Contacts of the helix formed by residues 58 - 80 (chain A) in PDB entry 1KO1
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 ASN 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LYS* 3.9 8.9 - - - +
57A LEU* 1.3 69.9 - - - +
59A ASP* 1.3 57.6 + - - +
60A ASP* 2.4 17.9 + - - +
61A ASP* 2.1 89.4 + - - +
62A ARG* 2.8 15.7 + - - +
91A LYS* 6.0 0.2 - - - +
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Residues in contact with ASP 59 (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* 1.3 75.9 + - - +
60A ASP* 1.3 61.7 + - - +
62A ARG* 3.1 4.8 + - - +
63A LYS* 3.1 22.0 + - - +
66A LEU* 5.6 0.5 - - - +
91A LYS* 2.4 36.9 + - - +
93A HIS* 5.4 8.5 + - + +
94A TYR* 2.6 29.3 + - + -
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Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 2.4 25.9 + - - +
59A ASP* 1.3 70.8 - - - +
61A ASP* 1.3 65.3 + - - +
63A LYS* 3.7 18.8 + - - +
64A PRO* 3.8 9.0 - - - +
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Residues in contact with ASP 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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44A PRO* 5.3 0.3 - - - +
47A ASN* 3.2 34.2 + - - +
50A LYS* 2.8 20.3 + - - +
57A LEU* 3.3 16.2 - - + -
58A ASN* 2.1 81.6 + - - +
60A ASP* 1.3 72.9 - - - +
62A ARG* 1.3 59.5 + - - +
63A LYS 3.2 0.5 + - - -
64A PRO* 3.3 10.4 - - - +
65A TRP 4.7 0.2 + - - -
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASN* 4.3 1.1 - - - -
56A PRO* 6.0 0.2 - - - +
57A LEU* 3.4 56.0 + - + +
58A ASN 2.8 9.0 + - - +
59A ASP* 3.1 5.6 + - - +
61A ASP* 1.3 79.8 - - + +
63A LYS* 1.3 63.1 + - - +
64A PRO* 3.6 0.4 - - - -
65A TRP* 3.1 36.1 - - + +
66A LEU* 3.0 33.6 + - + +
90A LEU* 5.4 2.7 - - - +
91A LYS* 4.0 12.1 - - - +
94A TYR* 2.4 54.9 + - + -
137A GLN* 5.1 9.7 - - - +
140A THR* 4.1 17.9 + - - +
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Residues in contact with LYS 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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59A ASP 3.1 14.1 + - - +
60A ASP* 4.0 16.8 - - - +
61A ASP 3.2 0.4 + - - -
62A ARG* 1.3 76.2 - - - +
64A PRO* 1.3 71.2 - - + +
66A LEU* 3.3 10.4 + - - +
67A GLN* 3.0 22.6 + - + +
93A HIS* 5.4 6.0 + - + -
97A LEU* 4.8 25.3 - - + +
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Residues in contact with PRO 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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44A PRO* 4.4 16.6 - - + -
60A ASP 3.8 5.4 - - - +
61A ASP 3.3 15.7 - - - +
63A LYS* 1.3 95.6 - - + +
65A TRP* 1.3 65.3 - - - +
67A GLN* 3.8 8.3 - - + +
68A ALA* 3.0 25.3 + - - +
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Residues in contact with TRP 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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39A GLY 2.9 31.1 + - - -
40A ASP* 4.8 7.4 - - - -
42A LEU* 3.9 7.6 - - + +
43A HIS* 3.2 62.8 + + + -
44A PRO* 4.2 9.2 - - + +
47A ASN* 4.3 1.3 - - - +
62A ARG* 3.1 46.0 - - + +
64A PRO* 1.3 79.5 - - - +
66A LEU* 1.3 72.0 + - + +
68A ALA* 3.2 4.9 + - - +
69A LEU* 2.9 47.5 + - + +
87A CYS* 3.7 21.8 - - + -
88A SER* 4.2 15.5 - - - -
89A ALA 5.1 1.1 - - - -
94A TYR* 5.6 3.6 - + - -
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Residues in contact with LEU 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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59A ASP 5.6 0.2 - - - +
62A ARG* 3.0 25.4 + - + +
63A LYS* 3.7 4.9 - - - +
65A TRP* 1.3 92.1 - - + +
67A GLN* 1.3 56.1 + - - +
69A LEU* 3.1 6.9 + - + +
70A ASN* 2.8 29.9 + - - +
87A CYS* 4.2 15.0 - - - -
94A TYR* 3.5 49.1 - - + +
97A LEU* 3.9 31.8 - - + +
98A LEU* 3.7 19.7 - - + +
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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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63A LYS* 3.0 17.8 + - + +
64A PRO* 3.8 9.2 - - + +
66A LEU* 1.3 76.0 - - - +
68A ALA* 1.3 58.8 + - - +
70A ASN* 3.3 12.7 + - - +
71A ASP* 2.9 60.5 + - - +
97A LEU* 5.2 11.0 - - - +
100A GLU* 5.4 3.6 - - - +
45B ARG* 3.6 18.0 - - - +
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Residues in contact with ALA 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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42A LEU* 3.8 25.4 - - + +
64A PRO 3.0 17.6 + - - +
65A TRP 3.2 3.8 + - - +
67A GLN* 1.3 77.5 - - - +
69A LEU* 1.3 56.9 + - - +
71A ASP* 3.4 9.9 + - - +
72A ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 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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37A LEU* 4.2 3.4 - - + -
39A GLY* 3.3 29.6 - - - +
42A LEU* 3.7 16.2 - - + -
65A TRP* 2.9 50.5 + - + +
66A LEU* 3.6 10.1 - - - +
68A ALA* 1.3 73.2 - - - +
70A ASN* 1.3 61.4 + - - +
72A ALA* 3.2 2.2 + - - +
73A ALA* 2.9 31.2 + - - +
85A ILE* 3.9 24.2 - - + +
87A CYS* 3.7 26.0 - - + -
98A LEU* 3.6 13.0 - - + -
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Residues in contact with ASN 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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66A LEU 2.8 13.2 + - - +
67A GLN* 3.4 17.9 - - - +
69A LEU* 1.3 76.8 - - - +
71A ASP* 1.3 62.1 + - - +
73A ALA* 3.3 1.9 + - - +
74A PHE* 3.2 18.4 + - - +
97A LEU 2.8 28.9 + - - +
98A LEU* 3.2 17.8 + - - +
100A GLU* 2.8 26.4 + - - +
102A ASN* 3.4 14.8 + - - +
45B ARG* 3.1 30.1 + - - -
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Residues in contact with ASP 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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67A GLN* 2.9 38.3 + - - +
68A ALA* 3.6 8.8 - - - +
70A ASN* 1.3 76.0 - - - +
72A ALA* 1.3 57.5 + - - +
74A PHE* 3.3 8.2 + - - +
75A ALA* 2.9 27.4 + - - +
41B PHE 4.9 0.4 - - - -
43B HIS 5.2 7.8 - - - +
44B PRO* 5.6 0.8 - - + +
45B ARG* 3.0 52.5 + - - +
48B ILE* 5.2 0.9 - - - +
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Residues in contact with ALA 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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37A LEU* 3.5 31.2 - - + -
42A LEU* 3.9 7.4 - - + -
68A ALA 2.9 17.6 + - - +
69A LEU 3.2 3.6 + - - +
71A ASP* 1.3 75.8 - - - +
73A ALA* 1.3 58.9 + - - +
75A ALA* 3.3 1.8 + - - +
76A MET* 2.8 37.5 + - - +
85A ILE* 5.0 0.4 - - + -
41B PHE* 3.5 24.9 - - + +
42B LEU* 4.7 1.8 - - + -
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Residues in contact with ALA 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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10A ILE* 3.5 15.2 - - + +
69A LEU 2.9 16.0 + - - +
70A ASN* 3.5 6.1 - - - +
72A ALA* 1.3 77.9 - - - +
74A PHE* 1.3 61.8 + - - +
76A MET* 3.3 3.4 + - - +
77A GLN* 3.0 25.3 + - - +
85A ILE* 3.5 23.7 - - + +
98A LEU* 6.4 0.2 - - + -
102A ASN* 4.1 5.2 - - - +
105A LEU* 4.0 23.8 - - + -
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Residues in contact with PHE 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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3A THR* 4.1 31.4 - - - -
4A THR* 4.2 10.8 - - - -
70A ASN 3.2 8.2 + - - +
71A ASP* 3.6 7.9 - - - +
73A ALA* 1.3 80.0 - - - +
75A ALA* 1.3 63.6 + - - +
77A GLN* 3.0 47.9 + - - +
78A ARG* 3.2 10.8 - - - +
101A GLY 4.7 3.4 - - - -
102A ASN* 3.8 18.1 + - - +
45B ARG* 4.2 28.7 - - - +
48B ILE* 3.1 36.6 - - + -
49B GLU* 4.3 19.5 - - - -
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Residues in contact with ALA 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 ASP 2.9 13.9 + - - +
72A ALA 3.3 6.7 + - - +
74A PHE* 1.3 77.3 - - - +
76A MET* 1.3 62.8 - - - +
78A ARG* 2.9 18.0 + - - +
79A THR* 4.3 3.5 + - - +
40B ASP 4.5 3.6 - - - +
41B PHE* 3.8 31.6 - - + +
43B HIS 5.1 2.2 - - - +
48B ILE* 3.0 33.3 - - + +
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Residues in contact with MET 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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35A ALA* 3.7 28.5 - - + -
36A PHE 3.8 3.1 - - - +
37A LEU* 3.8 17.5 - - + +
72A ALA 2.8 26.3 + - - +
73A ALA* 3.7 4.0 - - - +
75A ALA* 1.3 73.1 - - - +
77A GLN* 1.3 63.4 + - - +
78A ARG 3.2 0.9 + - - -
79A THR 3.4 0.7 + - - -
80A ASN* 3.1 34.3 + - - +
83A SER* 3.5 21.5 - - - +
84A LEU 3.7 22.0 - - - +
85A ILE* 3.7 24.9 - - - -
41B PHE* 3.5 32.1 - - + -
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Residues in contact with GLN 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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3A THR 3.3 19.6 + - - -
4A THR* 3.4 4.2 - - - -
5A ASN* 2.7 28.6 + - - +
8A HIS* 2.5 40.0 + - + +
9A HIS 5.2 0.9 - - - +
10A ILE* 3.5 26.9 - - + -
73A ALA 3.0 13.6 + - - +
74A PHE* 3.0 41.2 + - + +
76A MET* 1.3 76.3 - - - +
78A ARG* 1.3 63.0 + - - +
79A THR 3.3 0.2 - - - -
80A ASN 4.0 7.0 - - - -
83A SER* 4.2 3.1 + - - -
102A ASN* 5.0 1.1 - - - +
104A ASN* 3.1 20.4 + - - +
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Residues in contact with ARG 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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3A THR 4.7 18.1 + - - +
5A ASN* 5.4 3.1 - - - +
8A HIS* 3.5 12.0 - - - -
74A PHE* 3.2 17.7 - - - +
75A ALA* 2.9 19.3 - - - +
76A MET 3.2 0.2 - - - -
77A GLN* 1.3 84.1 - - - +
79A THR* 1.3 74.5 + - + +
48B ILE* 3.3 46.0 + - + +
51B MET* 4.2 34.3 + - - +
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Residues in contact with THR 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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8A HIS* 4.5 4.9 - - - -
75A ALA 4.3 1.5 + - - +
76A MET 3.4 2.7 + - - -
78A ARG* 1.3 100.5 - - + +
80A ASN* 1.3 76.8 + - - +
41B PHE* 5.4 2.6 - - - -
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Residues in contact with ASN 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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8A HIS* 3.2 22.0 + - - +
9A HIS 4.6 0.7 + - - +
33A HIS 5.4 1.9 - - - +
34A ALA 5.1 0.7 - - - -
35A ALA* 3.5 27.2 + - - +
76A MET* 3.1 22.8 + - - +
77A GLN* 3.5 6.2 - - - +
78A ARG 3.7 0.4 - - - -
79A THR* 1.3 95.0 + - - +
81A LYS* 1.3 63.3 + - - +
82A VAL 3.9 7.9 - - - +
83A SER* 3.4 14.7 + - - +
41B PHE* 3.9 17.4 - - - -
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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
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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