Contacts of the helix formed by residues 44 - 71 (chain G) in PDB entry 2PYO
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 ALA 44 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ARG* 4.6 5.2 + - - +
30G HIS* 4.6 10.7 - - + -
42G VAL 3.9 0.4 + - - -
43G GLY* 1.3 71.7 - - - -
45G GLY* 1.3 61.3 + - - +
47G PRO* 3.3 16.2 - - - +
48G VAL* 3.5 12.7 - - - +
118H TYR* 4.5 21.1 - - + +
1015H CL 4.0 0.2 - - - +
38I A 2.7 27.1 + - - +
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Residues in contact with GLY 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G ALA* 1.3 77.2 - - - +
46G ALA* 1.3 67.7 + - - +
48G VAL* 2.8 21.9 + - - +
49G TYR* 2.9 12.6 + - - +
88H SER* 3.9 11.7 - - - -
115H VAL* 3.9 13.1 - - - +
118H TYR* 5.5 2.9 - - - -
1015H CL 3.2 15.2 - - - +
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Residues in contact with ALA 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G LEU* 4.2 6.5 - - + -
42G VAL* 4.1 6.7 - - + -
43G GLY 3.5 4.0 + - - +
45G GLY* 1.3 74.0 - - - +
47G PRO* 1.3 65.2 - - + +
49G TYR* 3.3 1.6 + - - +
50G LEU* 2.8 33.0 + - - +
86H ILE* 3.5 27.8 - - + +
87H THR 3.9 9.4 - - - -
88H SER* 3.7 12.0 - - - +
91H ILE* 4.0 12.6 - - + +
1015H CL 3.7 5.5 - - - +
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Residues in contact with PRO 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ARG* 4.2 4.9 - - - +
26G VAL* 3.7 11.8 - - + +
29G ILE* 3.9 12.4 - - + +
30G HIS* 3.5 49.8 - - + +
33G LEU* 4.1 6.0 - - + -
42G VAL* 4.4 5.6 - - + -
43G GLY 3.0 26.2 - - - +
44G ALA 3.3 12.6 - - - +
46G ALA* 1.3 83.7 - - + +
48G VAL* 1.3 53.5 + - - +
50G LEU* 3.9 0.5 - - - +
51G ALA* 2.8 36.2 + - - +
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Residues in contact with VAL 48 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ARG* 5.6 0.2 - - - +
20G ALA* 3.9 14.6 - - + -
22G LEU* 3.5 1.7 - - - +
26G VAL* 3.7 24.0 - - + -
44G ALA 3.5 17.0 - - - +
45G GLY* 2.8 13.9 + - - +
47G PRO* 1.3 73.0 - - - +
49G TYR* 1.3 57.6 + - - +
51G ALA* 3.3 2.9 + - - +
52G ALA* 2.9 28.5 + - - +
114H ALA* 3.3 36.1 - - + +
115H VAL* 3.9 8.7 - - + +
118H TYR* 3.8 29.8 - - + -
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Residues in contact with TYR 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G GLY 2.9 9.8 + - - +
46G ALA 3.7 6.1 - - - +
48G VAL* 1.3 76.5 - - - +
50G LEU* 1.3 62.5 + - - +
52G ALA* 3.2 3.6 + - - +
53G VAL* 2.9 34.4 + - + +
88H SER* 4.1 18.6 - - - -
91H ILE* 3.5 24.5 - - + -
92H GLN* 2.6 54.6 + - + +
95H VAL* 4.5 3.6 - - + -
107H ALA 4.2 2.2 - - - -
108H VAL* 3.3 17.7 + - - +
111H GLY* 3.7 29.4 - - - -
112H THR* 3.6 15.0 - - - -
115H VAL* 3.9 16.1 - - + +
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Residues in contact with LEU 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ILE* 4.1 7.2 - - + -
33G LEU* 4.0 17.7 - - + -
46G ALA 2.8 21.7 + - - +
47G PRO 3.9 2.9 - - - +
49G TYR* 1.3 74.6 - - - +
51G ALA* 1.3 63.6 + - - +
53G VAL* 3.1 3.2 + - + -
54G MET* 2.9 41.1 + - + +
67H PHE* 3.7 37.2 - - + +
70H ILE* 3.9 39.0 - - + -
71H ALA 4.8 1.3 - - - +
91H ILE* 4.2 20.2 - - + +
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Residues in contact with ALA 51 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LEU* 3.9 13.2 - - + -
24G PHE* 3.9 11.6 - - + +
26G VAL* 4.0 14.4 - - + -
29G ILE* 3.2 28.6 - - + +
47G PRO 2.8 22.5 + - - +
48G VAL 3.5 4.3 - - - +
50G LEU* 1.3 72.7 - - - +
52G ALA* 1.3 58.7 + - - +
54G MET* 3.7 1.8 - - - +
55G GLU* 2.9 31.5 + - - +
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Residues in contact with ALA 52 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LEU* 3.5 17.8 - - + +
48G VAL 2.9 13.8 + - - +
49G TYR 3.5 8.3 - - - +
50G LEU 3.1 0.2 - - - -
51G ALA* 1.3 78.4 - - - +
53G VAL* 1.3 57.4 + - - +
55G GLU* 3.8 1.2 - - - +
56G TYR* 2.9 30.0 + - - +
110H GLU* 3.6 33.2 - - + +
111H GLY* 4.0 1.3 - - - -
114H ALA* 3.6 15.3 - - + -
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Residues in contact with VAL 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G TYR* 2.9 35.7 + - + +
50G LEU* 3.1 7.2 + - - +
52G ALA* 1.3 75.5 - - - +
54G MET* 1.3 62.7 + - - +
56G TYR* 3.4 6.9 + - - +
57G LEU* 3.0 34.3 + - + +
70H ILE* 3.8 26.0 - - + -
95H VAL* 4.0 14.1 - - + -
99H LEU* 4.5 2.2 - - + -
107H ALA* 3.4 40.2 - - + +
111H GLY* 4.6 0.7 - - - -
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Residues in contact with MET 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G PHE* 4.1 11.0 - - + -
29G ILE* 3.6 23.1 - - + -
50G LEU* 2.9 25.1 + - + +
51G ALA 3.7 2.9 - - - +
53G VAL* 1.3 74.1 - - - +
55G GLU* 1.3 66.7 + - - +
57G LEU* 3.2 4.6 + - - +
58G ALA* 2.9 24.1 + - - +
34H TYR* 3.6 29.4 - - + +
63H VAL* 3.1 42.5 - - + +
66H ILE* 4.1 27.4 - - + -
67H PHE* 3.9 22.7 - - + +
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Residues in contact with GLU 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G GLY 5.0 1.4 - - - +
22G LEU* 3.4 20.1 - - + +
23G GLN* 2.6 50.1 + - - +
24G PHE* 3.2 31.4 + - + -
51G ALA 2.9 15.2 + - - +
52G ALA* 3.8 4.0 - - - +
54G MET* 1.3 77.0 - - - +
56G TYR* 1.3 65.3 + - - +
58G ALA* 3.1 3.3 + - - +
59G ALA* 2.8 23.5 + - + +
41H VAL* 4.0 11.6 - - + +
44H GLN* 4.2 10.0 + - - +
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Residues in contact with TYR 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G ALA 2.9 18.2 + - - +
53G VAL* 3.4 4.9 - - - +
55G GLU* 1.3 77.8 - - - +
57G LEU* 1.3 79.4 + - + +
59G ALA* 2.9 10.8 + - + +
60G GLU* 2.9 49.0 + - + +
103H LEU* 3.7 26.3 - - + +
106H HIS* 3.2 33.9 - + + +
107H ALA* 3.8 32.5 - - + -
110H GLU* 3.8 28.5 - - + -
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Residues in contact with LEU 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G VAL* 3.0 18.1 + - + +
54G MET* 3.8 3.6 - - - +
56G TYR* 1.3 99.7 - - + +
58G ALA* 1.3 62.3 + - - +
60G GLU* 3.4 4.9 + - + +
61G VAL* 3.1 29.8 + - - +
92G LEU* 4.8 5.4 - - + -
95G LEU* 4.6 7.0 - - + -
62H PHE* 4.0 13.9 - - + -
66H ILE* 3.8 41.7 - - + -
99H LEU* 4.0 31.2 - - + -
103H LEU* 4.1 23.6 - - + -
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Residues in contact with ALA 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G PHE* 4.1 20.9 - - + -
54G MET 2.9 13.7 + - - +
55G GLU 3.4 10.3 - - - +
57G LEU* 1.3 78.1 - - - +
59G ALA* 1.3 57.6 + - - +
62G LEU* 2.9 39.4 + - + +
38H ILE* 5.4 2.7 - - + -
41H VAL* 4.8 4.9 - - + -
59H MET* 3.9 20.0 - - + +
62H PHE* 4.2 4.2 - - - -
63H VAL* 4.3 8.1 - - + -
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Residues in contact with ALA 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G GLU* 2.8 14.4 + - + +
56G TYR* 2.9 13.0 + - + +
58G ALA* 1.3 75.8 - - - +
60G GLU* 1.3 57.0 + - - +
62G LEU* 4.4 2.5 - - - -
63G GLU* 2.6 39.2 + - - +
41H VAL* 3.7 21.3 - - + +
44H GLN* 5.9 1.1 - - - +
45H VAL* 4.4 15.4 - - + +
----------------------------------------------------------
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Residues in contact with GLU 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G TYR* 2.9 36.9 + - + +
57G LEU* 3.4 13.0 + - + +
59G ALA* 1.3 75.7 - - - +
61G VAL* 1.3 61.4 + - + +
63G GLU* 3.7 9.4 - - - +
64G LEU* 3.2 44.5 + - - +
89G ASP* 5.5 2.1 - - - +
92G LEU* 4.6 14.4 - - + -
103H LEU* 4.3 21.3 - - + -
----------------------------------------------------------
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Residues in contact with VAL 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G LEU 3.1 17.6 + - - +
58G ALA 4.2 2.5 - - - +
60G GLU* 1.3 76.2 - - - +
62G LEU* 1.3 61.2 + - - +
64G LEU* 3.2 4.9 + - - +
65G ALA* 2.8 29.0 + - + +
82G LEU* 3.8 26.7 - - + -
85G ALA* 5.1 2.6 - - + +
86G ILE* 4.7 19.7 - - + -
92G LEU* 3.9 32.5 - - + -
96G LEU* 5.8 0.4 - - + -
59H MET* 3.9 12.6 - - + -
62H PHE* 3.8 20.2 - - + -
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Residues in contact with LEU 62 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G ALA* 2.9 28.3 + - + +
59G ALA* 3.9 3.6 - - - +
61G VAL* 1.3 75.6 - - - +
63G GLU* 1.3 57.6 + - - +
65G ALA* 3.9 2.8 - - - +
66G GLY* 2.8 26.2 + - - -
77G ILE* 4.0 14.7 - - + +
82G LEU* 5.2 2.7 - - + -
38H ILE* 3.6 36.3 - - + +
41H VAL* 4.3 5.8 - - + -
42H LEU* 3.8 35.8 - - + +
45H VAL* 4.5 5.6 - - + -
46H HIS* 3.5 9.1 - - - -
51H ILE* 4.2 21.3 - - + -
59H MET* 3.8 18.8 - - + -
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Residues in contact with GLU 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G ALA 2.6 24.2 + - - +
60G GLU* 3.7 12.1 - - - +
62G LEU* 1.3 72.9 - - - +
64G LEU* 1.3 71.3 + - + +
66G GLY 3.4 1.0 + - - -
67G ASN* 3.4 25.7 + - - +
45H VAL* 4.2 22.8 - - + +
46H HIS* 2.9 34.3 + - - -
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Residues in contact with LEU 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G GLU* 3.2 31.1 + - - +
61G VAL* 3.2 4.1 + - - +
63G GLU* 1.3 81.5 - - + +
65G ALA* 1.3 65.7 + - - +
67G ASN* 3.1 19.4 + - - +
68G ALA* 3.0 20.3 + - - +
85G ALA* 3.7 26.6 - - + +
89G ASP* 4.6 11.2 - - + +
92G LEU* 3.7 26.5 - - + -
----------------------------------------------------------
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Residues in contact with ALA 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G VAL 2.8 21.7 + - - +
62G LEU* 3.9 0.7 - - - +
64G LEU* 1.3 72.8 - - - +
66G GLY* 1.3 63.1 + - - +
68G ALA* 3.3 9.6 + - - +
69G ALA* 3.0 22.3 + - - +
77G ILE* 3.7 25.1 - - + +
81G HIS* 4.0 11.6 - - + +
82G LEU* 3.8 24.9 - - + -
85G ALA* 4.1 6.9 - - + +
----------------------------------------------------------
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Residues in contact with GLY 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G LEU 2.8 12.7 + - - -
64G LEU 3.1 0.4 - - - -
65G ALA* 1.3 77.6 - - - +
67G ASN* 1.3 61.9 + - - +
69G ALA* 3.1 13.8 + - - +
70G ARG* 3.2 12.6 + - - +
77G ILE* 3.6 12.5 - - - +
46H HIS* 3.5 27.8 - - - -
49H THR* 4.6 8.2 + - - -
----------------------------------------------------------
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Residues in contact with ASN 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G GLU* 3.4 26.4 + - - +
64G LEU* 3.1 19.4 + - - +
66G GLY* 1.3 73.6 - - - +
68G ALA* 1.3 63.5 + - - +
70G ARG* 2.9 23.2 + - - +
71G ASP* 2.8 35.0 + - - +
46H HIS* 3.4 18.9 - - - -
----------------------------------------------------------
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Residues in contact with ALA 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G LEU 3.0 13.1 + - - +
65G ALA* 3.6 13.5 - - - +
66G GLY 3.2 0.2 - - - -
67G ASN* 1.3 77.2 - - - +
69G ALA* 1.3 60.1 + - - +
71G ASP* 3.4 14.6 + - - +
72G ASN* 3.4 21.3 + - - +
81G HIS* 4.1 24.8 - - + +
84G LEU* 5.4 10.4 - - + +
85G ALA* 5.1 4.9 - - + +
----------------------------------------------------------
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Residues in contact with ALA 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G ALA 3.0 10.4 + - - +
66G GLY* 3.4 10.3 - - - +
67G ASN 3.1 0.2 - - - -
68G ALA* 1.3 78.0 - - - +
70G ARG* 1.3 52.5 + - - +
72G ASN* 3.5 1.4 + - - +
73G LYS 3.3 4.5 + - - -
74G LYS* 2.7 47.0 + - - +
75G THR 4.9 2.0 - - - -
76G ARG 4.4 5.2 - - - +
77G ILE* 4.3 12.1 - - + +
81G HIS* 3.6 33.1 - - + +
49H THR* 5.0 2.0 - - + -
----------------------------------------------------------
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Residues in contact with ARG 70 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G GLY 3.2 10.0 + - - +
67G ASN* 2.9 23.9 + - - +
69G ALA* 1.3 77.7 - - - +
71G ASP* 1.3 81.2 + - - +
72G ASN 3.1 5.4 - - - -
73G LYS* 3.3 14.3 + - - +
74G LYS 4.0 7.4 - - - +
----------------------------------------------------------
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Residues in contact with ASP 71 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G ASN* 2.8 30.5 + - - +
68G ALA* 3.4 11.6 + - - +
69G ALA 3.4 0.4 - - - -
70G ARG* 1.3 96.1 + - - +
72G ASN* 1.3 57.3 + - - +
73G LYS* 3.4 3.8 - - - +
----------------------------------------------------------
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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