Contacts of the helix formed by residues 56 - 78 (chain G) in PDB entry 1LNU
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 ASP 56 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55G PHE* 1.3 87.4 - - - +
57G PRO* 1.3 68.2 - - - +
58G GLN* 2.5 52.5 + - - +
59G GLY* 3.0 20.3 + - - -
2H GLU* 2.8 17.0 + - - +
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Residues in contact with PRO 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G VAL* 3.8 12.9 - - + +
40G LYS* 3.7 23.6 - - + +
41G GLU* 3.8 11.7 - - + -
42G THR* 3.5 30.7 - - - +
55G PHE* 3.0 8.5 - - + +
56G ASP* 1.3 89.6 - - - +
58G GLN* 1.3 63.1 + - - +
59G GLY 3.1 0.9 + - - -
60G GLY 3.3 8.7 + - - -
61G LEU* 3.3 17.4 + - + +
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Residues in contact with GLN 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G ASP* 2.5 45.7 + - - +
57G PRO* 1.3 79.0 - - - +
59G GLY* 1.3 81.7 + - - +
61G LEU* 3.7 14.3 - - + +
62G GLN* 2.7 59.8 + - - +
5H LYS* 5.5 1.0 - - - +
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Residues in contact with GLY 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G TYR* 4.7 1.1 - - - -
55G PHE* 4.8 1.3 - - - -
56G ASP 3.0 7.9 + - - -
58G GLN* 1.3 97.3 - - - +
60G GLY* 1.3 61.5 + - - +
62G GLN* 3.1 3.9 - - - +
63G ASN 3.1 5.7 + - - -
5H LYS* 2.3 52.1 + - - -
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Residues in contact with GLY 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G TYR* 3.5 37.2 - - - -
35G VAL* 4.6 3.6 - - - -
37G LEU* 4.8 1.8 - - - -
55G PHE* 4.2 4.8 - - - -
56G ASP 4.1 2.0 + - - -
57G PRO 3.3 7.0 + - - -
58G GLN 3.2 0.4 - - - -
59G GLY* 1.3 74.4 - - - +
61G LEU* 1.3 65.6 + - - +
63G ASN* 3.1 3.6 + - - +
64G ILE* 3.1 28.3 + - - +
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Residues in contact with LEU 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G VAL* 5.4 1.1 - - + -
37G LEU* 3.5 43.4 - - + +
40G LYS* 3.2 42.6 - - + +
57G PRO 3.3 15.3 + - - +
58G GLN* 3.4 15.7 + - + +
60G GLY* 1.3 73.7 - - - +
62G GLN* 1.3 63.2 + - - +
64G ILE* 3.2 17.9 + - + +
65G ALA* 3.3 13.0 + - - +
68G LYS* 5.4 0.3 + - - -
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Residues in contact with GLN 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G GLN* 2.7 47.3 + - - +
59G GLY* 3.1 8.1 - - - +
61G LEU* 1.3 77.5 - - - +
63G ASN* 1.3 56.1 + - - -
65G ALA* 3.6 12.5 - - - +
66G VAL* 3.2 19.0 - - + +
5H LYS* 3.1 26.8 + - - +
7H LYS* 4.1 14.8 - - - -
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Residues in contact with ASN 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G GLY 3.8 3.0 + - - -
12G SER* 2.6 33.4 + - - +
23G TYR* 3.8 6.3 - - + -
59G GLY 3.1 7.7 + - - +
60G GLY 3.1 4.7 + - - +
62G GLN* 1.3 74.3 - - - +
64G ILE* 1.3 60.7 + - - +
65G ALA 3.2 1.8 - - - -
66G VAL* 3.2 8.3 + - - +
67G VAL* 2.9 33.9 + - - +
5H LYS* 3.2 21.7 + - - +
6H ALA 3.6 9.2 + - - +
7H LYS* 3.6 1.9 - - - +
8H ALA* 3.2 26.3 + - - +
37H PHE* 3.5 20.8 - - - -
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Residues in contact with ILE 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G SER* 4.5 6.7 - - - -
13G VAL 4.3 10.1 - - - +
14G TYR* 4.1 20.9 - - + -
22G GLN 4.0 24.2 - - - +
23G TYR* 4.0 14.1 - - + -
37G LEU* 4.0 32.1 - - + -
60G GLY 3.1 15.7 + - - +
61G LEU* 3.2 10.0 + - + +
63G ASN* 1.3 77.5 - - - +
65G ALA* 1.3 52.7 + - - +
67G VAL* 3.1 4.5 + - + +
68G LYS* 2.5 54.4 + - - +
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Residues in contact with ALA 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G LEU 3.3 8.2 + - - +
62G GLN* 3.6 13.2 - - - +
64G ILE* 1.3 79.4 - - - +
66G VAL* 1.3 52.6 + - + +
68G LYS* 3.3 19.4 - - - +
69G HIS* 2.7 35.3 + - - +
10H LYS* 6.4 0.4 - - - -
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Residues in contact with VAL 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G GLN* 3.2 19.7 - - + +
63G ASN* 3.2 13.7 + - - +
65G ALA* 1.3 74.1 - - + +
67G VAL* 1.3 57.1 + - - +
69G HIS* 2.9 6.4 + - - +
70G ASN* 2.6 55.2 + - - +
8H ALA* 3.2 44.6 - - + +
9H ASN 3.7 6.7 - - - +
10H LYS* 4.1 20.6 - - + +
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Residues in contact with VAL 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G SER* 3.1 41.3 - - - +
13G VAL 4.2 0.9 - - - -
14G TYR* 3.4 25.4 - - + +
63G ASN* 2.9 24.6 + - - +
64G ILE* 3.5 7.9 - - - +
66G VAL* 1.3 77.2 - - + +
68G LYS* 1.3 63.4 + - - +
70G ASN* 3.7 5.0 - - - +
71G LEU* 3.0 23.7 + - - +
8H ALA* 4.9 2.9 - - + -
35H TYR* 3.3 29.1 - - + -
37H PHE* 4.4 9.0 - - + -
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Residues in contact with LYS 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G TYR* 2.7 54.2 - - + +
19G ASP* 4.3 6.5 + - - +
61G LEU 5.4 0.2 + - - -
64G ILE* 2.5 31.2 + - - +
65G ALA* 3.3 26.3 - - - +
67G VAL* 1.3 75.7 - - - +
69G HIS* 1.3 64.5 + - - +
71G LEU* 3.4 11.4 + - - +
72G GLY* 3.6 4.3 + - - -
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Residues in contact with HIS 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G ALA 2.7 17.9 + - - +
66G VAL* 2.9 10.5 + - - +
68G LYS* 1.3 75.7 - - - +
70G ASN* 1.3 73.8 + - - +
71G LEU 2.8 2.4 + - - -
72G GLY* 3.0 11.6 + - - -
73G VAL* 3.4 19.5 + - + +
10H LYS* 4.2 29.3 - - + +
11H ALA 3.9 21.8 + - - -
13H ASP* 5.8 0.8 + - - -
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Residues in contact with ASN 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G VAL* 2.6 46.5 + - - +
67G VAL* 3.7 4.9 - - - +
69G HIS* 1.3 72.0 - - - +
71G LEU* 1.3 61.3 + - - +
73G VAL* 3.4 3.8 - - - +
74G LEU* 3.1 26.7 + - - +
8H ALA* 5.0 1.0 - - - +
9H ASN 2.6 25.2 + - - -
10H LYS* 3.4 2.3 - - - -
11H ALA* 3.4 32.3 + - + +
35H TYR* 3.8 31.6 + - + -
56H TYR* 4.4 4.4 - - - -
63H TYR* 4.3 0.4 + - - +
87H TRP* 4.2 7.1 - - - -
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Residues in contact with LEU 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G TYR* 3.7 26.9 - - + +
15G GLN 4.1 0.9 - - - -
16G SER* 3.3 38.8 - - - +
67G VAL 3.0 17.4 + - - +
68G LYS 3.5 6.7 - - - +
69G HIS 2.8 4.8 + - - -
70G ASN* 1.3 69.6 - - - +
72G GLY* 1.3 63.4 + - - +
73G VAL 2.9 0.5 + - - -
74G LEU* 3.1 2.8 + - - -
75G THR* 2.4 49.3 + - - +
33H PHE* 3.9 12.8 - - + +
34H VAL 4.6 0.2 - - - -
35H TYR* 3.9 22.9 - - + +
58H TYR* 3.9 22.9 - - + -
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Residues in contact with GLY 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G LYS 3.6 4.2 + - - -
69G HIS 3.0 8.1 + - - -
71G LEU* 1.3 77.3 - - - +
73G VAL* 1.3 50.5 + - - +
75G THR* 2.8 11.1 - - - -
76G LYS* 2.7 57.5 + - - +
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Residues in contact with VAL 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G HIS* 3.4 25.5 + - + +
70G ASN* 3.4 7.9 - - - +
71G LEU 2.9 0.6 + - - -
72G GLY* 1.3 72.8 - - - +
74G LEU* 1.3 54.1 + - - +
76G LYS* 2.7 23.0 + - - +
77G ARG* 2.6 57.5 + - - +
11H ALA* 3.7 25.6 - - + +
12H VAL 3.6 2.9 - - - +
13H ASP 4.0 9.2 - - - +
14H GLY* 3.4 28.9 - - - -
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Residues in contact with LEU 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G ASN 3.1 13.8 + - - +
71G LEU 3.1 8.1 + - - +
73G VAL* 1.3 76.3 - - - +
75G THR* 1.3 67.1 + - - +
77G ARG* 3.4 16.7 - - - +
78G SER* 2.8 26.4 + - - -
11H ALA* 4.4 4.3 - - + -
35H TYR* 4.2 6.1 - - + -
58H TYR* 3.6 27.1 - - + -
63H TYR* 3.4 59.7 - - + +
79H LEU* 3.7 28.9 - - + +
83H ASP* 4.1 5.4 - - - +
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Residues in contact with THR 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G SER* 5.2 5.5 - - - +
71G LEU* 2.4 49.7 + - - +
72G GLY* 2.8 17.4 - - - -
74G LEU* 1.3 75.3 - - - +
76G LYS* 1.3 64.7 - - + +
78G SER* 2.9 6.2 + - - -
80G SER* 3.3 30.7 + - - +
33H PHE* 4.5 28.5 - - + +
58H TYR* 3.7 11.1 - - - +
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Residues in contact with LYS 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G GLY* 2.7 43.7 + - - +
73G VAL* 2.7 16.7 + - - +
75G THR* 1.3 69.6 - - - +
77G ARG* 1.3 54.5 + - - +
78G SER 2.4 18.4 + - - -
79G ASN* 2.8 13.7 + - - -
80G SER* 5.1 4.7 - - - -
310G NAG 5.3 0.2 + - - -
13H ASP 5.0 3.4 - - - +
14H GLY 3.7 13.5 - - - +
15H GLY 4.4 3.4 - - - +
16H GLY* 3.2 28.0 - - - +
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Residues in contact with ARG 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G VAL* 2.6 45.8 + - + +
74G LEU* 3.4 13.9 - - - +
76G LYS* 1.3 71.8 - - - +
78G SER* 1.3 52.2 + - - +
11H ALA* 3.8 2.0 - - - +
12H VAL* 3.5 17.2 + - - +
14H GLY* 4.3 10.2 - - - -
16H GLY* 3.3 2.8 - - - +
17H GLY* 2.6 32.3 - - - +
19H LEU* 2.9 15.5 - - + +
63H TYR* 3.9 2.6 - - - -
79H LEU* 2.5 53.5 + - + +
82H PRO* 3.6 18.8 - - + +
83H ASP* 2.4 47.1 + - - -
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Residues in contact with SER 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G LEU 2.8 17.3 + - - -
75G THR 3.5 2.9 - - - -
76G LYS 2.4 17.4 + - - -
77G ARG* 1.3 69.8 - - - +
79G ASN* 1.3 61.9 + - - +
80G SER 2.8 4.7 + - - -
81G THR* 2.7 29.1 + - - -
17H GLY 3.6 1.3 - - - -
19H LEU* 4.2 13.9 - - - +
58H TYR* 3.6 26.8 - - - -
79H LEU* 4.1 13.7 - - - +
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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