Contacts of the helix formed by residues 42 - 70 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G HIS* 4.7 3.5 + + - -
148G ASN* 5.3 6.6 + - - +
149G LEU* 4.1 16.3 - - + +
37M LEU* 2.9 16.7 + - + +
38M ASP* 5.6 0.2 - - - -
40M MET* 3.5 45.8 - - + -
41M ASP* 1.3 75.8 - - - +
43M GLY* 1.3 58.2 + - - +
44M GLU 3.5 1.6 - - - -
45M LEU* 3.2 19.7 + - + -
46M ALA* 3.0 28.3 + - - +
88M VAL* 4.4 8.7 - - + -
154M LEU* 3.9 57.7 - - + +
157M ILE* 4.0 7.4 - - + -
158M ALA* 3.9 26.2 - - + -
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Residues in contact with GLY 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M ASP* 5.2 0.9 - - - -
41M ASP* 3.4 8.3 + - - -
42M TYR* 1.3 71.5 - - - +
44M GLU* 1.3 62.0 + - - +
46M ALA* 3.4 1.9 + - - +
47M ALA* 3.1 18.5 + - - +
160M THR* 3.1 28.8 + - - -
161M PRO 3.2 8.5 - - - +
162M SER* 3.4 23.8 - - - -
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Residues in contact with GLU 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M TYR 3.5 0.4 - - - -
43M GLY* 1.3 73.3 - - - +
45M LEU* 1.3 64.5 + - + +
47M ALA* 3.4 4.4 + - + +
48M ASN* 3.2 43.6 + - - +
153M TYR* 4.6 5.4 + - - -
157M ILE* 3.6 27.6 - - + +
160M THR* 3.0 22.2 + - + +
161M PRO 3.5 6.2 + - - +
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Residues in contact with LEU 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M LEU* 3.8 17.1 - - + +
42M TYR* 3.2 19.3 + - + +
44M GLU* 1.3 77.8 - - + +
46M ALA* 1.3 65.5 + - - +
48M ASN* 4.0 1.0 - - - +
49M MET* 3.1 25.5 + - - +
88M VAL* 5.0 3.6 - - + -
92M TYR* 3.3 31.9 + - + +
138M TYR* 3.8 14.6 + - - +
142M ILE* 3.8 23.6 - - + -
146M ILE* 5.2 0.2 - - + -
153M TYR* 4.2 15.5 - - + +
154M LEU* 3.8 29.4 - - + -
157M ILE* 4.1 11.0 - - + +
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Residues in contact with ALA 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M HIS* 2.5 35.2 + - + +
37M LEU* 3.7 12.3 - - + +
38M ASP* 3.7 41.3 - - - +
42M TYR 3.0 15.7 + - - +
43M GLY 3.8 4.9 - - - +
45M LEU* 1.3 76.7 - - - +
47M ALA* 1.3 61.2 + - - +
49M MET* 3.7 0.6 - - - +
50M LYS 3.2 8.8 + - - -
162M SER* 4.7 1.3 - - - -
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Residues in contact with ALA 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M HIS* 4.8 0.7 - - - -
43M GLY 3.1 14.9 + - - +
44M GLU* 3.8 6.7 - - + +
45M LEU 3.2 0.2 - - - -
46M ALA* 1.3 76.2 - - - +
48M ASN* 1.3 63.3 + - - +
50M LYS* 3.2 5.5 + - - +
51M LEU* 2.9 34.2 + - + +
161M PRO 4.8 0.9 - - - +
162M SER* 3.2 29.6 - - - +
163M SER 4.2 9.2 - - - +
164M THR* 3.6 8.1 - - + +
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Residues in contact with ASN 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M GLU* 3.2 35.2 + - - +
45M LEU 4.3 0.2 - - - +
47M ALA* 1.3 77.9 - - - +
49M MET* 1.3 58.7 + - - +
51M LEU* 3.5 21.9 - - - +
52M ILE* 2.9 35.0 + - - +
138M TYR* 3.3 35.3 + - + +
171N PHE* 3.8 20.1 - - + -
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Residues in contact with MET 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M TYR* 3.3 29.5 - - - +
33M GLN* 3.4 19.3 - - + +
34M HIS* 4.0 11.0 - - + +
37M LEU* 3.9 8.7 - - + -
45M LEU 3.1 20.5 + - - +
46M ALA 3.7 4.9 - - - +
48M ASN* 1.3 77.8 - - - +
50M LYS* 1.3 57.1 + - - +
52M ILE* 3.4 6.6 + - - +
53M ALA* 3.1 25.7 + - - +
91M ILE* 3.6 16.6 - - + -
92M TYR* 3.9 16.2 - - + +
95M ASP* 3.3 17.7 - - - +
138M TYR* 4.9 1.9 + - + -
139M TYR* 3.2 35.7 - - + -
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Residues in contact with LYS 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M MET* 4.1 24.0 - - + +
34M HIS* 3.5 33.8 + - + +
46M ALA 3.2 2.2 + - - +
47M ALA 3.2 8.0 + - - +
49M MET* 1.3 76.0 - - - +
51M LEU* 1.3 61.1 + - - +
53M ALA* 3.4 3.3 + - - +
54M ILE* 3.0 36.9 + - + +
164M THR* 3.7 13.3 + - + -
2301M SO4 2.7 33.3 + - - +
61N GLU* 2.7 34.2 + - - +
2403N FEC 3.5 28.4 - - - +
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Residues in contact with LEU 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47M ALA* 2.9 19.5 + - + +
48M ASN* 3.3 30.3 + - - +
50M LYS* 1.3 76.5 - - - +
52M ILE* 1.3 62.0 + - - +
54M ILE* 3.2 10.3 + - + +
55M ASP 3.0 16.1 + - - -
164M THR* 3.6 33.7 - - + +
169N LYS* 3.6 24.5 - - + +
170N GLY 4.0 14.8 - - - +
171N PHE* 3.4 25.5 + - + +
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Residues in contact with ILE 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M TYR* 3.9 11.7 - - + -
48M ASN 2.9 20.2 + - - +
49M MET* 3.7 4.3 - - - +
51M LEU* 1.3 74.1 - - - +
53M ALA* 1.3 65.5 + - - +
55M ASP* 2.9 16.9 + - - +
56M GLU* 2.9 18.4 + - - +
135M HIS* 3.7 31.9 - - + +
138M TYR* 3.6 28.3 - - + -
139M TYR* 3.3 39.9 - - + +
171N PHE* 3.6 25.6 - - + -
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Residues in contact with ALA 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M ILE* 3.9 9.0 - - - +
30M TYR* 4.2 15.2 - - + -
31M MET* 3.9 30.3 - - + -
49M MET 3.1 14.0 + - - +
50M LYS 3.4 9.6 + - - +
52M ILE* 1.3 76.6 - - - +
54M ILE* 1.3 56.9 + - - +
56M GLU* 3.2 12.2 + - - +
57M MET* 2.9 34.6 + - + +
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Residues in contact with ILE 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M LYS* 3.0 37.8 + - + +
51M LEU* 3.3 13.5 - - + +
52M ILE 3.0 0.2 - - - -
53M ALA* 1.3 73.9 - - - +
55M ASP* 1.3 64.6 + - - +
57M MET* 3.1 23.0 + - + +
58M ARG* 3.1 21.9 + - - +
164M THR* 5.4 2.7 - - + -
168N SER* 3.8 24.0 - - - -
169N LYS 3.6 26.2 - - - +
170N GLY* 4.1 5.2 - - - -
2403N FEC 3.9 37.4 - - + +
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Residues in contact with ASP 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51M LEU 3.0 7.1 + - - -
52M ILE 2.9 8.9 + - - +
54M ILE* 1.3 77.7 - - - +
56M GLU* 1.3 57.8 - - - +
58M ARG* 2.5 41.9 + - - +
59M HIS* 2.9 33.7 + - - +
131M GLU* 4.8 0.2 - - - -
135M HIS* 2.6 34.8 + - + -
170N GLY* 3.5 2.6 - - - -
171N PHE* 3.2 22.6 + - - +
172N VAL* 3.0 24.6 + - - +
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Residues in contact with GLU 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M GLU* 3.1 25.2 - - - +
26M ALA* 4.2 4.6 - - + +
27M ILE* 4.0 14.8 - - + -
30M TYR* 3.5 17.8 - - + -
52M ILE* 2.9 16.8 + - - +
53M ALA* 3.5 12.6 - - - +
55M ASP* 1.3 72.7 - - - +
57M MET* 1.3 55.8 + - - +
59M HIS* 3.1 22.7 + - - +
60M ALA* 2.8 34.3 + - - +
99M GLU* 3.3 12.0 - - - +
132M GLU* 3.4 2.3 - - - +
135M HIS* 3.2 4.7 + - - -
200M FE 2.1 31.6 - - - -
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Residues in contact with MET 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M ILE* 3.7 25.8 - - + -
31M MET* 4.5 4.9 - - + -
53M ALA* 2.9 33.7 + - + +
54M ILE* 3.2 17.7 - - + +
56M GLU* 1.3 77.1 - - - +
58M ARG* 1.3 56.7 + - - +
60M ALA* 3.1 4.7 + - - +
61M GLU* 2.9 28.9 + - - +
2403N FEC 2.4 107.7 - - + +
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Residues in contact with ARG 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M ILE 3.1 7.6 + - - +
55M ASP* 2.5 39.6 + - - +
57M MET* 1.3 74.8 - - - +
59M HIS* 1.3 69.5 + - - +
61M GLU* 3.3 14.6 + - - +
62M ASN* 2.8 52.0 + - - +
131M GLU* 2.7 35.5 + - - -
167N ALA* 5.8 5.2 - - - +
168N SER* 3.6 31.6 + - - +
170N GLY* 4.7 2.4 - - - -
172N VAL* 3.8 12.8 + - - +
2403N FEC 4.0 11.1 - - + +
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Residues in contact with HIS 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M GLU* 2.9 30.1 + - + +
55M ASP 2.9 22.1 + - - -
56M GLU* 3.1 29.1 + - - +
58M ARG* 1.3 81.6 - - - +
60M ALA* 1.3 63.9 + - - +
62M ASN* 3.9 3.9 - - - +
63M PHE* 3.0 30.8 + - + -
128M ILE* 3.7 39.4 - - + +
131M GLU* 2.7 39.9 + - + +
132M GLU* 3.4 13.9 - - - -
135M HIS* 4.2 3.8 - + - -
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Residues in contact with ALA 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M ARG* 3.1 33.2 + - + +
23M GLU* 4.1 16.1 - - + +
24M LEU* 4.2 15.9 - - + -
27M ILE* 4.2 5.8 - - + -
56M GLU 2.8 16.2 + - - +
57M MET 3.4 9.0 - - - +
59M HIS* 1.3 72.6 - - - +
61M GLU* 1.3 58.1 + - - +
63M PHE* 3.4 3.7 + - - +
64M ALA 3.0 23.2 + - - -
2403N FEC 4.4 4.7 - - + +
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Residues in contact with GLU 61 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M MET 2.9 14.5 + - - +
58M ARG* 3.7 11.9 - - - +
60M ALA* 1.3 73.8 - - - +
62M ASN* 1.3 62.9 + - - +
64M ALA* 3.3 2.4 + - - +
65M GLU* 2.8 51.6 + - - +
31N MET* 4.5 0.3 - - - +
34N HIS* 4.3 6.2 + - - -
35N TYR* 3.2 27.3 + - + +
50N LYS* 3.0 29.8 + - - +
2401N SO4 3.9 9.0 + - - -
2403N FEC 3.3 38.9 - - + +
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Residues in contact with ASN 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M ARG* 2.8 44.7 + - - +
59M HIS* 3.9 7.1 - - - +
61M GLU* 1.3 75.5 + - - +
63M PHE* 1.3 66.5 + - - +
65M GLU* 3.1 20.5 + - - +
66M ARG* 3.1 24.1 + - - +
124M LEU* 4.0 24.2 - - + +
128M ILE* 4.6 9.0 - - + +
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Residues in contact with PHE 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M LEU* 3.5 27.6 - - + +
19M ALA* 3.7 5.6 - - + -
20M ARG* 3.8 30.1 - - + -
23M GLU* 3.8 9.6 - - + -
59M HIS* 3.0 24.3 + - + +
60M ALA 3.6 4.5 - - - +
62M ASN* 1.3 75.5 - - - +
64M ALA* 1.3 64.5 + - - +
66M ARG* 3.2 3.5 + - - +
67M ILE* 2.9 27.9 + - - +
106M TYR* 3.6 30.1 - + - -
124M LEU* 4.1 11.7 - - + -
125M PHE* 3.6 36.1 - + - -
128M ILE* 3.5 27.1 - - + -
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Residues in contact with ALA 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M ARG* 3.8 5.7 - - - +
60M ALA 3.0 16.5 + - - +
61M GLU 3.6 5.4 - - - +
63M PHE* 1.3 77.4 - - - +
65M GLU* 1.3 62.1 + - - +
67M ILE* 3.1 12.9 + - - +
68M LYS* 3.0 27.2 + - - +
74M PRO* 3.7 18.2 - - + +
35N TYR* 3.6 31.9 - - + -
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Residues in contact with GLU 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M GLU* 2.8 42.8 + - + +
62M ASN* 3.1 28.1 + - - +
64M ALA* 1.3 72.9 - - - +
66M ARG* 1.3 58.9 + - - +
68M LYS* 3.4 9.7 - - - +
69M GLU* 3.0 33.4 + - + +
34N HIS* 5.1 4.3 + - - -
35N TYR* 4.6 12.1 - - + -
38N ASP* 4.3 16.2 - - - +
2401N SO4 4.5 8.1 + - - -
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Residues in contact with ARG 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M LEU* 3.7 18.8 - - + -
62M ASN 3.1 15.1 + - - +
63M PHE 3.7 3.8 - - - +
65M GLU* 1.3 74.8 - - - +
67M ILE* 1.3 65.6 + - - +
69M GLU* 2.8 46.2 + - - +
70M LEU* 3.0 42.4 + - + +
118M ASP* 3.1 24.4 + - - -
120M VAL* 3.5 31.3 - - - +
121M THR* 3.1 19.6 + - + +
124M LEU* 3.9 16.2 - - + -
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Residues in contact with ILE 67 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M ILE* 4.3 11.2 - - + +
16M LEU* 3.6 32.3 - - + +
17M ASN* 3.2 31.9 - - - +
20M ARG* 4.2 5.2 - - - -
63M PHE 2.9 29.6 + - - +
64M ALA* 3.1 11.4 + - - +
66M ARG* 1.3 75.8 - - - +
68M LYS* 1.3 60.4 + - - +
70M LEU* 3.1 12.9 + - - +
71M GLY 3.2 0.2 + - - -
72M GLY* 2.8 50.4 + - - -
73M GLU 3.5 14.6 - - - +
74M PRO* 3.7 7.0 - - + -
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Residues in contact with LYS 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M ALA 3.0 15.7 + - - +
65M GLU* 3.4 11.4 - - - +
67M ILE* 1.3 76.1 - - - +
69M GLU* 1.3 57.6 + - + +
71M GLY* 2.9 19.9 + - - -
72M GLY 3.7 14.0 + - - +
73M GLU* 3.6 23.0 + - - -
74M PRO* 3.7 15.9 - - + -
35N TYR* 3.6 41.5 - - + +
36N SER* 3.7 19.1 + - - +
39N ASP* 3.8 34.8 + - + +
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Residues in contact with GLU 69 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M LYS* 5.0 4.0 - - - -
65M GLU* 3.0 22.0 + - - +
66M ARG* 2.8 53.7 + - - +
68M LYS* 1.3 76.5 - - + +
70M LEU* 1.3 61.1 + - - +
71M GLY 3.2 0.7 + - - -
120M VAL* 5.0 2.9 - - - +
39N ASP* 4.9 3.6 - - - +
----------------------------------------------------------
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Residues in contact with LEU 70 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M LYS* 3.6 46.0 - - + +
12M VAL* 3.9 19.7 - - + -
13M ILE* 3.7 28.4 - - + +
16M LEU* 3.6 29.8 - - + -
66M ARG* 3.0 44.2 + - - +
67M ILE 3.1 7.5 + - - +
69M GLU* 1.3 77.3 - - - +
71M GLY* 1.3 60.1 + - - +
72M GLY 3.4 0.4 - - - -
118M ASP* 3.9 8.3 - - - +
121M THR* 4.3 1.8 - - - +
----------------------------------------------------------
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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).
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