Contacts of the helix formed by residues 59 - 82 (chain A) in PDB entry 2NUN
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 THR 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A SER* 3.7 3.0 - - - -
58A ASN* 1.3 78.2 + - - +
60A PRO* 1.3 82.1 - - + +
61A GLU* 2.9 18.0 + - + +
62A ASN* 3.1 19.0 + - - +
63A ARG* 3.0 21.1 + - - +
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Residues in contact with PRO 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASN 4.8 0.2 - - - +
59A THR* 1.3 96.6 - - + +
61A GLU* 1.3 57.1 + - + +
63A ARG* 3.7 28.1 + - + +
64A ALA* 3.0 28.4 + - - +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR* 2.9 10.7 + - + +
60A PRO* 1.3 77.6 - - + +
62A ASN* 1.3 73.4 + - - +
63A ARG 3.1 0.9 - - - -
64A ALA* 2.8 8.1 + - - +
65A TYR* 2.8 25.6 + - - +
104A GLN* 4.9 7.8 - - - +
600A ADP 5.2 4.0 - - - +
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Residues in contact with ASN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A CYS 5.0 0.4 - - - -
57A SER* 2.6 34.8 + - - +
58A ASN* 3.9 3.6 - - - -
59A THR* 3.1 27.1 + - - +
61A GLU* 1.3 78.2 - - - +
63A ARG* 1.3 62.1 + - - +
65A TYR* 3.4 1.6 + - - +
66A CYS* 3.1 30.1 + - - -
600A ADP 3.4 39.2 + - + +
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A CYS* 3.6 41.4 - - + +
58A ASN* 2.8 48.6 + - + +
59A THR* 3.0 13.1 + - - +
60A PRO* 3.7 31.7 - - - +
62A ASN* 1.3 79.1 - - - +
64A ALA* 1.3 57.8 + - - +
66A CYS 3.6 0.3 + - - -
67A GLN* 3.0 26.9 + - - +
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PRO 3.0 18.8 + - - +
61A GLU* 2.8 7.2 + - - +
63A ARG* 1.3 75.4 - - - +
65A TYR* 1.3 60.1 + - - +
67A GLN* 3.7 6.9 - - - +
68A SER* 3.0 30.1 + - - -
102A LYS* 4.8 1.5 + - - -
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Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY 3.9 6.7 - - - -
61A GLU 2.8 15.1 + - - +
62A ASN 3.5 4.5 - - - +
64A ALA* 1.3 78.7 - - - +
66A CYS* 1.3 63.0 + - - +
68A SER* 3.4 3.7 + - - -
69A MET* 3.0 23.7 + - - -
98A TRP* 3.5 32.7 - + - -
99A ARG* 2.8 34.3 + - - -
102A LYS* 4.0 29.2 - - + -
270A ALA* 3.5 8.0 - - - +
600A ADP 3.0 79.5 + + - +
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Residues in contact with CYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLN 3.4 6.7 - - - +
43A CYS* 3.2 32.5 - - - +
45A ILE* 3.1 26.7 - - - +
47A ALA* 3.6 29.4 - - - -
62A ASN* 3.1 16.8 + - - +
63A ARG 3.9 0.2 - - - +
65A TYR* 1.3 88.2 - - - +
67A GLN* 1.3 64.4 + - - +
69A MET* 3.0 5.2 + - - +
70A TYR* 2.9 19.2 + - - +
600A ADP 4.4 2.7 - - - -
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 4.1 15.0 - - - +
42A GLN* 2.9 40.2 + - - +
43A CYS* 3.4 20.2 - - - -
63A ARG 3.0 19.8 + - - +
64A ALA* 3.7 8.2 - - - +
65A TYR 3.4 0.2 - - - -
66A CYS* 1.3 75.1 - - - +
68A SER* 1.3 62.1 + - - +
70A TYR* 3.3 5.7 + - - +
71A ASN* 3.1 35.7 + - - +
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ALA 3.0 17.0 + - - -
65A TYR 3.5 5.4 - - - -
67A GLN* 1.3 75.7 - - - +
69A MET* 1.3 65.7 + - - +
71A ASN* 3.2 9.3 + - - +
72A SER* 2.9 25.5 + - - -
98A TRP* 2.8 14.1 + - - -
102A LYS* 2.7 34.3 + - - -
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Residues in contact with MET 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 3.5 20.2 - - + +
46A GLY* 3.4 33.7 - - - +
65A TYR* 3.0 8.9 + - - +
66A CYS* 3.0 10.8 + - - +
68A SER* 1.3 75.6 - - - +
70A TYR* 1.3 52.7 + - - +
72A SER* 3.8 1.4 - - - -
73A ILE* 2.8 41.7 + - + +
98A TRP* 3.3 39.7 - - + +
270A ALA* 4.2 11.4 - - - +
273A GLU* 3.7 22.7 - - + -
274A PHE* 3.9 25.8 - - + +
277A ARG* 4.3 3.1 - - - -
600A ADP 4.8 5.4 - - - -
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLN* 3.2 29.8 + - - +
37A LEU* 3.7 22.1 + - + -
42A GLN* 3.3 50.9 - - + +
45A ILE* 4.1 14.8 - - + +
66A CYS 2.9 11.3 + - - +
67A GLN* 3.4 9.0 - - - +
68A SER 3.1 0.2 - - - -
69A MET* 1.3 77.8 - - - +
71A ASN* 1.3 75.3 + - - +
73A ILE* 3.3 8.8 + - + +
74A ARG* 3.1 52.6 + - + +
286A GLU* 2.3 38.1 + - - -
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Residues in contact with ASN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLN* 5.5 1.0 + - - -
42A GLN* 4.7 3.6 + - - -
67A GLN* 3.1 26.2 + - - +
68A SER* 3.2 9.8 + - - +
70A TYR* 1.3 96.6 - - - +
72A SER* 1.3 62.2 + - - +
74A ARG* 3.4 8.4 + - - +
75A SER* 3.1 21.5 + - - -
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Residues in contact with SER 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A SER* 2.9 16.0 + - - -
69A MET 3.9 0.7 - - - -
71A ASN* 1.3 74.1 - - - +
73A ILE* 1.3 61.2 + - - +
75A SER* 3.1 8.6 + - - -
76A ALA* 2.8 31.9 + - - +
94A ARG* 5.7 0.6 - - - +
98A TRP* 3.1 31.3 - - - -
274A PHE* 3.7 16.8 - - - -
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Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 4.8 2.9 - - + -
69A MET* 2.8 38.6 + - + +
70A TYR* 3.4 10.5 - - + +
72A SER* 1.3 76.5 - - - +
74A ARG* 1.3 60.9 + - + +
76A ALA* 3.2 3.5 + - - +
77A GLY* 2.9 25.5 + - - -
274A PHE* 2.9 63.3 - - + +
277A ARG* 3.4 39.0 - - + +
278A ALA* 3.7 2.8 - - - +
281A SER* 4.1 5.3 + - - -
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO* 2.8 48.3 + - + +
33A SER* 2.4 35.0 + - - +
36A GLN* 3.5 31.1 + - - +
70A TYR* 3.1 54.7 + - + +
71A ASN* 3.9 8.0 - - - +
73A ILE* 1.3 79.3 - - + +
75A SER* 1.3 57.0 + - - +
77A GLY 3.3 0.2 + - - -
78A ASP* 2.9 13.7 + - - +
281A SER* 3.4 13.9 - - - +
286A GLU* 3.6 10.7 + - - +
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASN 3.1 14.4 + - - -
72A SER* 3.4 12.6 - - - -
74A ARG* 1.3 75.8 - - - +
76A ALA* 1.3 59.4 + - - +
78A ASP* 3.2 9.7 + - - +
79A GLU* 3.0 33.9 + - - +
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A SER 2.8 15.9 + - - +
73A ILE 3.8 3.6 - - - +
75A SER* 1.3 77.0 - - - +
77A GLY* 1.3 59.0 + - - +
79A GLU* 3.3 14.4 + - - +
80A ILE* 2.9 33.3 + - - +
85A ILE* 3.9 14.3 - - + +
91A LEU* 4.1 2.2 - - + -
94A ARG* 4.3 10.1 - - + -
274A PHE* 4.0 21.1 - - + -
278A ALA* 4.1 8.1 - - + -
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO* 4.2 3.1 - - - +
73A ILE 2.9 12.8 + - - -
74A ARG 3.3 4.2 + - - -
75A SER 3.1 0.2 - - - -
76A ALA* 1.3 74.4 - - - +
78A ASP* 1.3 65.2 + - - +
80A ILE* 4.3 0.4 - - - -
81A SER* 3.1 19.8 + - - -
278A ALA 3.4 24.8 + - - -
281A SER* 4.3 2.5 - - - -
282A ALA* 3.3 23.6 - - - +
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Residues in contact with ASP 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLY* 5.0 1.4 - - - -
32A PRO* 3.7 18.3 - - + +
74A ARG 2.9 14.5 + - - +
75A SER* 3.2 13.1 + - - +
77A GLY* 1.3 76.6 - - - +
79A GLU* 1.3 63.1 + - - +
81A SER* 2.8 20.5 + - - -
82A ARG* 3.3 41.8 + - - -
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A SER* 3.0 18.2 + - - +
76A ALA* 3.4 17.8 - - - +
78A ASP* 1.3 78.9 - - + +
80A ILE* 1.3 59.4 + - - +
82A ARG* 3.0 11.7 + - - +
84A GLY* 2.7 37.5 + - - +
85A ILE* 3.7 15.7 - - + +
94A ARG* 2.8 47.5 + - - -
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 5.2 1.2 - - - +
27A ARG 5.5 0.7 - - - +
29A LEU* 4.6 5.8 - - + +
76A ALA 2.9 22.5 + - - +
77A GLY 3.7 4.5 - - - +
78A ASP 3.3 0.2 - - - -
79A GLU* 1.3 76.1 - - - +
81A SER* 1.3 58.8 + - - +
82A ARG 3.0 0.2 - - - -
83A GLY* 3.0 18.4 + - - -
85A ILE* 3.9 19.8 - - + +
91A LEU* 4.0 23.3 - - + -
234A TYR* 3.5 26.9 - - + +
238A ILE* 3.8 21.0 - - + +
278A ALA* 3.8 30.1 - - + +
279A ILE* 4.1 6.1 - - - +
282A ALA* 3.8 12.3 - - + -
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.7 3.3 - - - -
27A ARG 4.3 0.8 - - - +
28A ALA* 3.7 10.4 - - - +
29A LEU* 3.3 57.5 + - - +
31A GLY* 3.6 13.7 + - - -
77A GLY 3.1 11.0 + - - -
78A ASP* 2.8 23.7 + - - -
80A ILE* 1.3 77.0 - - - +
82A ARG* 1.3 64.9 + - - +
83A GLY 3.4 0.4 - - - -
282A ALA* 3.9 7.8 - - - +
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ASN* 2.7 31.1 + - - +
26A PHE* 3.3 22.0 - - + -
29A LEU 5.8 1.0 + - - -
31A GLY* 6.0 1.6 - - - +
78A ASP* 3.3 40.9 + - - +
79A GLU* 3.0 11.2 + - - +
81A SER* 1.3 83.1 + - - +
83A GLY* 1.3 51.0 + - - +
84A GLY* 3.1 4.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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