1 15.3 - - + +
75H LEU* 3.3 29.0 - - + +
133H VAL* 3.1 36.8 + - - +
134H SER* 5.2 7.9 - - - +
137H LEU* 3.4 40.6 - - + +
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Residues in contact with ILE 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ALA* 4.7 11.7 - - + +
21H LEU* 3.5 47.1 - - + +
22H GLN* 3.8 8.3 - - + +
68H VAL 3.6 13.9 - - - +
69H ALA 3.7 8.3 - - - +
70H GLU 2.8 0.4 - - - -
71H ARG* 1.3 82.5 - - - +
73H ALA* 1.3 58.0 + - - +
74H THR 3.4 0.4 - - - -
75H LEU* 3.5 6.1 - - - +
76H GLY 3.2 6.6 + - - -
77H LYS* 2.7 49.3 + - + +
78H SER 4.1 0.7 - - - -
79H PRO* 3.5 35.7 - - + -
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Residues in contact with ALA 73 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H ALA 3.6 9.2 + - - +
70H GLU* 2.9 9.7 + - - +
72H ILE* 1.3 77.8 - - - +
74H THR* 1.3 64.8 + - + +
76H GLY* 3.2 13.5 + - - -
77H LYS 3.2 14.7 + - - +
79H PRO* 4.5 3.3 - - + +
40J TRP 4.7 13.9 - - - +
41J ASN* 5.0 2.0 - - - +
99J ARG* 6.1 0.3 - - - -
----------------------------------------------------------
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Residues in contact with THR 74 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H GLU* 2.7 34.6 + - + +
71H ARG* 3.1 16.8 - - + +
73H ALA* 1.3 70.0 - - + +
75H LEU* 1.3 66.2 + - - +
76H GLY* 2.8 10.7 + - - -
----------------------------------------------------------
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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