Contacts of the helix formed by residues 42 - 70 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G LEU* 3.0 16.6 + - + +
40G MET* 3.6 42.6 - - + -
41G ASP* 1.3 80.1 - - - +
43G GLY* 1.3 54.7 + - - +
44G GLU 3.3 2.5 - - - -
45G LEU* 2.8 34.9 + - + -
46G ALA* 2.9 11.8 + - - +
88G VAL* 4.6 11.7 - - + -
154G LEU* 3.7 50.8 - - + +
157G ILE* 3.7 22.4 - - + -
158G ALA* 3.9 21.8 - - + -
145I HIS* 4.4 7.6 + + - -
148I ASN* 5.1 9.4 + - - +
149I LEU* 4.3 11.8 - - + +
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Residues in contact with GLY 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G ASP* 5.0 1.3 - - - -
41G ASP* 3.5 6.1 + - - -
42G TYR* 1.3 73.0 - - - +
44G GLU* 1.3 50.9 + - - +
46G ALA* 3.2 4.5 + - - +
47G ALA* 2.7 37.6 + - - +
160G THR* 3.2 26.7 + - - -
161G PRO 3.2 9.3 - - - +
162G SER* 3.6 14.8 - - - -
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Residues in contact with GLU 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G TYR 3.2 0.2 + - - -
43G GLY* 1.3 73.3 - - - +
45G LEU* 1.3 66.5 + - + +
47G ALA* 3.4 3.8 + - - +
48G ASN* 3.2 40.1 + - - +
153G TYR* 5.1 3.3 + - - -
156G LYS* 5.0 6.6 - - - +
157G ILE* 3.9 29.4 - - + +
160G THR* 3.1 30.3 + - - +
161G PRO 3.4 5.3 + - - -
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Residues in contact with LEU 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G LEU* 3.9 20.0 - - + +
42G TYR* 2.8 25.0 + - + +
44G GLU* 1.3 83.4 - - + +
46G ALA* 1.3 62.5 + - - +
48G ASN* 4.1 1.2 - - - +
49G MET* 3.2 24.9 + - - +
88G VAL* 5.0 2.2 - - + -
92G TYR* 3.4 31.6 + - + +
138G TYR* 3.7 17.1 + - - +
142G ILE* 3.9 26.5 - - + -
146G ILE* 4.9 4.9 - - + -
153G TYR* 4.3 7.6 - - + +
154G LEU* 4.8 10.8 - - + -
157G ILE* 3.9 20.4 - - + +
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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
----------------------------------------------------------
34G HIS* 2.8 31.3 + - + +
37G LEU* 3.9 10.6 - - + +
38G ASP* 3.7 44.2 - - - +
42G TYR 2.9 10.0 + - - +
43G GLY* 3.5 8.5 - - - +
45G LEU* 1.3 78.3 - - - +
47G ALA* 1.3 62.8 + - - +
49G MET* 3.5 1.3 + - - +
50G LYS* 3.4 9.7 + - - +
162G SER* 4.8 1.6 - - - -
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G HIS* 5.3 0.4 - - - -
43G GLY 2.7 21.6 + - - +
44G GLU* 3.8 6.3 - - - +
45G LEU 3.3 0.4 - - - -
46G ALA* 1.3 74.5 - - - +
48G ASN* 1.3 66.6 + - - +
49G MET 3.3 0.3 + - - -
50G LYS 3.3 2.4 + - - -
51G LEU* 3.0 29.3 + - + +
161G PRO 4.6 1.8 - - - +
162G SER* 3.6 19.7 + - - +
163G SER 4.0 9.0 - - - +
164G THR* 3.4 18.4 - - + +
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Residues in contact with ASN 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 3.2 27.8 + - - +
47G ALA* 1.3 79.2 - - - +
49G MET* 1.3 56.7 + - - +
51G LEU* 3.3 19.6 + - - +
52G ILE* 2.8 34.9 + - - +
138G TYR* 3.3 39.5 + - + +
171H PHE* 3.8 19.1 - - + -
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Residues in contact with MET 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G TYR* 3.1 32.5 - - - +
33G GLN* 3.4 21.3 - - + +
34G HIS* 3.8 11.2 - - + +
37G LEU* 4.0 15.0 - - + -
45G LEU 3.2 16.4 + - - +
46G ALA 3.8 4.5 - - - +
47G ALA 3.2 0.2 - - - -
48G ASN* 1.3 76.1 - - - +
50G LYS* 1.3 53.8 + - - +
52G ILE* 3.4 6.8 + - - +
53G ALA* 2.8 31.9 + - - +
91G ILE* 4.0 15.5 - - + -
92G TYR* 4.1 9.0 - - + +
95G ASP* 3.4 16.2 - - - +
138G TYR* 5.3 1.9 - - + -
139G TYR* 3.5 30.7 - - + -
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Residues in contact with LYS 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G MET* 4.1 25.1 - - + -
34G HIS* 3.9 20.8 + - + +
46G ALA 3.4 9.8 + - - +
47G ALA 3.3 7.5 + - - +
49G MET* 1.3 77.2 - - - +
51G LEU* 1.3 57.1 + - - +
53G ALA* 3.2 1.2 + - - +
54G ILE* 2.7 49.8 + - + +
164G THR* 3.7 16.2 - - + -
1701G SO4 2.9 31.9 + - - +
1704G FEC 3.5 28.3 - - + +
61H GLU* 2.5 37.1 + - - +
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Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G ALA* 3.0 21.2 + - + +
48G ASN* 3.6 26.9 - - - +
50G LYS* 1.3 77.4 - - - +
52G ILE* 1.3 56.3 + - - +
54G ILE* 3.1 9.6 + - + +
55G ASP 3.0 22.2 + - - -
164G THR* 3.8 26.2 - - + +
169H LYS* 3.4 47.8 - - - +
170H GLY* 4.0 11.2 - - - +
171H PHE* 3.3 28.1 + - + +
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Residues in contact with ILE 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G TYR* 3.9 14.4 - - + -
48G ASN 2.8 22.0 + - - +
49G MET* 3.7 4.0 - - - +
51G LEU* 1.3 74.3 - - - +
53G ALA* 1.3 66.6 + - - +
55G ASP* 3.1 6.7 + - - +
56G GLU* 3.0 25.2 + - - +
135G HIS* 3.6 30.7 - - + +
138G TYR* 3.5 29.6 - - + -
139G TYR* 3.3 39.5 - - + +
171H PHE* 3.6 25.6 - - + -
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Residues in contact with ALA 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ILE* 4.0 7.3 - - - +
30G TYR* 4.0 15.7 - - + -
31G MET* 3.8 32.1 - - + -
49G MET 2.8 21.5 + - - +
50G LYS 3.2 5.8 + - - +
52G ILE* 1.3 73.7 - - - +
54G ILE* 1.3 58.2 + - - +
56G GLU* 3.1 13.2 + - - +
57G MET* 2.9 32.9 + - + +
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Residues in contact with ILE 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G LYS* 2.7 46.6 + - + +
51G LEU* 3.5 10.8 - - + +
52G ILE 3.1 0.4 - - - -
53G ALA* 1.3 72.2 - - - +
55G ASP* 1.3 64.3 + - - +
57G MET* 3.2 27.6 + - + +
58G ARG* 3.1 21.5 + - - +
164G THR* 5.3 1.6 - - - +
1704G FEC 4.1 31.2 - - + -
168H SER* 3.5 32.1 - - - +
169H LYS 3.8 20.2 - - - +
170H GLY* 4.3 3.6 - - - -
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Residues in contact with ASP 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G LEU 3.0 9.1 + - - -
52G ILE 3.1 8.3 + - - +
54G ILE* 1.3 76.0 - - - +
56G GLU* 1.3 59.3 + - - +
58G ARG* 2.9 34.6 + - - +
59G HIS* 3.0 31.6 + - - +
131G GLU* 4.6 1.8 - - - +
135G HIS* 2.8 33.8 + - + -
170H GLY* 3.4 7.6 - - - -
171H PHE* 3.2 21.3 + - - +
172H VAL* 3.0 26.4 + - + +
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Residues in contact with GLU 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G GLU* 3.5 27.4 - - - +
26G ALA* 4.2 7.4 - - + +
27G ILE* 3.7 15.3 - - + +
30G TYR* 3.5 16.2 - - + -
52G ILE* 3.0 17.9 + - - +
53G ALA* 3.1 12.1 + - - +
55G ASP* 1.3 73.7 - - - +
57G MET* 1.3 58.2 + - - +
59G HIS* 3.3 16.9 + - - +
60G ALA 3.0 23.2 + - - -
99G GLU* 3.3 11.6 - - - +
132G GLU* 3.4 2.2 - - - +
135G HIS* 3.1 12.8 + - - -
200G FE 2.1 32.8 - - - -
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Residues in contact with MET 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ILE* 3.6 24.9 - - + +
31G MET* 4.3 6.5 - - + -
53G ALA* 2.9 31.4 + - + +
54G ILE* 3.4 19.1 - - + +
56G GLU* 1.3 75.5 - - - +
58G ARG* 1.3 57.6 + - - +
60G ALA* 3.3 4.0 + - - +
61G GLU* 3.0 28.1 + - - +
1704G FEC 2.4 109.0 - - + +
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Residues in contact with ARG 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G ILE 3.1 5.3 + - - +
55G ASP* 2.9 40.7 + - - +
57G MET* 1.3 74.9 - - - +
59G HIS* 1.3 63.9 + - - +
61G GLU* 3.2 10.1 + - - +
62G ASN* 2.8 47.0 + - - +
131G GLU* 2.8 35.6 + - - -
1704G FEC 3.7 22.2 - - + +
167H ALA* 5.1 8.1 - - - -
168H SER* 3.1 33.7 + - - +
170H GLY* 5.4 0.4 - - - -
172H VAL* 3.4 8.3 - - - +
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Residues in contact with HIS 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G GLU* 2.8 30.2 + - + +
55G ASP 3.0 18.4 + - - -
56G GLU* 3.3 21.9 + - - +
57G MET 3.3 0.2 - - - -
58G ARG* 1.3 81.9 - - + +
60G ALA* 1.3 64.0 + - - +
62G ASN* 3.0 6.5 + - - +
63G PHE* 2.9 29.5 + - + -
128G ILE* 3.6 40.5 - - + +
131G GLU* 3.1 36.5 + - + +
132G GLU* 3.3 21.5 - - - -
135G HIS* 4.4 2.5 - + - -
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Residues in contact with ALA 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ARG* 3.1 38.2 + - + +
23G GLU* 3.9 17.0 - - + +
24G LEU* 4.8 2.7 - - + +
27G ILE* 4.1 12.6 - - + -
56G GLU 3.0 10.5 + - - +
57G MET 3.6 7.6 - - - +
59G HIS* 1.3 77.8 - - - +
61G GLU* 1.3 62.8 + - - +
63G PHE* 3.4 4.1 + - - +
64G ALA 3.0 18.5 + - - -
1704G FEC 3.9 6.7 - - + +
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Residues in contact with GLU 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G MET 3.0 12.0 + - - +
58G ARG* 3.4 10.9 - - - +
60G ALA* 1.3 75.7 - - - +
62G ASN* 1.3 74.2 + - - +
64G ALA* 3.4 2.8 + - - +
65G GLU* 2.9 38.2 + - - +
1704G FEC 3.1 45.3 + - + +
31H MET* 4.2 4.3 - - - +
34H HIS* 4.4 6.1 + - - -
35H TYR* 3.5 23.0 + - + +
50H LYS* 2.6 31.5 + - - +
1801H SO4 4.6 3.8 + - - -
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Residues in contact with ASN 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G ARG* 2.8 35.4 + - - +
59G HIS* 3.7 7.2 + - - +
61G GLU* 1.3 85.0 + - - +
63G PHE* 1.3 63.4 + - - +
65G GLU* 3.2 24.9 + - - +
66G ARG* 3.0 22.2 + - - +
124G LEU* 3.9 28.4 - - + +
128G ILE* 4.8 5.6 - - + +
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Residues in contact with PHE 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G LEU* 3.3 29.2 - - + +
19G ALA* 3.4 21.5 - - + -
20G ARG* 3.9 30.5 - - + -
23G GLU* 4.0 8.3 - - + -
59G HIS 2.9 23.9 + - - +
60G ALA 3.7 4.5 - - - +
62G ASN* 1.3 75.7 - - - +
64G ALA* 1.3 57.8 + - - +
66G ARG* 3.0 4.7 + - - +
67G ILE* 2.8 34.1 + - - +
106G TYR* 3.7 21.1 - + - -
124G LEU* 3.7 13.2 - - + -
125G PHE* 3.7 27.6 - + - -
128G ILE* 3.6 27.6 - - + -
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Residues in contact with ALA 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ARG* 3.7 16.3 - - - +
60G ALA 3.0 16.9 + - - +
61G GLU 3.6 5.2 - - - +
63G PHE* 1.3 76.3 - - - +
65G GLU* 1.3 61.4 + - - +
67G ILE* 3.4 13.6 + - - +
68G LYS* 2.9 30.0 + - - +
74G PRO* 3.7 19.0 - - + +
35H TYR* 3.7 19.5 - - + -
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Residues in contact with GLU 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G GLU* 2.9 28.2 + - + +
62G ASN* 3.2 33.2 + - - +
63G PHE 3.2 0.2 - - - -
64G ALA* 1.3 75.7 - - - +
66G ARG* 1.3 58.9 + - - +
68G LYS* 3.5 6.9 + - - +
69G GLU* 3.1 36.2 + - - +
34H HIS* 5.7 0.9 + - - -
35H TYR* 4.9 10.5 - - + -
38H ASP* 3.8 18.4 - - - +
1801H SO4 5.6 1.9 + - - -
----------------------------------------------------------
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Residues in contact with ARG 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN* 3.3 27.1 - - - +
16G LEU* 3.6 14.6 - - + -
62G ASN 3.0 10.5 + - - +
63G PHE 3.0 7.8 + - - +
65G GLU* 1.3 74.8 - - - +
67G ILE* 1.3 67.3 + - - +
69G GLU* 3.0 37.9 + - - +
70G LEU* 3.0 45.6 + - + +
118G ASP* 3.2 23.2 + - - -
120G VAL* 3.5 27.7 - - - +
121G THR* 2.9 26.6 + - + +
124G LEU* 4.1 14.8 - - + -
----------------------------------------------------------
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Residues in contact with ILE 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ILE* 4.5 10.0 - - + +
16G LEU* 3.5 37.0 - - + +
17G ASN* 3.4 30.5 - - - +
20G ARG* 4.2 4.7 - - - -
63G PHE 2.8 25.9 + - - +
64G ALA* 3.5 9.9 - - - +
66G ARG* 1.3 76.8 - - - +
68G LYS* 1.3 60.1 + - - +
70G LEU* 3.2 11.3 + - - +
72G GLY* 2.8 50.8 + - - +
73G GLU 3.6 2.9 - - - +
74G PRO* 3.6 19.5 - - + -
----------------------------------------------------------
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Residues in contact with LYS 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G ALA 2.9 19.7 + - - +
65G GLU* 3.6 7.9 - - - +
67G ILE* 1.3 75.8 - - - +
69G GLU* 1.3 64.2 + - + +
71G GLY* 3.0 14.4 + - - -
72G GLY 3.5 15.5 + - - +
73G GLU* 3.4 21.6 + - - -
74G PRO* 3.6 19.0 - - + +
32H ASN 5.5 0.2 + - - -
35H TYR* 3.7 33.4 - - + +
36H SER* 3.7 19.7 + - - +
39H ASP* 3.9 38.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN* 4.4 10.8 - - - +
137B THR* 4.0 23.9 + - + +
140B GLU* 5.6 1.6 - - - +
9G LYS* 5.5 2.1 - - - -
65G GLU* 3.1 21.5 + - - +
66G ARG* 3.0 44.5 + - - +
68G LYS* 1.3 77.5 - - + +
70G LEU* 1.3 60.5 + - - +
71G GLY 3.3 1.2 + - - -
120G VAL* 5.1 1.2 - - - +
39H ASP* 5.0 4.0 - - - +
----------------------------------------------------------
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Residues in contact with LEU 70 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G LYS* 3.7 44.2 - - + +
12G VAL* 3.7 35.7 - - + -
13G ILE* 3.6 26.5 - - + +
16G LEU* 4.0 14.6 - - + -
66G ARG* 3.0 41.6 + - - +
67G ILE 3.6 5.6 - - - +
68G LYS 3.1 0.8 - - - -
69G GLU* 1.3 80.2 - - - +
71G GLY* 1.3 59.4 + - - +
72G GLY 3.4 0.7 - - - -
118G ASP* 3.8 7.9 - - - +
121G THR* 4.2 1.6 - - - +
----------------------------------------------------------
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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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