Contacts of the helix formed by residues 42 - 70 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LEU* 3.1 15.6 + - + +
38E ASP* 4.9 0.2 - - - +
40E MET* 3.6 44.9 - - + -
41E ASP* 1.3 74.1 - - - +
43E GLY* 1.3 54.4 + - - +
44E GLU 3.4 2.2 - - - -
45E LEU* 3.2 14.2 + - + -
46E ALA* 3.0 33.2 + - - +
88E VAL* 4.8 3.8 - - + -
154E LEU* 3.3 58.3 - - + +
157E ILE* 3.7 16.8 - - + -
158E ALA* 3.9 20.0 - - + -
145P HIS* 4.4 9.6 - + - -
148P ASN* 5.3 6.2 + - - +
149P LEU* 4.5 14.0 - - + +
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Residues in contact with GLY 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ASP* 5.3 0.9 - - - -
41E ASP* 3.4 7.1 + - - -
42E TYR* 1.3 71.0 - - - +
44E GLU* 1.3 56.7 + - - +
46E ALA* 3.4 2.2 + - - +
47E ALA* 2.9 31.0 + - - +
160E THR* 2.8 32.1 + - - -
161E PRO 3.0 11.4 - - - +
162E SER* 3.4 11.9 - - - -
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Residues in contact with GLU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C GLY 5.7 0.7 - - - +
42E TYR 3.3 0.6 + - - -
43E GLY* 1.3 72.1 - - - +
45E LEU* 1.3 67.2 + - + +
47E ALA* 3.1 7.0 + - + +
48E ASN* 2.9 44.4 + - - +
153E TYR* 5.1 3.3 + - - -
156E LYS* 5.7 0.9 - - - -
157E ILE* 3.5 26.9 - - + +
160E THR* 3.0 19.7 + - - +
161E PRO 3.4 5.1 + - - +
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Residues in contact with LEU 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LEU* 4.1 17.9 - - + +
42E TYR* 3.2 12.9 + - + +
44E GLU* 1.3 78.9 - - + +
46E ALA* 1.3 62.8 + - - +
48E ASN* 3.4 1.8 + - - +
49E MET* 3.0 26.2 + - - +
88E VAL* 4.9 0.9 - - + -
92E TYR* 3.2 35.8 + - + +
138E TYR* 3.9 15.9 + - - +
142E ILE* 3.9 22.4 - - + -
146E ILE* 4.9 1.3 - - + -
153E TYR* 4.1 15.5 - - + +
154E LEU* 4.0 26.5 - - + -
157E ILE* 4.2 13.4 - - + +
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Residues in contact with ALA 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E HIS* 2.7 29.6 + - + +
37E LEU* 3.8 12.0 - - + +
38E ASP* 3.6 45.8 - - + +
42E TYR 3.0 16.6 + - - +
43E GLY 3.7 4.9 - - - +
45E LEU* 1.3 76.8 - - - +
47E ALA* 1.3 61.6 + - - +
49E MET* 3.6 1.5 + - - +
50E LYS 3.4 9.2 + - - -
162E SER* 4.6 1.3 - - - -
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Residues in contact with ALA 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E HIS* 5.2 0.4 - - - -
43E GLY 2.9 17.8 + - - +
44E GLU* 3.1 9.6 + - + +
46E ALA* 1.3 77.6 - - - +
48E ASN* 1.3 64.9 + - - +
50E LYS 3.5 1.4 + - - -
51E LEU* 3.2 29.1 + - + +
161E PRO 4.6 1.1 - - - +
162E SER* 3.4 27.8 + - - +
163E SER 4.0 9.6 - - - +
164E THR* 3.5 10.1 - - + +
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Residues in contact with ASN 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E GLU* 2.9 34.6 + - - +
45E LEU* 5.9 0.2 - - - +
47E ALA* 1.3 75.7 - - - +
49E MET* 1.3 64.8 + - - +
51E LEU* 3.4 19.0 + - - +
52E ILE* 3.0 30.6 + - - +
138E TYR* 3.0 42.9 + - + +
171F PHE* 4.2 14.2 - - + -
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Residues in contact with MET 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E TYR* 3.3 29.3 - - - +
33E GLN* 3.5 23.6 - - + +
34E HIS* 3.8 13.2 - - + +
37E LEU* 3.7 22.7 - - + -
45E LEU 3.0 16.1 + - - +
46E ALA 3.6 6.5 - - - +
48E ASN* 1.3 77.2 - - - +
50E LYS* 1.3 57.9 + - - +
52E ILE* 3.3 7.4 + - - +
53E ALA* 2.9 25.2 + - - +
91E ILE* 3.8 11.0 - - + -
92E TYR* 4.0 8.5 - - + +
95E ASP* 3.6 14.1 - - - +
138E TYR* 4.7 1.7 + - + -
139E TYR* 3.6 30.1 - - + -
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Residues in contact with LYS 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E MET* 3.8 27.4 - - + -
34E HIS* 3.6 32.3 + - + +
46E ALA 3.4 1.4 + - - -
47E ALA 3.8 7.2 - - - +
48E ASN 3.3 0.2 - - - -
49E MET* 1.3 75.8 - - - +
51E LEU* 1.3 62.5 + - - +
53E ALA* 2.9 3.8 + - - +
54E ILE* 2.7 37.9 + - + +
164E THR* 3.6 14.9 + - + -
1501E SO4 2.5 39.2 + - - +
61F GLU* 3.1 24.2 + - - +
1604F FEC 3.7 28.0 - - + +
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Residues in contact with LEU 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ALA* 3.2 19.5 + - + +
48E ASN* 3.7 21.5 - - - +
49E MET 3.4 0.2 - - - -
50E LYS* 1.3 76.4 - - - +
52E ILE* 1.3 63.7 + - - +
54E ILE* 3.0 12.4 + - + +
55E ASP 2.9 17.5 + - - -
163E SER 6.0 0.2 - - - +
164E THR* 3.6 34.3 - - + +
169F LYS* 3.4 24.2 - - + +
170F GLY 3.9 11.9 - - - +
171F PHE* 3.5 27.5 + - + +
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Residues in contact with ILE 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E TYR* 4.0 13.9 - - + -
48E ASN 3.0 19.3 + - - +
49E MET 3.6 6.3 - - - +
51E LEU* 1.3 75.9 - - - +
53E ALA* 1.3 65.8 + - - +
55E ASP* 2.9 15.3 + - - +
56E GLU* 3.0 11.1 + - - +
135E HIS* 3.7 30.5 - - + +
138E TYR* 3.5 27.6 - - + -
139E TYR* 3.3 38.1 - - + +
171F PHE* 3.6 28.5 - - + -
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Residues in contact with ALA 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ILE* 4.2 7.6 - - - +
30E TYR* 3.9 15.5 - - + -
31E MET* 3.8 31.4 - - + -
49E MET 2.9 14.9 + - - +
50E LYS 2.9 7.6 + - - +
52E ILE* 1.3 76.9 - - - +
54E ILE* 1.3 58.7 + - - +
56E GLU* 3.1 12.8 + - - +
57E MET* 2.9 35.0 + - + +
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Residues in contact with ILE 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E LYS* 2.7 31.4 + - + +
51E LEU* 3.5 13.2 - - + +
53E ALA* 1.3 75.6 - - - +
55E ASP* 1.3 65.7 + - - +
57E MET* 3.2 30.4 + - + +
58E ARG* 3.2 13.0 + - - +
164E THR* 5.4 1.8 - - - +
168F SER* 3.5 32.1 - - - +
169F LYS 3.9 20.6 - - - +
170F GLY* 4.3 3.6 - - - -
1604F FEC 3.6 38.4 - - + +
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Residues in contact with ASP 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E LEU 2.9 8.0 + - - -
52E ILE 2.9 10.1 + - - +
54E ILE* 1.3 76.8 - - - +
56E GLU* 1.3 62.9 + - - +
58E ARG* 3.0 34.4 + - - +
59E HIS* 3.0 16.6 + - - -
131E GLU* 4.5 2.5 - - - +
135E HIS* 2.8 32.1 + - + +
170F GLY* 3.3 9.5 - - - -
171F PHE* 3.3 21.1 + - - +
172F VAL* 2.9 36.3 + - - +
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Residues in contact with GLU 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLU* 3.6 24.9 - - - +
26E ALA* 4.2 5.1 - - + +
27E ILE* 3.9 15.3 - - + -
30E TYR* 3.6 18.7 - - + -
52E ILE 3.0 12.1 + - - +
53E ALA* 3.1 13.2 + - - +
55E ASP* 1.3 76.2 - - - +
57E MET* 1.3 58.1 + - - +
59E HIS* 3.2 21.9 + - - +
60E ALA* 3.0 27.2 + - - +
99E GLU* 3.1 13.2 - - - +
132E GLU* 3.3 1.7 - - - +
135E HIS* 3.3 10.4 + - - -
200E FE 2.1 31.8 - - - -
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Residues in contact with MET 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ILE* 3.8 27.6 - - + -
31E MET* 4.4 5.4 - - + -
53E ALA* 2.9 33.9 + - + +
54E ILE* 3.3 19.1 - - + +
55E ASP 3.2 0.2 - - - -
56E GLU* 1.3 77.5 - - - +
58E ARG* 1.3 60.6 - - - +
60E ALA* 3.4 4.7 + - - +
61E GLU* 3.1 21.7 + - - +
1604F FEC 2.4 110.6 - - + +
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Residues in contact with ARG 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E ILE 3.2 4.8 + - - +
55E ASP* 3.0 25.5 + - - +
57E MET* 1.3 76.1 - - - +
59E HIS* 1.3 59.5 + - - +
61E GLU* 3.1 11.7 + - - +
62E ASN* 2.7 54.6 + - - +
131E GLU* 3.1 35.7 + - - -
167F ALA* 4.9 9.2 - - - -
168F SER* 2.8 32.8 + - - +
172F VAL* 3.4 22.6 - - - +
1604F FEC 3.7 19.1 - - + +
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Residues in contact with HIS 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLU* 2.9 30.7 + - + +
55E ASP 3.0 13.3 + - - -
56E GLU* 3.2 25.0 + - - +
58E ARG* 1.3 83.3 - - - +
60E ALA* 1.3 64.2 + - - +
62E ASN* 3.0 6.5 + - - +
63E PHE* 2.8 31.4 + - + -
128E ILE* 3.7 37.4 - - + +
131E GLU* 2.5 42.0 + - + +
132E GLU* 3.5 13.2 + - - -
135E HIS* 4.2 3.6 - + - -
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Residues in contact with ALA 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ARG* 2.8 39.2 + - + +
23E GLU* 4.1 18.5 - - + +
24E LEU* 4.7 5.6 - - + -
27E ILE* 4.2 13.2 - - + -
56E GLU 3.0 12.9 + - - +
57E MET 3.5 11.0 - - - +
58E ARG 3.3 0.2 - - - -
59E HIS* 1.3 75.2 - - - +
61E GLU* 1.3 56.6 + - - +
63E PHE* 3.5 4.0 + - - +
64E ALA 3.1 18.7 + - - -
1604F FEC 4.4 5.4 - - + +
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Residues in contact with GLU 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E MET 3.1 9.3 + - - +
58E ARG* 3.4 13.3 - - - +
60E ALA* 1.3 78.9 - - - +
62E ASN* 1.3 65.7 + - - +
64E ALA* 3.3 1.4 + - - +
65E GLU* 2.9 52.7 + - - +
31F MET* 4.6 0.6 - - + +
34F HIS* 4.4 5.4 + - - -
35F TYR* 3.6 28.7 + - + +
50F LYS* 2.8 33.1 + - - +
1601F SO4 4.3 5.4 + - - -
1604F FEC 3.7 31.8 - - + +
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Residues in contact with ASN 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E ARG* 2.7 44.3 + - - +
59E HIS* 3.8 8.9 + - - +
61E GLU* 1.3 80.7 + - - +
63E PHE* 1.3 62.8 + - - +
65E GLU* 3.4 22.2 + - - +
66E ARG* 3.1 23.0 + - - +
124E LEU* 4.0 26.6 - - + +
128E ILE* 4.6 3.2 - - + +
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Residues in contact with PHE 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LEU* 3.5 31.0 - - + +
19E ALA* 3.5 12.3 - - + -
20E ARG* 3.8 24.7 - - + -
23E GLU* 3.9 10.3 - - + -
59E HIS 2.8 22.0 + - - +
60E ALA 3.6 4.9 - - - +
62E ASN* 1.3 78.2 - - - +
64E ALA* 1.3 56.1 + - - +
66E ARG* 3.2 5.3 + - - +
67E ILE* 2.8 34.6 + - - +
106E TYR* 3.8 21.3 - + - -
124E LEU* 4.0 11.7 - - + -
125E PHE* 3.6 38.6 - + - -
128E ILE* 3.5 27.4 - - + -
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ARG* 3.9 3.3 - - - +
60E ALA 3.1 17.6 + - - +
61E GLU 3.3 0.6 + - - +
63E PHE* 1.3 73.3 - - - +
65E GLU* 1.3 62.2 + - - +
67E ILE* 3.2 12.0 + - - +
68E LYS* 2.9 35.9 + - - +
74E PRO* 3.5 25.4 - - + -
35F TYR* 3.7 28.0 - - + -
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Residues in contact with GLU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLU* 2.9 41.9 + - + +
62E ASN* 3.6 25.1 + - - +
63E PHE 3.3 0.4 - - - -
64E ALA* 1.3 77.1 - - - +
66E ARG* 1.3 61.3 + - - +
68E LYS* 3.4 6.5 + - - +
69E GLU* 3.1 31.9 + - - +
34F HIS* 5.0 3.8 + - - -
35F TYR* 4.7 10.1 - - + -
38F ASP* 3.7 19.5 - - - +
1601F SO4 5.4 2.4 + - - -
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Residues in contact with ARG 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LEU* 3.7 18.8 - - + -
62E ASN 3.1 14.1 + - - +
63E PHE 3.5 8.1 - - - +
65E GLU* 1.3 75.3 - - - +
67E ILE* 1.3 63.9 + - - +
69E GLU* 3.0 45.3 + - - +
70E LEU* 3.1 31.8 + - - +
118E ASP* 2.7 30.9 + - - -
120E VAL* 3.4 30.6 - - + +
121E THR* 2.7 15.6 + - + +
124E LEU* 3.9 20.6 - - + -
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Residues in contact with ILE 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E ILE* 4.4 11.4 - - + +
16E LEU* 3.7 32.1 - - + +
17E ASN* 3.2 26.9 - - - +
20E ARG* 3.9 12.1 - - - -
63E PHE 2.8 27.5 + - - +
64E ALA* 3.5 15.0 - - - +
66E ARG* 1.3 77.7 - - - +
68E LYS* 1.3 59.4 + - - +
70E LEU* 3.3 5.8 + - - +
71E GLY 3.2 4.2 + - - -
72E GLY* 2.8 51.1 + - - +
73E GLU 3.7 2.9 - - - +
74E PRO* 3.6 16.2 - - + -
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Residues in contact with LYS 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ALA 2.9 20.6 + - - +
65E GLU* 3.7 7.0 - - - +
67E ILE* 1.3 72.1 - - - +
69E GLU* 1.3 63.4 + - + +
71E GLY* 3.0 17.2 + - - -
72E GLY 3.6 8.9 + - - +
73E GLU* 3.4 23.0 + - - -
74E PRO* 3.5 26.0 - - + -
35F TYR* 3.7 37.0 - - + +
36F SER* 3.8 16.6 + - - +
39F ASP* 3.6 39.3 + - + +
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Residues in contact with GLU 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LYS* 5.6 1.6 - - - -
65E GLU* 3.1 25.9 + - + +
66E ARG* 3.0 43.4 + - - +
68E LYS* 1.3 77.3 - - + +
70E LEU* 1.3 60.7 + - - +
71E GLY 3.2 0.7 + - - -
120E VAL* 5.0 4.2 - - - +
39F ASP* 4.9 4.0 - - - +
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Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LYS* 3.9 47.2 - - + +
12E VAL* 3.5 35.9 - - + -
13E ILE* 3.9 24.8 - - + +
16E LEU* 3.8 15.9 - - + -
66E ARG* 3.1 40.5 + - - +
67E ILE 3.3 7.2 + - - +
69E GLU* 1.3 77.1 - - - +
71E GLY* 1.3 59.6 + - - +
72E GLY 3.4 0.4 + - - -
118E ASP* 4.1 7.2 - - - +
----------------------------------------------------------
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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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