Contacts of the helix formed by residues 23 - 47 (chain F) in PDB entry 1NU9
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 SER 23 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU* 4.2 14.6 - - - +
111C GLU* 3.5 33.9 + - - +
112C ASP* 5.3 3.9 + - - -
21F LEU 3.8 2.2 + - - -
22F ILE* 1.3 75.3 - - - +
24F ASP* 1.3 61.3 + - - +
25F TRP* 3.7 16.4 + - - -
26F TYR 3.0 4.3 + - - -
27F LEU* 2.8 24.9 + - - +
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Residues in contact with ASP 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASP* 4.3 33.6 - - + +
22F ILE 3.4 3.3 + - - -
23F SER* 1.3 70.6 - - - +
25F TRP* 1.3 63.8 + - - +
27F LEU* 3.0 32.4 + - - +
28F LYS* 2.8 48.2 + - - +
111F GLU* 5.1 5.9 - - - +
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Residues in contact with TRP 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C TYR* 3.8 30.8 - + - -
87C LEU* 3.1 32.7 - - + +
88C TYR* 4.1 10.5 - - - -
91C TYR* 3.9 45.2 - + + -
103C LYS* 5.9 3.6 - - - -
111C GLU* 3.3 26.8 + - - -
2001C IMD 3.9 36.8 - + + +
23F SER* 3.7 11.1 + - - -
24F ASP* 1.3 80.4 + - - +
26F TYR* 1.3 66.8 + + + +
28F LYS* 4.3 14.6 + - - +
29F GLY 4.6 1.7 + - - -
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Residues in contact with TYR 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 3.5 49.6 - - + -
90C LYS* 3.4 18.2 + - - -
91C TYR* 4.1 25.1 - + + -
94C GLU* 2.7 27.4 + - - -
22F ILE* 3.2 22.4 - - + -
23F SER 3.0 6.5 + - - +
25F TRP* 1.3 98.9 - + + +
27F LEU* 1.3 66.4 + - - +
28F LYS 3.3 0.7 - - - -
29F GLY* 3.3 11.0 + - - -
30F ARG* 3.4 41.1 + - + +
115F MET* 4.0 16.9 - - + +
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Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ILE* 3.5 18.1 - - + +
23F SER 2.8 12.7 + - - +
24F ASP* 3.2 26.9 - - - +
26F TYR* 1.3 74.6 - - - +
28F LYS* 1.3 69.9 + - - +
30F ARG* 2.8 14.8 + - - +
31F LEU* 2.9 30.0 + - + +
110F ILE* 3.3 26.0 - - + +
111F GLU 3.6 20.9 - - - +
113F LEU* 3.7 35.4 - - + +
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Residues in contact with LYS 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ASP* 2.8 48.4 + - - +
25F TRP* 4.3 10.5 - - - +
27F LEU* 1.3 86.5 - - + +
29F GLY* 1.3 63.2 + - - +
31F LEU* 3.3 10.4 + - + +
32F THR* 3.1 26.7 + - - +
109F THR* 4.4 15.2 + - - -
110F ILE 4.8 3.2 + - - -
111F GLU* 5.9 2.2 - - - +
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Residues in contact with GLY 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C TYR* 6.5 1.8 - - - -
95C ASN* 6.2 2.0 - - - -
25F TRP 4.6 2.2 + - - -
26F TYR 3.3 8.1 + - - -
27F LEU 3.1 0.6 - - - -
28F LYS* 1.3 80.2 - - - +
30F ARG* 1.3 73.4 + - - +
32F THR* 3.9 6.9 - - - -
33F SER* 3.1 23.9 + - - -
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Residues in contact with ARG 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C TYR* 6.4 0.4 - - - -
94C GLU* 3.9 26.8 + - - +
95C ASN* 4.7 12.5 + - - +
22F ILE* 4.1 17.9 - - + -
26F TYR* 3.4 50.6 + - + +
27F LEU 2.8 7.6 + - - +
29F GLY* 1.3 91.9 + - - +
31F LEU* 1.3 66.1 + - - +
33F SER* 3.4 10.1 + - - -
34F LEU* 3.1 27.7 + - - +
113F LEU* 4.5 5.6 - - + -
115F MET* 4.7 3.9 - - - +
118F TYR* 3.0 52.0 + - + -
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D TRP* 3.6 33.3 - - + -
27F LEU* 2.9 30.1 + - + +
28F LYS* 3.3 13.4 + - + +
30F ARG* 1.3 74.3 - - - +
32F THR* 1.3 65.2 + - - +
34F LEU* 3.0 10.2 + - + +
35F GLU* 2.9 20.3 + - - +
73F LEU* 5.4 1.1 - - + -
109F THR* 5.4 5.4 - - - -
110F ILE* 3.7 44.6 - - + +
113F LEU* 4.0 24.2 - - + -
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Residues in contact with THR 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LYS 3.1 17.7 + - - -
29F GLY* 3.9 7.4 - - - -
30F ARG 3.4 0.2 - - - -
31F LEU* 1.3 75.1 - - - +
33F SER* 1.3 58.0 + - - +
35F GLU* 3.2 19.9 + - - +
36F SER* 3.0 33.9 + - - +
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Residues in contact with SER 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F GLY 3.1 19.0 + - - -
30F ARG* 3.5 16.3 + - - -
31F LEU 3.2 0.2 - - - -
32F THR* 1.3 77.7 - - - +
34F LEU* 1.3 60.5 + - - +
36F SER* 3.4 8.2 + - - -
37F GLN* 3.1 32.3 + - - +
118F TYR* 2.7 27.6 + - - -
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Residues in contact with LEU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D TRP* 4.0 9.4 - - + -
30F ARG 3.1 18.7 + - - +
31F LEU* 3.0 18.3 + - + +
33F SER* 1.3 74.5 - - - +
35F GLU* 1.3 66.5 + - - +
37F GLN* 3.2 22.6 + - - +
38F PHE* 2.9 37.9 + - + -
73F LEU* 4.3 9.0 - - + -
113F LEU* 4.0 19.7 - - + -
118F TYR* 3.8 19.7 - - + -
121F LEU* 3.8 40.6 - - + -
122F THR* 4.1 2.9 - - - +
125F LEU* 5.5 1.8 - - + -
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Residues in contact with GLU 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D TRP* 3.8 12.3 - - + +
149D VAL* 2.7 78.6 + - + +
31F LEU 2.9 11.5 + - - +
32F THR* 3.3 22.1 + - - +
34F LEU* 1.3 77.2 - - - +
36F SER* 1.3 56.6 + - - +
38F PHE* 3.2 7.7 + - - +
39F ILE* 3.0 37.9 + - + +
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Residues in contact with SER 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F THR* 3.0 22.4 + - - +
33F SER* 3.7 11.1 - - - -
34F LEU 3.2 0.2 - - - -
35F GLU* 1.3 75.2 - - - +
37F GLN* 1.3 61.3 + - - +
39F ILE* 3.3 11.0 + - - +
40F ASN* 2.9 30.7 + - - +
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Residues in contact with GLN 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F SER* 3.1 19.9 + - - +
34F LEU* 3.2 19.4 + - - +
36F SER* 1.3 76.1 - - - +
38F PHE* 1.3 57.7 + - - +
40F ASN* 3.3 8.0 + - - +
41F ALA* 2.9 29.6 + - - +
118F TYR* 3.5 17.2 + - - -
122F THR* 3.0 54.5 + - - +
125F LEU* 3.8 20.3 - - + +
126F LYS* 5.6 0.7 - - - -
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Residues in contact with PHE 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D TRP* 3.4 26.5 - + - -
149D VAL* 4.0 19.7 - - + -
34F LEU* 2.9 34.0 + - + -
35F GLU* 3.5 6.7 - - - +
37F GLN* 1.3 74.5 - - - +
39F ILE* 1.3 66.3 + - - +
41F ALA* 3.2 4.6 + - - +
42F LEU* 2.9 31.0 + - + +
66F ILE* 3.5 26.7 - - + -
69F GLU* 3.7 32.8 - - + -
70F ASP* 3.5 28.5 - - + -
73F LEU* 3.6 14.6 - - + -
121F LEU* 5.0 1.1 - - + -
125F LEU* 3.9 19.5 - - + -
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Residues in contact with ILE 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D VAL* 3.4 45.5 - - + +
35F GLU* 3.0 26.4 + - + +
36F SER* 3.7 11.2 - - - +
38F PHE* 1.3 76.1 - - - +
40F ASN* 1.3 59.5 + - - +
42F LEU* 3.4 3.8 + - - +
43F GLY* 2.9 26.7 + - - -
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Residues in contact with ASN 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F SER 2.9 17.8 + - - +
37F GLN* 3.6 7.0 + - - +
39F ILE* 1.3 79.7 - - - +
41F ALA* 1.3 63.5 + - - +
43F GLY* 3.3 2.3 + - - -
44F ILE* 3.1 44.8 + - - +
129F VAL* 5.2 5.3 - - - +
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Residues in contact with ALA 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F GLN 2.9 16.9 + - - +
38F PHE* 3.8 5.6 - - - +
40F ASN* 1.3 77.0 - - - +
42F LEU* 1.3 66.4 + - - +
44F ILE* 3.3 5.6 + - - +
45F LEU* 3.1 20.3 + - - +
62F LEU* 4.4 3.7 - - + +
66F ILE* 3.5 28.9 - - + +
125F LEU* 4.9 9.2 - - + -
129F VAL* 4.2 23.8 - - + -
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Residues in contact with LEU 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D LYS* 3.8 68.4 - - + +
150D GLY* 4.0 5.2 - - - +
38F PHE 2.9 17.2 + - - +
39F ILE* 3.9 4.0 - - - +
41F ALA* 1.3 75.9 - - - +
43F GLY* 1.3 58.6 + - - +
45F LEU* 3.1 7.1 - - + +
46F GLU* 2.9 34.8 + - + +
63F MET* 4.0 31.9 - - + -
66F ILE* 4.1 22.7 - - + -
67F LEU* 5.6 2.7 - - + -
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Residues in contact with GLY 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ILE 2.9 16.0 + - - -
40F ASN* 3.7 4.5 - - - -
41F ALA 3.2 0.2 - - - -
42F LEU* 1.3 74.0 - - - +
44F ILE* 1.3 64.5 + - - +
46F GLU* 3.2 8.5 + - - +
47F THR* 3.2 21.7 + - - -
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Residues in contact with ILE 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ASN* 3.1 36.1 + - - +
41F ALA* 3.8 6.5 - - - +
42F LEU 3.3 0.2 - - - -
43F GLY* 1.3 76.5 - - - +
45F LEU* 1.3 63.6 - - - +
47F THR* 3.0 25.7 + - - +
50F TYR* 3.4 14.3 - - + +
62F LEU* 5.1 2.5 - - + -
129F VAL* 3.9 29.4 - - + -
132F PHE* 4.0 25.6 - - + -
133F GLU* 4.9 7.9 - - + +
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Residues in contact with LEU 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F ALA 3.1 9.6 + - - +
42F LEU* 3.1 13.7 + - + +
44F ILE* 1.3 82.1 - - - +
46F GLU* 1.3 66.6 + - + +
47F THR 3.4 0.9 + - - +
50F TYR* 4.3 6.9 - - - +
59F LYS* 3.3 61.0 + - + +
62F LEU* 3.6 35.9 - - + +
63F MET* 3.8 34.8 - - + +
66F ILE* 4.2 4.9 - - + -
132F PHE* 4.8 3.8 - - + -
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Residues in contact with GLU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ARG* 2.9 41.2 + - - -
74D THR* 5.5 2.8 - - - +
149D LYS 5.3 8.1 - - - -
151D GLN* 3.9 20.9 + - - +
42F LEU* 2.9 19.9 + - + +
43F GLY* 3.2 7.8 + - - +
45F LEU* 1.3 82.9 - - + +
47F THR* 1.3 66.2 + - - +
48F TYR* 3.1 4.3 + - - -
63F MET* 5.1 1.6 - - - +
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Residues in contact with THR 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F GLY 3.2 11.8 + - - -
44F ILE* 3.0 22.8 + - - +
45F LEU 3.3 0.4 - - - -
46F GLU* 1.3 75.4 - - - +
48F TYR* 1.3 69.9 + - + +
49F HIS* 3.9 20.4 - - + +
50F TYR* 2.8 35.2 + - + +
51F GLY* 3.7 2.8 + - - -
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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