Contacts of the helix formed by residues 56 - 85 (chain H) in PDB entry 1LP9
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 GLY 56 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H GLN 3.4 4.1 + - - -
55H GLU* 1.3 75.2 + - - +
57H PRO* 1.3 78.8 - - - +
58H GLU* 3.2 3.8 - - - -
59H TYR* 2.9 21.7 + - - +
60H TRP* 3.3 9.5 + - - -
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Residues in contact with PRO 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H ARG* 5.8 0.4 - - - +
56H GLY* 1.3 83.5 - - - +
58H GLU* 1.3 57.9 + - - +
60H TRP* 3.2 7.7 + - + +
61H ASP* 2.7 46.1 + - - +
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Residues in contact with GLU 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H GLY 3.1 1.7 + - - -
57H PRO* 1.3 79.5 - - - +
59H TYR* 1.3 56.2 + - - +
61H ASP* 4.0 5.4 - - - +
62H GLY* 2.9 26.2 + - - -
65H ARG* 5.3 1.3 + - - +
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Residues in contact with TYR 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H TYR* 4.6 0.7 + - - -
33H PHE* 3.7 9.9 - - - -
34H VAL* 4.3 3.5 - - + +
52H ILE* 3.6 26.6 - - + +
55H GLU* 3.6 27.8 - - + +
56H GLY 2.9 12.8 + - - +
58H GLU* 1.3 79.1 - - - +
60H TRP* 1.3 80.5 + + - +
62H GLY* 3.1 2.3 + - - -
63H GLU* 2.8 67.3 + - + +
167H TRP* 3.6 31.9 - + + -
171H TYR* 2.7 33.2 + + - -
1J ALA* 4.4 1.8 + - + -
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Residues in contact with TRP 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H VAL* 4.1 11.7 - - + -
44H ARG* 3.3 17.7 - - - +
45H MET* 3.4 34.5 - - + +
46H GLU 3.8 3.4 - - - -
47H PRO* 3.6 44.6 - - + -
52H ILE* 3.5 36.7 + - + -
53H GLU* 4.5 5.0 + - - +
55H GLU* 3.0 22.9 + - - +
56H GLY 3.3 23.7 + - - -
57H PRO* 3.2 7.6 + - + +
59H TYR* 1.3 87.8 - + - +
61H ASP* 1.3 55.2 + - - +
63H GLU* 3.9 1.1 - - + +
64H THR* 2.7 38.0 + - - +
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Residues in contact with ASP 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H ARG* 2.7 38.9 + - - +
57H PRO* 2.7 31.9 + - - +
58H GLU* 4.0 5.6 - - - +
60H TRP* 1.3 71.8 - - - +
62H GLY* 1.3 55.9 + - - +
64H THR* 3.4 1.7 + - - -
65H ARG* 3.0 50.9 + - - +
57M LYS* 6.0 0.2 + - - -
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Residues in contact with GLY 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H GLU 2.9 16.3 + - - -
59H TYR 3.1 2.2 + - - -
61H ASP* 1.3 74.3 - - - +
63H GLU* 1.3 64.4 + - - +
65H ARG* 3.5 19.0 + - - +
66H LYS* 3.1 39.5 + - - +
100L SER* 6.5 0.7 - - - -
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Residues in contact with GLU 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H TYR* 4.0 3.1 + - - -
34H VAL* 5.9 0.2 - - + -
45H MET* 4.0 27.0 - - + +
59H TYR* 2.8 56.1 + - + +
60H TRP* 4.2 2.5 - - - +
62H GLY* 1.3 69.8 - - - -
64H THR* 1.3 61.1 + - - +
66H LYS* 2.9 27.4 + - - +
67H VAL* 2.9 34.0 + - - +
1J ALA* 3.5 14.3 - - - +
2J LEU* 2.8 40.1 + - - +
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Residues in contact with THR 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H GLN 3.8 22.0 - - - +
44H ARG* 3.7 29.4 + - + +
45H MET* 3.1 19.7 + - - +
60H TRP 2.7 24.4 + - - -
61H ASP 3.6 4.3 - - - -
62H GLY 3.2 0.2 - - - -
63H GLU* 1.3 77.5 - - - +
65H ARG* 1.3 63.9 + - - +
67H VAL* 3.4 9.6 - - + +
68H LYS* 2.9 39.7 + - + +
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Residues in contact with ARG 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H GLU* 5.3 1.2 + - - +
61H ASP* 3.0 36.8 + - - +
62H GLY* 3.6 24.6 - - - +
64H THR* 1.3 77.8 - - + +
66H LYS* 1.3 64.5 + - - +
68H LYS* 3.4 7.0 + - - +
69H ALA* 3.1 22.9 + - - +
101L PHE* 3.8 26.3 - - + +
48M TYR* 3.2 25.6 + - - -
50M TYR* 4.3 3.0 + - + -
56M GLU* 3.0 42.5 + - - +
57M LYS* 5.2 14.8 + - - +
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Residues in contact with LYS 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H GLY* 3.1 24.0 + - - +
63H GLU* 2.9 32.5 + - - +
65H ARG* 1.3 76.4 - - - +
67H VAL* 1.3 63.0 + - - +
69H ALA* 3.1 3.1 + - - +
70H HIS* 2.8 29.4 + - - -
1J ALA* 4.2 4.0 - - - +
2J LEU* 2.7 38.7 + - + +
3J TRP 3.5 17.9 - - - +
4J GLY* 3.9 8.5 - - - -
6J PHE* 4.1 17.5 - - + -
99L SER 2.7 25.0 + - - +
100L SER* 4.7 0.9 - - - +
101L PHE* 4.2 17.5 - - + +
----------------------------------------------------------
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Residues in contact with VAL 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PHE* 4.7 4.0 - - + -
22H PHE* 3.8 8.2 - - + -
24H ALA* 3.8 29.2 - - + -
36H PHE* 3.6 38.1 - - + -
45H MET* 4.0 9.0 - - + -
63H GLU 2.9 22.9 + - - +
64H THR* 3.4 10.1 - - - +
66H LYS* 1.3 78.2 - - - +
68H LYS* 1.3 61.0 + - - +
70H HIS* 3.3 4.0 + - - +
71H SER* 3.0 26.7 + - - -
2J LEU* 3.6 17.9 - - + +
----------------------------------------------------------
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Residues in contact with LYS 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H PHE* 3.9 17.3 - - + -
43H GLN* 2.7 51.2 + - - +
44H ARG* 4.9 1.6 - - - +
64H THR* 2.9 33.2 + - + +
65H ARG* 3.9 2.2 - - - +
67H VAL* 1.3 77.0 - - - +
69H ALA* 1.3 57.6 + - - +
71H SER* 3.3 8.4 + - - -
72H GLN* 3.1 27.9 + - - +
50M TYR* 3.0 29.1 - - + +
56M GLU* 5.7 2.0 - - - +
----------------------------------------------------------
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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
----------------------------------------------------------
65H ARG 3.1 13.9 + - - +
66H LYS 3.5 8.1 - - - +
68H LYS* 1.3 75.9 - - - +
70H HIS* 1.3 63.0 + - - +
72H GLN* 3.5 2.8 + - - +
73H THR* 2.8 30.4 + - - -
6J PHE* 3.6 32.5 - - + -
101L PHE* 3.6 13.2 - - + -
31M TYR* 5.0 3.1 + - - +
50M TYR* 4.0 14.1 - - + -
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Residues in contact with HIS 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PHE* 3.6 20.4 - + + -
22H PHE* 4.0 14.4 - - + -
66H LYS 2.8 34.6 + - - -
67H VAL* 3.3 10.7 + - - +
69H ALA* 1.3 76.7 - - - +
71H SER* 1.3 61.9 + - - +
73H THR* 3.3 6.6 + - - -
74H HIS* 3.0 32.5 + - + -
97H ARG* 3.4 19.9 + - - +
99H TYR* 2.8 37.6 + + - -
2J LEU* 4.2 4.8 - - + +
3J TRP* 3.3 22.9 + - + -
5J PHE 5.1 1.3 - - - -
6J PHE* 3.6 18.1 - + - -
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Residues in contact with SER 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H PHE* 3.5 45.3 - - - +
36H PHE* 4.7 7.3 - - - -
38H SER* 4.7 4.7 - - - -
67H VAL 3.0 11.1 + - - -
68H LYS* 3.4 13.9 - - - -
70H HIS* 1.3 76.5 - - - +
72H GLN* 1.3 57.3 + - - +
74H HIS* 3.4 2.3 + - - +
75H ARG* 2.9 28.9 + - - +
----------------------------------------------------------
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Residues in contact with GLN 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H LYS 3.1 15.9 + - - +
69H ALA* 3.8 7.4 - - - +
70H HIS 3.4 0.2 - - - -
71H SER* 1.3 73.7 - - - +
73H THR* 1.3 65.0 + - - +
75H ARG* 3.1 27.4 + - - +
76H VAL* 3.0 42.3 + - + +
30M ASP* 3.7 13.8 + - + +
50M TYR* 4.4 15.5 - - + +
51M VAL* 3.5 39.6 - - + +
----------------------------------------------------------
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Residues in contact with THR 73 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H ALA 2.8 22.4 + - - -
70H HIS* 3.5 7.2 - - - -
72H GLN* 1.3 78.7 - - - +
74H HIS* 1.3 63.0 + - + +
76H VAL* 3.0 9.8 + - - +
77H ASP* 2.9 38.2 + - - +
97H ARG* 5.9 1.3 - - - +
6J PHE* 3.7 19.6 + - + +
7J PRO 3.2 27.8 - - - +
8J VAL* 3.9 18.4 - - + +
31M TYR* 4.5 5.7 + - - -
----------------------------------------------------------
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Residues in contact with HIS 74 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PHE* 3.7 30.7 - + + +
11H SER* 3.7 25.9 + - - +
22H PHE* 3.4 19.8 - + + -
70H HIS* 3.0 18.0 + - + +
71H SER 4.0 2.5 - - - +
73H THR* 1.3 78.6 - - + +
75H ARG* 1.3 65.6 + - - +
77H ASP* 3.5 21.9 - - + +
78H LEU* 3.1 28.5 + - - +
95H VAL* 5.0 7.1 + - + +
97H ARG* 3.5 43.1 + - + -
116H TYR* 4.4 7.7 + + - -
----------------------------------------------------------
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Residues in contact with ARG 75 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H SER* 5.3 0.8 - - - -
18H GLY 3.5 22.6 + - - -
19H GLU* 3.9 15.4 - - - +
20H PRO* 3.8 30.7 - - + +
71H SER 2.9 15.8 + - - +
72H GLN* 3.1 34.0 + - - +
74H HIS* 1.3 76.9 - - - +
76H VAL* 1.3 63.0 + - - +
78H LEU* 3.6 20.2 + - - +
79H GLY* 3.8 3.1 + - - -
----------------------------------------------------------
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Residues in contact with VAL 76 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H GLN* 3.0 38.7 + - + +
73H THR* 3.0 8.9 + - - +
75H ARG* 1.3 78.6 - - + +
77H ASP* 1.3 60.7 + - - +
79H GLY* 3.0 6.1 + - - -
80H THR* 2.9 32.9 + - - +
8J VAL* 5.4 11.4 - - + -
30M ASP* 4.3 10.3 - - - +
----------------------------------------------------------
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Residues in contact with ASP 77 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H THR* 2.9 24.0 + - - +
74H HIS* 3.2 30.0 + - - +
76H VAL* 1.3 75.5 - - - +
78H LEU* 1.3 66.8 + - - +
80H THR* 3.5 7.7 + - - -
81H LEU* 2.8 29.5 + - - +
95H VAL* 4.6 8.0 - - + +
116H TYR* 4.4 3.6 - - - -
7J PRO 4.7 0.7 - - - +
8J VAL* 3.7 9.9 - - - +
9J LEU* 3.1 52.8 + - + +
----------------------------------------------------------
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Residues in contact with LEU 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H SER* 4.1 16.8 - - - +
13H SER* 3.9 21.8 - - - +
20H PRO* 3.8 34.5 - - + -
74H HIS 3.1 16.2 + - - +
75H ARG* 3.7 6.7 - - - +
76H VAL 3.3 0.2 - - - -
77H ASP* 1.3 74.3 - - - +
79H GLY* 1.3 63.3 + - - +
81H LEU* 4.1 2.2 - - - +
82H ARG* 3.1 24.5 + - - +
93H HIS* 3.6 32.7 - - + +
94H THR 4.5 0.2 - - - -
95H VAL* 3.7 24.4 - - + +
118H TYR* 4.8 4.0 + - + -
----------------------------------------------------------
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Residues in contact with GLY 79 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H ARG 3.8 3.0 + - - -
76H VAL* 3.0 9.2 + - - -
78H LEU* 1.3 78.4 - - - +
80H THR* 1.3 63.3 + - - +
82H ARG* 3.4 21.1 + - - +
83H GLY* 3.2 15.9 + - - -
----------------------------------------------------------
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Residues in contact with THR 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H VAL* 2.9 24.5 + - - +
77H ASP* 3.5 12.1 + - - -
79H GLY* 1.3 75.7 - - - +
81H LEU* 1.3 58.6 + - + +
83H GLY* 3.0 6.1 + - - -
84H TYR* 2.9 59.3 + - + +
146H LYS* 4.3 5.0 + - - +
8J VAL* 6.0 0.3 - - - +
9J LEU* 3.5 20.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H ASP 2.8 20.6 + - - +
78H LEU 4.1 1.1 - - - +
80H THR* 1.3 70.7 - - - +
82H ARG* 1.3 66.9 + - - +
84H TYR* 3.0 30.9 + - + -
85H TYR* 3.0 34.2 + - + +
95H VAL* 4.4 5.2 - - + -
118H TYR* 3.4 56.1 - - + -
123H TYR* 3.3 26.0 - - + +
9J LEU* 4.0 25.6 - - + -
----------------------------------------------------------
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Residues in contact with ARG 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H LEU 3.1 18.4 + - - +
79H GLY* 3.5 16.4 + - - +
81H LEU* 1.3 75.7 - - - +
83H GLY* 1.3 80.4 + - - +
86H ASN* 3.0 5.7 + - - -
87H GLN* 2.8 65.8 + - + +
88H SER 4.1 7.0 - - - +
89H GLU* 3.0 46.7 + - - +
93H HIS* 5.6 4.3 - - + +
118H TYR* 4.2 5.0 + - - +
----------------------------------------------------------
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Residues in contact with GLY 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H GLY 3.2 7.5 + - - -
80H THR* 3.0 8.2 + - - -
82H ARG* 1.3 90.5 - - - +
84H TYR* 1.3 61.8 + - - +
86H ASN* 2.9 31.3 + - - -
----------------------------------------------------------
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Residues in contact with TYR 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H THR* 2.9 28.5 + - + -
81H LEU* 3.0 28.0 + - + +
83H GLY* 1.3 76.5 - - - +
85H TYR* 1.3 64.6 + - + +
86H ASN* 3.6 7.3 + - - +
123H TYR* 3.4 16.2 - - - -
139H ALA* 3.8 28.0 - - + +
142H THR* 3.6 23.5 - - + +
143H THR* 3.8 1.3 - - - -
146H LYS* 3.1 24.9 + - - -
9J LEU* 2.8 28.8 + - - -
----------------------------------------------------------
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Residues in contact with TYR 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H LEU* 3.0 27.5 + - + +
84H TYR* 1.3 78.3 - - + +
86H ASN* 1.3 71.8 + - - +
87H GLN* 3.0 28.4 + - + +
118H TYR* 3.5 34.6 - + - +
123H TYR* 3.3 29.0 - + - -
137H ASP* 2.5 30.5 + - - -
139H ALA* 3.6 17.9 - - + -
----------------------------------------------------------
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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