Contacts of the helix formed by residues 42 - 70 (chain O) in PDB entry 1NF6
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 TYR 42 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K HIS* 4.5 10.2 + + - -
148K ASN* 5.1 9.5 + - - +
149K LEU* 4.4 13.9 - - + +
37O LEU* 3.1 15.2 + - + +
40O MET* 3.6 44.0 - - + -
41O ASP* 1.3 74.8 - - - +
43O GLY* 1.3 52.1 + - - +
44O GLU 3.5 2.2 - - - -
45O LEU* 3.1 16.3 + - + +
46O ALA* 2.9 31.8 + - - +
88O VAL* 4.6 8.7 - - + -
154O LEU* 3.8 51.3 - - + +
157O ILE* 3.7 20.4 - - + -
158O ALA* 4.0 23.6 - - + -
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Residues in contact with GLY 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O ASP* 5.1 0.9 - - - -
41O ASP* 3.4 9.0 + - - -
42O TYR* 1.3 68.9 - - - +
44O GLU* 1.3 57.3 + - - +
46O ALA* 3.0 4.0 + - - +
47O ALA* 2.7 36.9 + - - +
160O THR* 3.4 23.5 + - - -
161O PRO 3.1 8.5 - - - -
162O SER* 3.4 15.8 - - - -
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Residues in contact with GLU 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43O GLY* 1.3 73.5 - - - +
45O LEU* 1.3 60.7 + - + +
47O ALA* 3.6 3.9 + - - +
48O ASN* 3.1 48.4 + - - +
153O TYR* 6.1 0.2 - - - -
156O LYS* 5.4 0.9 - - - +
157O ILE* 2.8 37.9 - - + +
160O THR* 3.4 24.4 + - - +
161O PRO 3.2 9.7 + - - -
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Residues in contact with LEU 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O LEU* 3.8 13.1 - - + +
42O TYR* 3.1 23.6 + - + +
44O GLU* 1.3 80.1 - - + +
46O ALA* 1.3 64.9 - - - +
48O ASN* 3.5 1.7 + - - +
49O MET* 3.1 24.8 + - - +
88O VAL* 4.9 4.0 - - + -
92O TYR* 3.5 30.2 + - + +
138O TYR* 3.6 20.2 + - - +
142O ILE* 4.1 23.8 - - + -
146O ILE* 5.2 0.9 - - + -
153O TYR* 4.6 7.9 - - + +
154O LEU* 4.3 21.3 - - + -
157O ILE* 4.0 17.5 - - + -
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Residues in contact with ALA 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O HIS* 2.5 31.3 + - + +
37O LEU* 3.9 10.9 - - + +
38O ASP* 3.6 43.3 - - + +
42O TYR 2.9 12.4 + - - +
43O GLY* 3.0 10.1 + - - +
45O LEU* 1.3 76.7 - - - +
47O ALA* 1.3 62.5 + - - +
49O MET* 3.4 2.1 + - - +
50O LYS 3.2 7.6 + - - -
162O SER* 4.5 1.8 - - - -
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Residues in contact with ALA 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O HIS* 4.7 1.1 - - - -
43O GLY 2.7 17.5 + - - +
44O GLU* 3.9 6.1 - - - +
46O ALA* 1.3 75.4 - - - +
48O ASN* 1.3 63.3 + - - +
50O LYS 3.3 1.2 + - - -
51O LEU* 3.1 31.1 + - + +
161O PRO 4.8 0.7 - - - +
162O SER* 2.9 32.0 + - - +
163O SER 3.7 10.8 - - - +
164O THR* 3.7 11.0 - - + +
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Residues in contact with ASN 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O GLU* 3.1 35.2 + - - +
47O ALA* 1.3 78.3 - - - +
49O MET* 1.3 56.6 + - - +
51O LEU* 3.6 15.3 + - - +
52O ILE* 3.1 33.7 + - - +
138O TYR* 3.3 36.1 + - + +
171P PHE* 3.7 23.0 - - + -
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Residues in contact with MET 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O TYR* 3.3 29.6 - - - +
33O GLN* 3.0 22.0 - - + +
34O HIS* 3.9 9.9 - - + +
37O LEU* 3.9 16.2 - - + -
45O LEU 3.1 18.1 + - - +
46O ALA 3.6 5.4 - - - +
47O ALA 3.2 0.2 - - - -
48O ASN* 1.3 79.3 - - - +
50O LYS* 1.3 56.8 + - - +
52O ILE* 3.6 3.5 + - - +
53O ALA* 3.1 25.3 + - - +
91O ILE* 3.5 17.5 - - + -
92O TYR* 4.0 7.6 - - + +
95O ASP* 3.0 19.7 - - - +
138O TYR* 5.0 1.9 + - + -
139O TYR* 3.4 32.8 - - + -
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Residues in contact with LYS 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O MET* 3.8 22.9 - - + -
34O HIS* 3.4 34.9 + - + +
46O ALA 3.2 5.1 + - - -
47O ALA 3.8 6.3 - - - +
49O MET* 1.3 74.5 - - - +
51O LEU* 1.3 60.9 + - - +
53O ALA* 3.4 2.3 + - - +
54O ILE* 2.9 35.2 + - + +
164O THR* 3.6 20.9 + - + -
2501O SO4 2.8 33.5 + - - +
2502O FEC 3.6 27.6 - - - +
61P GLU* 3.0 29.1 + - - +
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Residues in contact with LEU 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O ALA* 3.1 24.9 + - + +
48O ASN* 3.8 19.3 - - - +
50O LYS* 1.3 74.3 - - - +
52O ILE* 1.3 59.3 + - - +
54O ILE* 3.3 9.9 + - + +
55O ASP 3.1 20.1 + - - -
163O SER 5.7 0.4 - - - +
164O THR* 4.0 35.9 - - + +
169P LYS* 3.2 33.2 - - + +
170P GLY* 3.7 10.1 - - - +
171P PHE* 3.4 26.0 + - + +
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Residues in contact with ILE 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O TYR* 3.8 15.5 - - + -
48O ASN 3.1 21.8 + - - +
49O MET 3.9 1.8 - - - +
50O LYS 3.3 0.2 - - - -
51O LEU* 1.3 75.2 - - - +
53O ALA* 1.3 66.3 + - - +
55O ASP* 3.0 14.8 + - - +
56O GLU* 3.1 12.6 + - - +
135O HIS* 3.8 30.7 - - + +
138O TYR* 3.6 25.6 - - + -
139O TYR* 3.1 43.1 - - + +
171P PHE* 3.5 26.0 - - + -
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Residues in contact with ALA 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O ILE* 4.0 7.4 - - - +
30O TYR* 4.0 16.1 - - + -
31O MET* 3.8 29.4 - - + +
49O MET 3.1 19.1 + - - +
50O LYS 3.5 6.3 - - - +
51O LEU 3.3 0.2 - - - -
52O ILE* 1.3 76.6 - - - +
54O ILE* 1.3 57.5 + - - +
56O GLU* 3.2 11.8 + - - +
57O MET* 2.9 35.8 + - + +
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Residues in contact with ILE 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O LYS* 2.9 34.5 + - + +
51O LEU* 3.6 11.2 - - + +
52O ILE 3.1 0.4 - - - -
53O ALA* 1.3 75.6 - - - +
55O ASP* 1.3 63.3 + - - +
57O MET* 3.4 27.7 + - + +
58O ARG* 3.2 22.8 + - + +
164O THR* 5.5 2.0 - - - +
2502O FEC 3.9 37.7 - - + -
168P SER* 3.9 22.9 - - - +
169P LYS 3.5 27.4 - - - +
170P GLY* 4.5 1.8 - - - -
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Residues in contact with ASP 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51O LEU 3.1 7.5 + - - -
52O ILE 3.0 9.5 + - - +
54O ILE* 1.3 76.3 - - - +
56O GLU* 1.3 59.6 + - - +
58O ARG* 2.8 37.4 + - - +
59O HIS* 2.9 34.0 + - - +
131O GLU* 4.7 0.4 - - - -
135O HIS* 2.6 35.2 + - + -
170P GLY* 3.6 6.9 - - - -
171P PHE* 3.3 21.6 + - - +
172P VAL* 3.1 24.0 + - - +
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Residues in contact with GLU 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O GLU* 3.3 23.4 - - - +
26O ALA* 4.4 4.3 - - + +
27O ILE* 4.0 13.5 - - + +
30O TYR* 3.5 18.1 - - + -
52O ILE 3.1 17.0 + - - +
53O ALA* 3.5 11.9 - - - +
55O ASP* 1.3 72.3 - - - +
57O MET* 1.3 56.5 + - - +
59O HIS* 2.9 27.1 + - - +
60O ALA* 2.7 35.9 + - - +
99O GLU* 3.3 11.6 - - - +
132O GLU* 3.4 1.5 - - - +
135O HIS* 3.4 4.6 + - - -
200O FE 2.1 30.9 - - - -
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Residues in contact with MET 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O ILE* 3.6 27.3 - - + +
31O MET* 4.4 5.4 - - + -
53O ALA* 2.9 37.8 + - + +
54O ILE* 3.5 24.2 - - + +
55O ASP 3.3 0.2 - - - -
56O GLU* 1.3 76.2 - - - +
58O ARG* 1.3 56.8 + - - +
60O ALA* 3.4 2.8 + - - +
61O GLU* 3.0 28.8 + - - +
2502O FEC 2.4 103.2 - - + +
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Residues in contact with ARG 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54O ILE* 3.2 13.1 + - - +
55O ASP* 2.8 40.6 + - - +
56O GLU 3.1 0.4 - - - -
57O MET* 1.3 73.8 - - - +
59O HIS* 1.3 63.8 + - - +
61O GLU* 3.8 9.7 - - - +
62O ASN* 2.9 43.3 + - - +
131O GLU* 3.7 23.8 + - - -
2502O FEC 3.3 18.6 - - + +
167P ALA* 5.3 5.8 - - - -
168P SER* 2.9 35.0 + - - +
170P GLY* 5.3 0.8 - - - -
172P VAL* 3.7 14.6 + - - +
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Residues in contact with HIS 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O GLU* 2.6 30.9 + - + +
55O ASP* 2.9 25.1 + - - +
56O GLU* 2.9 28.0 + - - +
58O ARG* 1.3 79.4 - - - +
60O ALA* 1.3 66.5 + - - +
62O ASN* 3.1 3.9 + - - +
63O PHE* 2.9 30.6 + - + -
128O ILE* 3.9 38.0 - - + +
131O GLU* 2.7 32.3 + - + +
132O GLU* 3.3 19.0 + - - -
135O HIS* 4.1 7.0 - + - -
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Residues in contact with ALA 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20O ARG* 2.7 41.6 + - + +
23O GLU* 3.9 19.2 - - + +
24O LEU* 4.4 6.7 - - + -
27O ILE* 4.1 14.4 - - + -
56O GLU 2.7 19.0 + - - +
57O MET 3.4 5.6 + - - +
59O HIS* 1.3 73.3 - - - +
61O GLU* 1.3 55.1 + - - +
63O PHE* 3.6 0.6 + - - -
64O ALA 3.2 16.8 + - - -
2502O FEC 4.1 6.7 - - - +
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Residues in contact with GLU 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57O MET 3.0 15.7 + - - +
58O ARG* 3.8 7.1 - - - +
60O ALA* 1.3 74.5 - - - +
62O ASN* 1.3 66.4 + - - +
63O PHE 3.2 0.2 - - - -
64O ALA* 3.4 2.3 + - - +
65O GLU* 2.8 50.5 + - - +
2502O FEC 3.2 40.6 + - + +
31P MET* 4.4 1.3 - - - +
34P HIS* 4.1 8.1 + - - -
35P TYR* 3.6 23.7 + - + +
50P LYS* 3.0 29.5 + - - +
2601P SO4 4.5 5.1 + - - -
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Residues in contact with ASN 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58O ARG* 2.9 35.8 + - - +
59O HIS* 3.9 5.0 - - - +
61O GLU* 1.3 77.5 + - - +
63O PHE* 1.3 61.7 + - - +
65O GLU* 3.3 24.0 + - - +
66O ARG* 3.1 24.1 + - - +
124O LEU* 3.9 28.8 - - + +
128O ILE* 4.7 7.0 - - + +
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Residues in contact with PHE 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O LEU* 3.6 26.6 - - + +
19O ALA* 3.5 11.7 - - + -
20O ARG* 3.8 30.3 - - + -
23O GLU* 3.9 9.9 - - + -
59O HIS 2.9 21.8 + - - +
60O ALA 3.7 4.5 - - - +
62O ASN* 1.3 77.8 - - - +
64O ALA* 1.3 57.6 + - - +
66O ARG* 3.5 2.9 + - - +
67O ILE* 3.0 33.2 + - - +
106O TYR* 3.9 14.6 - + - -
124O LEU* 3.9 13.2 - - + -
125O PHE* 3.3 39.5 - + - -
128O ILE* 3.4 32.5 - - + -
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Residues in contact with ALA 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20O ARG* 3.7 10.2 - - - +
60O ALA 3.2 14.9 + - - +
61O GLU 3.4 1.1 + - - +
63O PHE* 1.3 76.6 - - - +
65O GLU* 1.3 64.5 + - - +
67O ILE* 3.5 4.5 - - - +
68O LYS* 3.0 30.1 + - - +
74O PRO* 3.6 31.8 - - + +
35P TYR* 3.7 22.2 - - + -
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Residues in contact with GLU 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O GLU* 2.8 50.7 + - + +
62O ASN* 3.3 26.3 + - - +
63O PHE 3.3 0.4 - - - -
64O ALA* 1.3 77.8 - - - +
66O ARG* 1.3 59.7 + - - +
68O LYS* 3.5 7.0 + - - +
69O GLU* 2.9 34.1 + - - +
34P HIS* 5.2 2.6 + - - -
35P TYR* 4.6 10.8 - - + -
38P ASP* 4.5 13.4 - - - +
2601P SO4 5.2 4.9 + - - -
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Residues in contact with ARG 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O LEU* 3.6 15.5 - - + -
62O ASN 3.1 17.0 + - - +
63O PHE 3.8 4.7 - - - +
64O ALA 3.2 0.2 - - - -
65O GLU* 1.3 76.3 - - - +
67O ILE* 1.3 65.2 + - - +
69O GLU* 3.0 45.3 + - - +
70O LEU* 3.2 33.0 + - - +
118O ASP* 3.1 29.7 + - - -
120O VAL* 3.9 28.3 - - - +
121O THR* 2.5 26.4 + - + +
124O LEU* 3.9 15.5 - - + -
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Residues in contact with ILE 67 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O ILE* 4.2 12.2 - - + +
16O LEU* 3.5 32.3 - - + -
17O ASN* 3.5 32.5 - - - +
20O ARG* 4.1 4.7 - - - -
63O PHE 3.0 28.9 + - - +
64O ALA* 3.5 7.0 - - - +
66O ARG* 1.3 77.9 - - - +
68O LYS* 1.3 60.2 + - - +
70O LEU* 3.3 6.9 + - - +
71O GLY 3.2 4.9 + - - -
72O GLY* 3.0 49.0 + - - +
73O GLU 3.7 2.7 - - - +
74O PRO* 3.7 21.8 - - + -
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Residues in contact with LYS 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64O ALA 3.0 21.8 + - - +
65O GLU* 3.6 9.2 - - - +
66O ARG 3.2 0.2 - - - -
67O ILE* 1.3 73.4 - - - +
69O GLU* 1.3 65.1 + - + +
71O GLY* 3.1 13.7 + - - -
72O GLY 3.7 16.7 + - - +
73O GLU* 4.0 17.7 + - - -
74O PRO* 4.0 13.5 - - + -
35P TYR* 3.3 42.6 - - + +
36P SER* 3.8 20.1 + - - +
39P ASP* 3.9 37.3 + - + +
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Residues in contact with GLU 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O LYS* 4.7 6.4 + - - -
65O GLU* 2.9 28.4 - - - +
66O ARG* 3.0 40.0 + - - +
68O LYS* 1.3 76.6 - - + +
70O LEU* 1.3 60.4 + - - +
71O GLY* 3.7 0.3 + - - -
120O VAL* 5.1 2.9 - - - +
39P ASP* 5.0 4.7 - - - +
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Residues in contact with LEU 70 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O LYS* 3.4 58.6 + - + +
12O VAL* 3.8 32.5 - - + -
13O ILE* 4.0 17.2 - - + +
16O LEU* 3.9 18.4 - - + -
66O ARG* 3.2 39.3 + - - +
67O ILE 3.6 8.5 - - - +
68O LYS 3.2 0.6 - - - -
69O GLU* 1.3 75.8 - - - +
71O GLY* 1.3 58.1 + - - +
72O GLY 3.6 0.2 - - - -
118O ASP* 3.9 9.4 - - - +
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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).
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