Contacts of the helix formed by residues 42 - 70 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LEU* 3.1 16.7 + - + +
40J MET* 3.6 44.6 - - + -
41J ASP* 1.3 77.6 - - - +
43J GLY* 1.3 63.3 + - - +
44J GLU 3.4 2.0 - - - -
45J LEU* 2.9 31.3 + - + -
46J ALA* 3.0 12.0 + - - +
88J VAL* 5.1 5.6 - - + -
154J LEU* 3.5 48.7 - - + +
157J ILE* 3.8 27.4 - - + -
158J ALA* 4.0 15.5 - - + -
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Residues in contact with GLY 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J ASP* 5.4 0.9 - - - -
41J ASP* 3.4 8.2 + - - -
42J TYR* 1.3 71.4 - - - +
44J GLU* 1.3 52.7 + - - +
46J ALA* 3.2 4.2 + - - +
47J ALA* 2.8 33.3 + - - +
157J ILE 3.9 0.2 + - - -
160J THR* 3.2 27.4 + - - -
161J PRO 3.1 12.1 - - - +
162J SER* 3.6 15.2 - - - -
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Residues in contact with GLU 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J GLY* 1.3 72.5 - - - +
45J LEU* 1.3 63.2 + - + +
47J ALA* 4.0 4.4 - - - +
48J ASN* 3.3 39.0 + - - +
156J LYS* 5.8 1.7 - - - +
157J ILE* 3.7 29.9 - - + +
160J THR* 3.0 35.1 + - - +
161J PRO* 3.4 6.1 + - - +
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Residues in contact with LEU 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LEU* 3.8 18.5 - - + +
42J TYR* 2.9 24.3 + - + +
44J GLU* 1.3 78.2 - - + +
46J ALA* 1.3 57.1 + - - +
48J ASN* 3.9 2.3 - - - +
49J MET* 3.1 28.8 + - - +
88J VAL* 5.3 1.8 - - + -
92J TYR* 3.3 31.2 + - + +
138J TYR* 3.7 17.3 + - - +
142J ILE* 3.8 26.0 - - + -
146J ILE* 4.8 2.5 - - + -
153J TYR* 4.5 7.2 - - + +
154J LEU* 4.3 22.9 - - + -
157J ILE* 4.0 15.9 - - + -
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Residues in contact with ALA 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J HIS* 2.8 29.7 + - + +
37J LEU* 3.9 10.9 - - + +
38J ASP* 3.7 42.6 - - - +
42J TYR 3.0 11.5 + - - +
43J GLY* 3.2 9.2 + - - +
45J LEU* 1.3 76.0 - - - +
47J ALA* 1.3 64.0 + - - +
49J MET* 3.4 1.2 + - - +
50J LYS 3.2 10.2 + - - -
162J SER* 4.7 1.3 - - - -
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Residues in contact with ALA 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J HIS* 5.0 0.4 - - - -
43J GLY 2.8 19.4 + - - +
44J GLU* 4.0 5.8 - - - +
46J ALA* 1.3 73.7 - - - +
48J ASN* 1.3 59.6 + - - +
50J LYS* 3.2 5.2 + - - +
51J LEU* 2.8 35.4 + - + +
161J PRO 4.7 1.3 - - - +
162J SER* 3.4 25.2 + - - +
163J SER 3.9 9.9 - - - +
164J THR* 3.6 13.1 - - + +
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Residues in contact with ASN 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171I PHE* 3.5 26.2 - - + -
44J GLU* 3.3 27.1 + - - +
45J LEU 3.9 0.2 - - - +
47J ALA* 1.3 81.9 - - - +
49J MET* 1.3 57.4 + - - +
51J LEU* 3.3 14.9 + - - +
52J ILE* 2.9 34.5 + - - +
138J TYR* 3.3 38.7 + - + +
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Residues in contact with MET 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J TYR* 3.2 31.5 - - - +
33J GLN* 3.5 17.9 - - + +
34J HIS* 3.7 12.1 - - + +
37J LEU* 4.0 14.8 - - + -
45J LEU 3.1 15.3 + - - +
46J ALA 3.8 4.7 - - - +
47J ALA 3.2 0.4 - - - -
48J ASN* 1.3 72.1 - - - +
50J LYS* 1.3 60.9 + - - +
52J ILE* 3.4 5.9 + - - +
53J ALA* 3.0 27.4 + - - +
91J ILE* 3.8 17.3 - - + -
92J TYR* 4.1 8.5 - - + +
95J ASP* 3.2 19.5 - - - +
138J TYR* 5.2 1.7 + - + -
139J TYR* 3.4 32.3 - - + -
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Residues in contact with LYS 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I GLU* 2.8 27.9 + - - +
1903I FEC 2.6 53.1 + - - +
31J MET* 4.0 17.9 - - + -
34J HIS* 3.5 26.2 + - + +
46J ALA 3.2 3.4 + - - +
47J ALA 3.6 7.0 - - - +
49J MET* 1.3 75.7 - - - +
51J LEU* 1.3 60.8 + - - +
53J ALA* 3.2 2.8 + - - +
54J ILE* 2.9 36.6 + - + +
164J THR* 3.6 15.8 + - + +
2001J SO4 2.9 29.0 + - - +
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Residues in contact with LEU 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169I LYS* 3.5 24.9 - - + +
170I GLY 4.0 12.6 - - - +
171I PHE* 3.4 25.6 + - + +
47J ALA* 2.8 23.0 + - + +
48J ASN* 3.6 22.0 - - - +
49J MET 3.3 0.2 - - - -
50J LYS* 1.3 78.3 - - - +
52J ILE* 1.3 62.2 + - - +
54J ILE* 3.0 17.8 + - + +
55J ASP 3.1 9.5 + - - -
164J THR* 3.7 35.7 - - + +
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Residues in contact with ILE 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171I PHE* 3.6 23.6 - - + -
30J TYR* 3.7 17.7 - - + -
48J ASN 2.9 21.8 + - - +
49J MET 3.4 2.7 + - - +
51J LEU* 1.3 75.9 - - - +
53J ALA* 1.3 63.6 + - - +
55J ASP* 3.2 11.8 + - - +
56J GLU* 3.2 13.3 + - - +
135J HIS* 3.8 31.0 - - + +
138J TYR* 3.6 24.0 - - + -
139J TYR* 3.1 48.0 - - + +
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Residues in contact with ALA 53 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J ILE* 4.0 6.0 - - - +
30J TYR* 4.0 14.6 - - + -
31J MET* 3.6 32.1 - - + +
49J MET 3.0 14.7 + - - +
50J LYS 3.4 9.2 - - - +
52J ILE* 1.3 76.8 - - - +
54J ILE* 1.3 62.4 + - - +
56J GLU* 3.3 11.0 + - - +
57J MET* 3.0 31.1 + - + +
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Residues in contact with ILE 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I SER* 3.9 25.8 - - - +
169I LYS 3.8 26.2 - - - +
170I GLY* 4.2 4.5 - - - -
1903I FEC 4.3 35.0 - - + +
50J LYS* 2.9 33.3 + - + +
51J LEU* 3.0 14.1 + - + +
53J ALA* 1.3 77.8 - - - +
55J ASP* 1.3 63.9 + - - +
57J MET* 3.2 26.6 + - + +
58J ARG* 3.0 19.9 + - - +
164J THR* 5.2 2.9 - - - +
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Residues in contact with ASP 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170I GLY* 3.0 5.0 - - - -
171I PHE* 2.9 23.3 + - - +
172I VAL* 3.1 24.8 + - - +
51J LEU 3.1 4.1 + - - -
52J ILE 3.2 7.4 + - - +
54J ILE* 1.3 78.1 - - - +
56J GLU* 1.3 58.7 + - - +
58J ARG* 2.5 42.7 + - - +
59J HIS* 2.8 32.5 + - - +
131J GLU* 4.8 0.2 - - - +
135J HIS* 2.8 32.0 + - + -
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Residues in contact with GLU 56 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J GLU* 3.3 27.3 - - - +
26J ALA* 4.0 12.2 - - + +
27J ILE* 3.9 14.7 - - + +
30J TYR* 3.5 14.2 - - + -
52J ILE 3.2 16.5 + - - +
53J ALA* 3.3 7.6 + - - +
55J ASP* 1.3 72.2 - - - +
57J MET* 1.3 59.4 + - - +
59J HIS* 3.0 22.5 + - - +
60J ALA* 2.8 29.6 + - - +
99J GLU* 3.2 12.3 - - - +
132J GLU* 3.4 1.8 - - - +
135J HIS* 3.4 4.6 + - - -
200J FE 2.1 31.4 - - - -
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Residues in contact with MET 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1903I FEC 2.4 108.4 - - + +
27J ILE* 3.7 22.6 - - + +
31J MET* 4.3 5.6 - - + -
53J ALA* 3.0 37.1 + - + +
54J ILE* 3.2 17.9 - - + +
56J GLU* 1.3 75.3 - - - +
58J ARG* 1.3 57.4 + - - +
60J ALA* 3.4 2.6 + - - +
61J GLU* 2.9 28.9 + - - +
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Residues in contact with ARG 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I ALA* 5.8 7.1 - - - +
168I SER* 4.1 22.4 + - - +
170I GLY* 4.4 6.1 - - - +
172I VAL* 4.0 9.2 - - - +
1903I FEC 5.2 1.3 - - - +
54J ILE* 3.0 9.4 + - - +
55J ASP* 2.5 46.7 + - - +
57J MET* 1.3 73.6 - - - +
59J HIS* 1.3 60.3 + - - +
61J GLU* 3.1 16.5 + - - +
62J ASN* 2.7 59.5 + - - +
131J GLU* 2.9 37.4 + - - -
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Residues in contact with HIS 59 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J GLU* 2.8 31.7 + - + +
55J ASP* 2.8 20.4 + - - +
56J GLU* 3.0 28.6 + - - +
57J MET 3.3 0.2 - - - -
58J ARG* 1.3 76.8 + - - +
60J ALA* 1.3 64.6 + - - +
62J ASN* 3.0 8.4 + - - +
63J PHE* 2.8 30.6 + - + -
128J ILE* 3.8 34.0 - - + +
131J GLU* 2.6 38.1 + - + +
132J GLU* 3.3 16.4 + - - -
135J HIS* 4.3 3.6 - + - -
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Residues in contact with ALA 60 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1903I FEC 4.6 4.0 - - + -
20J ARG* 2.8 37.0 + - + +
23J GLU* 3.9 18.2 - - + +
24J LEU* 4.4 7.9 - - + -
27J ILE* 4.2 13.0 - - + -
56J GLU 2.8 19.6 + - - +
57J MET 3.7 4.5 - - - +
59J HIS* 1.3 74.5 - - - +
61J GLU* 1.3 57.4 + - - +
63J PHE* 3.6 7.0 + - - +
64J ALA 3.0 17.0 + - - -
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Residues in contact with GLU 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I MET* 4.4 0.3 - - - +
34I HIS* 4.2 5.5 + - - -
35I TYR* 3.6 19.3 + - + -
50I LYS* 2.5 39.7 + - - +
1901I SO4 4.1 7.8 + - - -
1903I FEC 3.3 32.9 - - + +
57J MET 2.9 9.4 + - - +
58J ARG* 3.5 18.6 - - - +
59J HIS 3.1 0.2 - - - -
60J ALA* 1.3 74.8 - - - +
62J ASN* 1.3 65.3 + - - +
64J ALA* 3.3 1.9 + - - +
65J GLU* 2.9 49.8 + - - +
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Residues in contact with ASN 62 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J ARG* 2.7 49.6 + - - +
59J HIS* 3.8 9.3 - - - +
61J GLU* 1.3 76.8 - - - +
63J PHE* 1.3 61.2 + - - +
65J GLU* 3.4 19.6 + - - +
66J ARG* 3.1 23.6 + - - +
124J LEU* 3.9 26.5 - - + +
128J ILE* 4.6 8.1 - - + +
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Residues in contact with PHE 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J LEU* 3.6 32.5 - - + +
19J ALA* 3.5 12.8 - - + -
20J ARG* 3.8 21.8 - - + -
23J GLU* 3.7 24.7 - - + -
59J HIS* 2.8 22.3 + - + +
60J ALA 3.7 4.3 - - - +
62J ASN* 1.3 78.0 - - - +
64J ALA* 1.3 61.8 + - - +
66J ARG* 3.4 2.1 + - - +
67J ILE* 3.0 30.9 + - - +
106J TYR* 3.8 11.7 - + - -
124J LEU* 3.7 13.2 - - + -
125J PHE* 3.6 36.6 - + - -
128J ILE* 3.5 27.6 - - + -
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Residues in contact with ALA 64 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I TYR* 3.6 25.8 - - + -
20J ARG* 3.6 15.4 - - - +
60J ALA 3.0 18.5 + - - +
61J GLU 3.7 1.1 - - - +
62J ASN 3.3 0.2 - - - -
63J PHE* 1.3 73.2 - - - +
65J GLU* 1.3 66.6 + - - +
67J ILE* 3.3 12.6 + - - +
68J LYS* 2.9 28.0 + - - +
74J PRO* 3.7 16.3 - - + +
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Residues in contact with GLU 65 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I HIS* 5.0 4.2 + - - +
35I TYR* 4.5 11.4 - - + -
38I ASP* 4.2 16.3 - - - +
1901I SO4 5.2 4.0 + - - -
61J GLU* 2.9 42.5 + - + +
62J ASN* 3.4 24.2 - - - +
63J PHE 3.3 0.2 - - - -
64J ALA* 1.3 77.1 - - - +
66J ARG* 1.3 58.1 + - - +
68J LYS* 3.3 10.3 + - - +
69J GLU* 3.0 33.0 + - + +
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Residues in contact with ARG 66 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J LEU* 3.7 19.7 - - + -
62J ASN 3.1 16.2 + - - +
63J PHE 3.9 4.0 - - - +
65J GLU* 1.3 75.3 - - - +
67J ILE* 1.3 65.8 - - - +
69J GLU* 2.6 48.2 + - - +
70J LEU* 2.9 42.1 + - + +
118J ASP* 3.1 27.1 + - - -
120J VAL* 3.5 32.8 - - - +
121J THR* 3.0 17.7 + - + +
124J LEU* 4.0 17.9 - - + -
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Residues in contact with ILE 67 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J ILE* 4.1 11.9 - - + +
16J LEU* 3.5 36.3 - - + +
17J ASN* 3.1 31.4 - - - +
20J ARG* 4.1 7.0 - - - -
63J PHE 3.0 32.0 + - - +
64J ALA* 3.5 10.1 - - - +
66J ARG* 1.3 74.9 - - - +
68J LYS* 1.3 58.0 + - - +
70J LEU* 3.3 6.1 + - - +
71J GLY 3.2 3.8 + - - -
72J GLY* 2.7 57.0 + - - +
73J GLU 3.6 14.6 - - - +
74J PRO* 3.8 3.1 - - + -
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Residues in contact with LYS 68 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I ASN* 5.3 0.7 - - - -
35I TYR* 3.7 39.3 - - + +
36I SER* 3.7 22.1 + - - +
39I ASP* 3.7 37.4 + - + +
64J ALA 2.9 16.3 + - - +
65J GLU* 3.3 12.6 - - - +
66J ARG 3.1 0.2 - - - -
67J ILE* 1.3 74.5 - - - +
69J GLU* 1.3 64.8 + - + +
71J GLY* 3.0 14.0 + - - -
72J GLY 3.7 15.1 + - - +
73J GLU* 4.2 12.1 + - - -
74J PRO* 4.0 18.4 - - + -
----------------------------------------------------------
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Residues in contact with GLU 69 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I ASP* 5.0 2.9 - - - +
9J LYS* 5.3 2.8 - - - -
65J GLU* 3.0 19.5 + - + +
66J ARG* 2.6 53.6 + - - +
68J LYS* 1.3 77.0 - - + +
70J LEU* 1.3 61.8 + - - +
71J GLY 3.2 1.1 + - - -
120J VAL* 4.8 2.8 - - - +
----------------------------------------------------------
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Residues in contact with LEU 70 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J LYS* 3.7 47.1 - - + +
12J VAL* 3.5 35.0 - - + -
13J ILE* 3.3 31.2 - - + +
16J LEU* 4.0 13.7 - - + -
66J ARG* 2.9 38.7 + - - +
67J ILE 3.3 1.1 + - - +
68J LYS 3.1 0.4 - - - -
69J GLU* 1.3 77.4 - - - +
71J GLY* 1.3 57.3 + - - +
72J GLY 3.4 0.9 - - - -
118J ASP* 3.6 11.4 - - - +
121J THR* 3.9 5.4 - - - +
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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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