Contacts of the helix formed by residues 42 - 70 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N LEU* 3.0 15.9 + - + +
38N ASP* 5.5 0.2 - - - -
40N MET* 3.6 43.5 - - + -
41N ASP* 1.3 75.0 - - - +
43N GLY* 1.3 62.3 + - - +
44N GLU 3.5 1.8 - - - -
45N LEU* 3.1 12.8 + - + -
46N ALA* 3.0 22.3 + - - +
88N VAL* 4.7 6.5 - - + -
154N LEU* 3.5 58.2 - - + +
157N ILE* 3.8 17.5 - - + -
158N ALA* 3.6 29.2 - - + -
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Residues in contact with GLY 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N ASP* 5.4 0.9 - - - -
41N ASP* 3.3 8.1 + - - -
42N TYR* 1.3 71.6 - - - +
44N GLU* 1.3 57.2 - - - +
46N ALA* 3.0 5.6 + - - +
47N ALA 2.8 25.6 + - - -
160N THR* 3.2 28.5 + - - -
161N PRO 3.3 8.5 - - - -
162N SER* 3.5 18.2 - - - -
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Residues in contact with GLU 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY* 5.1 6.9 - - - +
42N TYR 3.5 0.2 - - - -
43N GLY* 1.3 71.2 - - - +
45N LEU* 1.3 62.8 + - + +
47N ALA* 3.8 4.9 - - + +
48N ASN* 3.1 45.9 + - - +
138N TYR* 5.9 0.2 - - - +
153N TYR* 5.4 2.3 + - - -
157N ILE* 4.0 25.6 - - + +
160N THR* 3.0 26.3 + - - +
161N PRO 3.4 7.2 + - - +
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Residues in contact with LEU 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N LEU* 3.9 16.1 - - + +
42N TYR* 3.1 19.3 + - + +
44N GLU* 1.3 79.4 - - + +
46N ALA* 1.3 57.8 + - - +
48N ASN* 4.0 1.0 - - - +
49N MET* 3.0 31.2 + - - +
88N VAL* 5.1 1.8 - - + -
92N TYR* 3.2 31.9 + - + +
138N TYR* 3.5 18.3 + - - +
142N ILE* 3.9 27.1 - - + -
146N ILE* 5.5 0.2 - - + -
153N TYR* 4.3 8.1 - - + +
154N LEU* 4.1 26.0 - - + -
157N ILE* 4.0 15.0 - - + +
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Residues in contact with ALA 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N HIS* 2.7 29.6 + - + +
37N LEU* 4.0 9.8 - - - +
38N ASP* 3.6 45.3 - - + +
42N TYR 3.0 13.2 + - - +
43N GLY* 3.4 8.5 - - - +
45N LEU* 1.3 76.7 - - - +
47N ALA* 1.3 63.0 + - - +
49N MET* 3.5 1.2 + - - +
50N LYS 3.1 10.4 + - - -
162N SER* 4.5 1.6 - - - -
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Residues in contact with ALA 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N HIS* 5.1 0.4 - - - -
43N GLY 2.8 13.6 + - - +
44N GLU* 3.8 7.9 - - + +
46N ALA* 1.3 74.4 - - - +
48N ASN* 1.3 62.6 + - - +
50N LYS* 3.0 7.2 + - - +
51N LEU* 3.0 33.1 + - + +
161N PRO 4.6 1.3 - - - +
162N SER* 3.3 29.5 + - - +
163N SER 3.9 10.3 - - - +
164N THR* 3.7 8.6 - - + +
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Residues in contact with ASN 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171M PHE* 3.8 22.5 - - + -
44N GLU* 3.1 37.0 + - - +
45N LEU 4.2 0.2 - - - +
47N ALA* 1.3 79.0 - - - +
49N MET* 1.3 61.5 + - - +
51N LEU* 3.8 16.7 - - - +
52N ILE* 3.1 30.3 + - - +
138N TYR* 3.3 37.4 + - + +
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Residues in contact with MET 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N TYR* 3.2 30.8 - - - +
33N GLN* 3.4 19.7 - - + +
34N HIS* 3.7 12.8 - - + +
37N LEU* 3.9 14.6 - - + -
45N LEU 3.0 19.5 + - - +
46N ALA 3.6 4.5 - - - +
48N ASN* 1.3 76.8 - - - +
50N LYS* 1.3 62.7 + - - +
52N ILE* 3.5 5.9 + - - +
53N ALA* 3.2 22.0 + - - +
91N ILE* 3.7 17.7 - - + -
92N TYR* 3.9 8.1 - - + +
95N ASP* 3.3 17.9 - - - +
138N TYR* 5.1 1.5 + - + -
139N TYR* 3.5 31.0 - - + -
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Residues in contact with LYS 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M GLU* 3.0 24.3 + - - +
31N MET* 3.9 27.1 - - + -
34N HIS* 3.7 21.5 + - + +
46N ALA 3.1 5.6 + - - +
47N ALA 3.0 9.4 + - - +
49N MET* 1.3 77.3 - - - +
51N LEU* 1.3 57.0 + - - +
53N ALA* 3.3 2.8 + - - +
54N ILE* 3.0 38.8 + - + +
57N MET* 5.8 0.2 - - + -
164N THR* 3.7 13.1 + - + -
2401N SO4 2.9 30.3 + - - +
2403N FEC 2.6 49.5 + - - -
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Residues in contact with LEU 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169M LYS* 3.2 34.8 - - + +
170M GLY* 3.5 23.7 - - - +
171M PHE* 3.0 24.6 + - + +
47N ALA* 3.0 19.9 + - + +
48N ASN* 3.8 24.5 - - - +
49N MET 3.3 0.2 - - - -
50N LYS* 1.3 76.3 - - - +
52N ILE* 1.3 61.7 + - - +
54N ILE* 3.5 5.7 + - + -
55N ASP 3.2 13.3 + - - -
164N THR* 3.9 29.4 - - + +
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Residues in contact with ILE 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171M PHE* 3.5 24.5 - - + -
30N TYR* 4.0 14.6 - - + -
48N ASN 3.1 20.3 + - - +
49N MET 3.9 1.8 - - - +
50N LYS 3.2 0.2 - - - -
51N LEU* 1.3 73.3 - - - +
53N ALA* 1.3 66.8 + - - +
54N ILE 3.1 0.2 - - - -
55N ASP* 3.0 6.0 + - - +
56N GLU* 3.0 25.7 + - - +
135N HIS* 3.7 31.6 - - + +
138N TYR* 3.7 28.9 - - + -
139N TYR* 3.2 42.8 - - + +
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Residues in contact with ALA 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N ILE* 3.9 6.8 - - - +
30N TYR* 4.0 16.8 - - + -
31N MET* 3.9 30.1 - - + -
49N MET 3.2 13.7 + - - +
50N LYS 3.3 8.7 + - - +
52N ILE* 1.3 77.7 - - - +
54N ILE* 1.3 58.6 + - - +
56N GLU* 3.2 13.0 + - - +
57N MET* 2.9 34.5 + - + +
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Residues in contact with ILE 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168M SER* 3.5 32.9 - - - +
169M LYS 3.9 20.6 - - - +
170M GLY* 4.2 4.0 - - - -
50N LYS* 3.0 47.3 + - + +
51N LEU* 3.8 9.6 - - + +
52N ILE 3.1 0.2 - - - -
53N ALA* 1.3 75.8 - - - +
55N ASP* 1.3 66.9 + - - +
57N MET* 3.1 29.9 + - + +
58N ARG* 3.1 19.4 + - - +
164N THR* 5.5 1.8 - - - +
2403N FEC 4.5 21.5 - - + -
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Residues in contact with ASP 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170M GLY* 3.5 1.4 - - - -
171M PHE* 3.0 36.3 + - - +
172M VAL* 3.0 14.1 + - - +
51N LEU 3.2 4.4 + - - -
52N ILE 3.0 9.2 + - - +
54N ILE* 1.3 75.5 - - - +
56N GLU* 1.3 57.6 + - - +
58N ARG* 2.5 48.5 + - - +
59N HIS* 2.8 31.2 + - - +
131N GLU* 4.7 0.4 - - - +
135N HIS* 2.8 33.2 + - + -
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Residues in contact with GLU 56 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N GLU* 3.5 27.4 - - - +
26N ALA* 4.3 3.9 - - + +
27N ILE* 4.0 14.3 - - + +
30N TYR* 3.8 15.7 - - + -
52N ILE* 3.0 17.5 - - - +
53N ALA* 3.3 12.3 - - - +
55N ASP* 1.3 72.2 - - - +
57N MET* 1.3 58.3 + - - +
59N HIS* 3.0 26.4 + - - +
60N ALA* 2.9 28.4 + - - +
99N GLU* 3.3 11.3 - - - +
132N GLU* 3.3 2.1 - - - +
135N HIS* 3.2 6.0 + - - -
200N FE 2.1 28.1 - - - -
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Residues in contact with MET 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N ILE* 3.5 23.1 - - + +
31N MET* 4.5 7.2 - - + -
53N ALA* 2.9 33.7 + - + +
54N ILE* 3.1 29.3 + - + +
56N GLU* 1.3 75.2 - - - +
58N ARG* 1.3 57.7 + - - +
60N ALA* 3.2 3.1 + - - +
61N GLU* 3.0 27.0 + - - +
2403N FEC 2.4 98.9 - - + +
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Residues in contact with ARG 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167M ALA* 5.6 7.4 - - + +
168M SER* 3.9 29.7 + - - +
170M GLY* 4.4 3.2 - - - -
172M VAL* 4.3 9.6 + - - +
54N ILE 3.1 5.2 + - - +
55N ASP* 2.5 58.2 + - - +
57N MET* 1.3 76.6 - - - +
59N HIS* 1.3 66.6 + - - +
61N GLU* 3.2 16.2 + - - +
62N ASN* 2.9 47.6 + - - +
131N GLU* 3.1 30.4 + - - -
2403N FEC 5.0 1.3 - - + +
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Residues in contact with HIS 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23N GLU* 2.6 31.6 + - + +
55N ASP* 2.8 17.4 + - - +
56N GLU* 3.0 27.7 + - - +
58N ARG* 1.3 80.6 + - - +
60N ALA* 1.3 64.4 + - - +
62N ASN* 3.1 8.8 + - - +
63N PHE* 2.9 30.5 + - + -
128N ILE* 3.6 40.5 - - + +
131N GLU* 3.0 29.8 + - + +
132N GLU* 3.2 18.8 - - + -
135N HIS* 4.3 5.6 - + - -
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Residues in contact with ALA 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M TYR* 4.5 0.2 - - - -
20N ARG* 2.8 42.1 + - + +
23N GLU* 4.0 17.2 - - + +
24N LEU* 4.5 7.6 - - + -
27N ILE* 4.3 12.1 - - + -
56N GLU 2.9 13.9 + - - +
57N MET 3.2 9.4 + - - +
59N HIS* 1.3 75.8 - - - +
61N GLU* 1.3 54.9 + - - +
63N PHE* 3.9 3.9 - - - +
64N ALA* 3.0 18.9 + - - +
2403N FEC 4.6 3.8 - - + -
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Residues in contact with GLU 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M MET* 4.6 0.4 - - + -
34M HIS* 4.2 7.0 + - - +
35M TYR* 3.7 21.5 + - + -
50M LYS* 2.7 38.5 + - - +
2301M SO4 4.0 7.2 + - - -
57N MET 3.0 12.4 + - - +
58N ARG* 3.5 19.9 - - - +
59N HIS 3.1 0.2 - - - -
60N ALA* 1.3 75.8 - - - +
62N ASN* 1.3 61.8 + - - +
64N ALA* 3.4 1.9 + - - +
65N GLU* 2.8 50.1 + - - +
2403N FEC 3.5 27.1 - - + +
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Residues in contact with ASN 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58N ARG* 2.9 47.2 + - - +
59N HIS* 3.8 7.8 - - - +
61N GLU* 1.3 74.2 - - - +
63N PHE* 1.3 67.7 + - - +
65N GLU* 3.2 20.1 + - - +
66N ARG* 3.0 23.9 + - - +
124N LEU* 3.9 26.0 - - + +
128N ILE* 4.7 7.3 - - + +
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Residues in contact with PHE 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N LEU* 3.5 27.6 - - + +
19N ALA* 3.5 14.1 - - + -
20N ARG* 3.9 25.6 - - + -
23N GLU* 3.8 12.3 - - + -
59N HIS 2.9 21.8 + - - +
60N ALA 3.9 3.4 - - - +
62N ASN* 1.3 75.1 - - - +
64N ALA* 1.3 63.3 + - - +
66N ARG* 3.3 3.5 + - - +
67N ILE* 3.0 29.7 + - - +
106N TYR* 3.6 23.8 - + - -
124N LEU* 3.9 12.8 - - + -
125N PHE* 3.6 38.8 - + - -
128N ILE* 3.5 27.8 - - + -
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Residues in contact with ALA 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M TYR* 3.6 20.9 - - + -
20N ARG* 3.6 16.7 - - - +
60N ALA 3.0 20.1 + - - +
61N GLU 3.5 4.9 - - - +
63N PHE* 1.3 78.3 - - - +
65N GLU* 1.3 61.3 + - - +
67N ILE* 3.4 1.9 + - - -
68N LYS* 3.3 27.0 + - - +
74N PRO* 3.6 25.2 - - + +
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Residues in contact with GLU 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M HIS* 5.0 4.7 + - - +
35M TYR* 4.6 12.3 - - + -
38M ASP* 3.9 18.6 - - + +
2301M SO4 5.3 4.5 + - - -
61N GLU* 2.8 45.6 + - + +
62N ASN* 3.2 26.8 + - - +
64N ALA* 1.3 71.9 - - - +
66N ARG* 1.3 57.9 + - - +
68N LYS* 3.4 9.1 - - - +
69N GLU* 3.1 33.1 + - - +
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Residues in contact with ARG 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G GLN* 3.4 21.6 + - - +
16N LEU* 3.9 13.5 - - + -
62N ASN 3.0 15.2 + - - +
63N PHE 3.6 4.3 - - - +
65N GLU* 1.3 75.4 - - - +
67N ILE* 1.3 64.9 + - - +
68N LYS 3.2 0.4 - - - -
69N GLU* 2.7 46.5 + - - +
70N LEU* 3.1 44.3 + - - +
118N ASP* 3.1 24.4 + - - -
120N VAL* 3.5 27.0 - - - +
121N THR* 3.1 21.5 + - + +
124N LEU* 3.9 19.5 - - + -
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Residues in contact with ILE 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N ILE* 4.3 14.8 - - + +
16N LEU* 3.5 38.8 - - + +
17N ASN* 3.3 29.4 - - - +
20N ARG* 4.4 3.6 - - - -
63N PHE 3.0 24.7 + - - +
64N ALA* 3.4 5.4 + - - +
66N ARG* 1.3 76.0 - - - +
68N LYS* 1.3 56.4 + - - +
70N LEU* 3.2 7.4 + - - +
71N GLY 3.2 4.9 + - - -
72N GLY* 2.9 51.9 + - - -
73N GLU 3.6 2.9 - - - +
74N PRO* 3.6 22.7 - - + -
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Residues in contact with LYS 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M TYR* 3.7 32.1 - - + +
36M SER* 3.4 26.5 + - - +
39M ASP* 4.0 35.1 + - + +
64N ALA 3.3 12.3 + - - +
65N GLU* 3.4 12.3 - - - +
67N ILE* 1.3 73.7 - - - +
69N GLU* 1.3 61.7 + - + +
70N LEU 3.0 1.6 - - - -
71N GLY* 2.8 20.1 + - - -
72N GLY 3.4 15.6 + - - +
73N GLU* 4.2 14.0 + - - -
74N PRO* 4.0 21.3 - - + -
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Residues in contact with GLU 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G GLN* 4.5 12.7 + - - +
137G THR* 4.4 19.6 + - + +
140G GLU* 5.5 2.6 - - - +
39M ASP* 5.0 4.3 - - - +
9N LYS* 5.3 2.8 - - - -
65N GLU* 3.1 18.4 + - - +
66N ARG* 2.7 55.0 + - - +
68N LYS* 1.3 80.1 - - + +
70N LEU* 1.3 61.0 + - - +
71N GLY 3.2 2.0 + - - -
120N VAL* 4.8 2.1 - - - +
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Residues in contact with LEU 70 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N LYS* 3.8 45.8 - - + +
12N VAL* 3.6 33.0 - - + -
13N ILE* 3.5 24.4 - - + +
16N LEU* 3.8 12.3 - - + -
66N ARG* 3.1 43.5 + - - +
67N ILE 3.7 6.3 - - - +
68N LYS 3.0 0.8 - - - -
69N GLU* 1.3 77.1 - - - +
71N GLY* 1.3 61.0 + - - +
72N GLY 3.4 1.3 - - - -
118N ASP* 3.8 10.3 - - - +
121N THR* 4.0 3.8 - - - +
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il