Contacts of the helix formed by residues 41 - 67 (chain H) in PDB entry 1R5I
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 THR 41 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H SER* 4.0 9.4 + - - -
38H LYS* 2.9 17.0 + - + +
39H GLU 3.0 0.4 + - - -
40H GLU* 1.3 82.8 - - + +
42H LYS* 1.3 64.5 + - - +
43H GLU 3.3 2.9 - - - -
44H VAL* 3.2 9.9 - - - +
45H LEU* 3.0 24.5 + - - +
94H ALA 4.6 2.9 - - - -
95H ASN* 2.5 65.6 + - + +
97H VAL* 3.8 16.8 - - + -
100H ILE* 4.7 1.6 - - - -
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Residues in contact with LYS 42 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H SER 5.9 1.6 - - - +
37H ASN 5.5 3.3 + - - +
38H LYS 4.1 3.8 - - - +
39H GLU* 2.9 64.3 + - + +
40H GLU 3.5 0.2 - - - -
41H THR* 1.3 78.8 + - - +
43H GLU* 1.3 66.8 + - + +
45H LEU* 3.5 10.1 + - - +
46H LYS* 3.4 29.9 + - - +
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Residues in contact with GLU 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ILE* 4.2 8.7 - - - +
39H GLU 4.8 0.4 + - - -
40H GLU 5.1 3.2 + - - +
41H THR 3.3 0.8 - - - -
42H LYS* 1.3 79.2 - - + +
44H VAL* 1.3 65.4 + - - +
46H LYS* 2.8 56.1 + - - +
47H LEU* 3.6 13.3 + - - +
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Residues in contact with VAL 44 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H GLU 5.6 0.4 + - - -
41H THR 3.2 14.9 + - - +
43H GLU* 1.3 74.4 - - - +
45H LEU* 1.3 65.2 + - - +
47H LEU* 3.0 17.8 + - + +
48H PHE* 2.9 27.1 + - - +
97H VAL* 4.0 21.3 - - + +
100H ILE* 3.5 41.1 - - + -
101H LYS* 3.6 33.2 - - + +
104H ILE* 4.7 5.4 - - + -
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Residues in contact with LEU 45 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H TYR* 4.1 21.3 - - + +
36H SER* 3.6 34.3 - - - +
41H THR 3.0 14.1 + - - +
42H LYS* 3.6 11.0 - - - +
44H VAL* 1.3 85.0 - - + +
46H LYS* 1.3 61.0 + - + +
48H PHE* 4.0 24.2 - - + -
49H LYS* 3.1 53.8 + - + +
90H GLN* 5.5 0.7 - - - +
100H ILE* 5.2 2.0 - - + -
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Residues in contact with LYS 46 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ILE* 3.6 40.9 - - + +
42H LYS* 3.4 18.4 - - - +
43H GLU* 2.8 45.9 + - - +
44H VAL 3.1 0.6 - - - -
45H LEU* 1.3 75.4 - - + +
47H LEU* 1.3 65.9 + - - +
49H LYS* 3.2 11.5 + - - +
50H LEU* 3.0 28.6 + - + +
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Residues in contact with LEU 47 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D LYS* 5.4 9.6 - - + +
144D ILE* 4.5 15.9 - - + -
193D TYR* 4.9 1.0 + - - -
213D ASP* 4.3 31.4 - - - +
43H GLU* 3.7 16.4 - - - +
44H VAL* 3.0 19.6 + - + +
46H LYS* 1.3 84.3 - - + +
48H PHE* 1.3 57.3 + - - +
50H LEU* 3.4 12.7 + - + +
51H LYS* 3.0 28.1 + - - +
101H LYS* 5.8 2.2 - - + -
104H ILE* 3.7 17.2 - - + +
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Residues in contact with PHE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ILE* 4.9 1.8 - - + -
33H TYR* 3.5 36.6 - + - -
44H VAL 2.9 12.1 + - - +
45H LEU* 3.4 18.8 - - + +
47H LEU* 1.3 73.4 - - - +
49H LYS* 1.3 64.6 + - - +
51H LYS* 3.0 5.7 + - - +
52H VAL* 2.9 30.2 + - + +
86H VAL* 5.6 2.0 - - + -
87H PHE* 3.9 23.6 - + - -
90H GLN* 3.6 40.4 - - + -
100H ILE* 3.8 24.7 - - + -
103H ASN* 4.5 12.3 - - + -
104H ILE* 3.5 18.1 - - + +
107H LEU* 4.9 9.0 - - + -
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Residues in contact with LYS 49 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D LYS* 3.5 33.1 - - - +
30H GLU* 5.0 5.5 + - - +
33H TYR* 3.6 55.0 - - + +
45H LEU* 3.1 43.8 + - + +
46H LYS* 3.2 10.8 + - - +
48H PHE* 1.3 77.0 - - - +
50H LEU* 1.3 63.8 + - - +
52H VAL* 3.2 2.9 + - - +
53H ASN* 3.0 29.4 + - - +
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Residues in contact with LEU 50 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D LYS* 3.9 38.6 - - + +
144D ILE* 4.1 21.8 - - + -
147D LYS* 3.6 36.6 - - + +
193D TYR* 4.2 21.6 + - + +
194D TYR* 4.6 12.3 - - + -
46H LYS* 3.0 17.7 + - + +
47H LEU* 3.5 15.0 - - + +
49H LYS* 1.3 76.6 - - - +
51H LYS* 1.3 57.7 + - - +
53H ASN* 3.4 9.1 + - + +
54H GLN* 2.9 27.9 + - - +
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Residues in contact with LYS 51 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D TYR* 3.2 21.6 + - - +
47H LEU 3.0 10.2 + - - +
48H PHE 3.0 10.4 + - - +
50H LEU* 1.3 74.7 - - - +
52H VAL* 1.3 56.8 + - - +
54H GLN* 2.6 30.7 + - - +
55H PHE* 2.7 35.9 + - - +
104H ILE* 3.4 46.5 - - + +
107H LEU* 4.1 16.8 - - + -
108H ASP* 3.0 27.6 + - - +
111H MET* 3.4 16.8 - - + -
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Residues in contact with VAL 52 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H LEU* 3.9 25.4 - - + -
33H TYR* 3.3 27.8 - - + +
48H PHE* 2.9 39.1 + - + +
49H LYS 3.7 2.5 - - - +
51H LYS* 1.3 74.4 - - - +
53H ASN* 1.3 66.0 + - - +
55H PHE* 3.0 10.2 + - - +
56H TYR* 2.9 35.1 + - + -
83H LEU* 5.1 2.0 - - + -
87H PHE* 4.3 14.1 - - + -
107H LEU* 4.2 12.3 - - + -
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Residues in contact with ASN 53 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D LYS* 4.2 32.5 + - - +
194D TYR* 4.8 6.5 - - + +
29H LEU* 5.7 2.1 - - - +
33H TYR* 4.7 3.5 + - - -
49H LYS* 3.0 18.0 + - - +
50H LEU* 3.5 11.9 - - + +
52H VAL* 1.3 82.7 - - - +
54H GLN* 1.3 61.5 + - - +
56H TYR* 3.1 9.8 + - - +
57H ARG* 3.0 28.3 + - + +
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Residues in contact with GLN 54 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D TYR* 2.9 52.9 + - + +
194D TYR* 4.2 12.0 - - - +
196D GLY* 3.6 8.4 - - - -
197D ASP 3.3 21.6 + - - -
198D ILE* 4.4 5.1 - - - +
50H LEU 2.9 14.8 + - - +
51H LYS* 2.6 42.9 + - - +
53H ASN* 1.3 74.8 - - - +
55H PHE* 1.3 57.3 + - - +
57H ARG* 3.3 2.6 + - - +
58H HIS* 2.9 27.9 + - - +
108H ASP* 4.2 1.0 + - - +
111H MET* 3.4 13.2 - - - +
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Residues in contact with PHE 55 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H LYS 2.7 16.5 + - - +
52H VAL* 3.0 15.2 + - + +
54H GLN* 1.3 72.8 - - - +
56H TYR* 1.3 72.6 + + + +
58H HIS* 3.0 4.3 + - - +
59H ALA* 3.0 19.4 + - - +
79H MET* 3.4 44.2 - - + +
80H PHE* 4.5 12.1 - + - -
83H LEU* 3.9 28.0 - - + -
107H LEU* 3.9 24.9 - - + -
110H ILE* 3.5 37.7 - - + -
111H MET* 3.8 24.9 - - + -
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Residues in contact with TYR 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H VAL* 3.4 18.2 - - + -
24H PHE* 2.6 45.9 + - - +
29H LEU* 3.7 11.9 - - + +
52H VAL* 2.9 36.8 + - + +
53H ASN* 3.1 10.5 + - - +
55H PHE* 1.3 80.4 - + - +
57H ARG* 1.3 67.8 + - - +
59H ALA* 3.0 12.1 + - - +
60H PHE* 3.0 38.4 + + + -
80H PHE* 3.5 27.4 - + - -
83H LEU* 4.5 7.9 - - + -
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Residues in contact with ARG 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D TYR 3.0 29.4 - - - +
195D GLU* 3.6 21.2 + - - +
53H ASN* 3.0 13.3 + - + +
54H GLN 3.8 1.3 - - - +
56H TYR* 1.3 82.0 - - - +
58H HIS* 1.3 58.6 + - - +
60H PHE* 3.9 34.8 + - - +
61H GLY* 2.9 27.2 + - - +
64H ASN* 6.1 1.8 - - - +
----------------------------------------------------------
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Residues in contact with HIS 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D GLU 4.3 1.1 + - - -
196D GLY* 3.0 26.9 + - - +
198D ILE* 4.4 13.4 - - + +
4H ARG* 3.5 15.3 + - - -
54H GLN 2.9 13.8 + - - +
55H PHE 3.0 8.5 + - - +
57H ARG* 1.3 77.7 - - - +
59H ALA* 1.3 64.1 + - - +
61H GLY* 3.1 2.5 + - - -
62H ILE* 3.1 32.9 + - + +
79H MET* 4.4 5.2 - - - -
111H MET* 3.6 39.3 + - + +
115H ASP* 3.0 39.8 + - - -
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Residues in contact with ALA 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H PHE* 3.0 12.9 + - + +
56H TYR 3.6 6.3 - - - +
58H HIS* 1.3 76.0 - - - +
60H PHE* 1.3 58.6 + - - +
62H ILE* 3.0 20.1 + - - +
63H VAL* 3.1 13.9 + - - +
76H PHE* 3.4 22.9 - - + -
79H MET* 3.2 31.1 - - + +
80H PHE* 3.7 17.0 - - + -
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Residues in contact with PHE 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H VAL* 4.9 13.5 - - + -
56H TYR* 3.0 51.1 + + + +
57H ARG* 4.1 31.3 + - - +
59H ALA* 1.3 73.8 - - + +
61H GLY* 1.3 60.4 + - - +
63H VAL* 3.6 16.4 - - + +
64H ASN* 2.8 31.4 + - - +
76H PHE* 3.7 29.8 - + - -
80H PHE* 4.8 4.3 - + - -
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Residues in contact with GLY 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D GLU 5.8 0.4 - - - -
4H ARG* 4.2 9.9 + - - -
57H ARG* 2.9 22.5 + - - +
58H HIS* 3.5 3.1 - - - -
59H ALA 3.0 0.6 - - - -
60H PHE* 1.3 79.9 - - - +
62H ILE* 1.3 62.0 + - - +
64H ASN* 3.1 15.1 + - - +
65H ASP* 3.2 18.2 + - - +
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Residues in contact with ILE 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ARG* 3.7 21.8 - - - +
58H HIS* 3.1 14.6 + - - +
59H ALA 3.0 8.4 + - - +
61H GLY* 1.3 77.4 - - - +
63H VAL* 1.3 60.1 + - + +
65H ASP 3.6 0.2 + - - -
66H TYR* 3.0 31.5 + - + +
72H TYR* 5.0 11.8 - - + +
75H ILE* 4.0 14.8 - - + -
76H PHE* 5.6 1.1 - - + +
79H MET* 3.6 25.1 - - + -
114H ALA* 3.9 19.3 - - + -
115H ASP* 4.1 11.7 - - - +
118H LEU* 4.2 28.3 - - + -
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Residues in contact with VAL 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H ALA 3.1 16.8 - - - +
60H PHE* 3.3 21.3 + - + +
62H ILE* 1.3 76.5 - - + +
64H ASN* 1.3 64.8 + - - +
67H ASN* 3.2 30.0 + - + +
72H TYR* 3.6 33.7 - - + +
76H PHE* 3.5 28.0 - - + -
----------------------------------------------------------
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Residues in contact with ASN 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ARG* 6.1 1.8 - - - +
60H PHE 2.8 17.4 + - - +
61H GLY* 3.1 8.7 + - - +
63H VAL* 1.3 82.9 - - + +
65H ASP* 1.3 62.3 + - - +
67H ASN* 3.6 8.9 + - - +
182H LEU* 5.0 0.9 - - - +
185H LYS* 2.7 52.7 + - - +
204H SER* 4.7 9.5 - - - -
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Residues in contact with ASP 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ARG* 4.2 6.5 + - - +
61H GLY 3.2 11.2 + - - +
64H ASN* 1.3 79.8 - - - +
66H TYR* 1.3 84.0 + - + +
67H ASN* 3.7 2.6 + - - -
68H GLY 5.2 0.2 + - - -
128H PHE* 4.9 0.2 - - - -
132H TRP* 3.3 25.7 + - + -
178H TRP* 6.1 0.3 - - - -
182H LEU* 4.8 9.1 - - - +
185H LYS* 5.4 1.6 + - - +
204H SER* 3.2 16.4 - - - -
205H ASP* 2.8 33.2 + - - +
206H PHE* 3.1 32.6 + - - +
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Residues in contact with TYR 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET* 5.2 4.7 - - - -
2H LYS* 4.8 9.4 + - - +
3H LEU* 6.0 0.3 - - - -
4H ARG* 4.2 7.1 + - + +
62H ILE* 3.0 22.6 + - - +
65H ASP* 1.3 99.4 - - + +
67H ASN* 1.3 55.6 + - - +
68H GLY 2.9 12.8 + - - +
69H LEU* 2.9 18.6 + - + +
72H TYR* 3.3 16.5 - - + +
118H LEU* 3.8 39.3 - - + -
122H ILE* 3.9 19.7 - - + +
128H PHE* 3.9 23.8 - + - -
132H TRP* 4.1 23.4 - + - -
205H ASP* 2.8 35.7 + - + +
----------------------------------------------------------
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Residues in contact with ASN 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H VAL* 3.2 27.8 + - + +
64H ASN* 3.6 15.4 + - - +
65H ASP 3.7 1.5 + - - -
66H TYR* 1.3 73.7 - - - +
68H GLY* 1.3 61.8 + - - +
69H LEU 3.2 2.1 + - - +
72H TYR* 3.7 33.6 - - + +
177H TRP* 5.2 11.2 - - - -
178H TRP* 3.2 27.7 - - - +
181H SER* 6.0 1.6 - - - -
182H LEU* 5.6 5.3 - - - +
185H LYS* 4.5 5.7 - - - +
----------------------------------------------------------
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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