Contacts of the helix formed by residues 55 - 77 (chain A) in PDB entry 1JK8
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 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A PHE* 1.3 85.2 - - - +
56A PRO* 1.3 73.3 - - - +
57A GLN* 2.8 29.5 + - - +
58A PHE* 3.0 51.1 + - + +
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Residues in contact with PRO 56 (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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34A VAL* 4.1 15.1 - - + +
39A LYS* 3.5 41.7 - - + +
40A GLU* 4.0 2.0 - - - +
41A THR* 3.2 27.4 - - - +
54A PHE 3.3 6.0 - - - +
55A ASP* 1.3 90.0 - - - +
57A GLN* 1.3 64.2 + - - +
59A ALA* 2.9 17.0 + - - +
60A LEU* 3.2 12.5 + - - +
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Residues in contact with GLN 57 (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 LYS* 2.5 42.0 + - + +
55A ASP* 2.8 28.2 + - - +
56A PRO* 1.3 75.3 - - - +
58A PHE* 1.3 63.8 + - + +
60A LEU* 3.2 18.5 + - - +
61A THR* 3.1 40.6 + - - +
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Residues in contact with PHE 58 (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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54A PHE* 4.1 8.5 - + + -
55A ASP* 3.0 48.4 + - + +
57A GLN* 1.3 78.4 - - + +
59A ALA* 1.3 66.8 - - - +
61A THR* 3.4 7.6 + - - -
62A ASN* 3.2 26.5 + - - +
2C VAL* 6.4 1.8 - - + -
3C GLU 5.1 8.7 - - - -
5C LEU* 3.8 37.2 - - + +
7C LEU* 6.0 3.0 - - + +
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Residues in contact with ALA 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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22A TYR* 3.5 44.2 - - + -
34A VAL* 3.6 24.2 - - + -
36A LEU* 4.7 1.3 - - + -
54A PHE* 4.3 1.9 - - + -
55A ASP 4.0 0.8 + - - -
56A PRO 2.9 11.6 + - - +
58A PHE* 1.3 79.1 - - - +
60A LEU* 1.3 64.1 + - - +
62A ASN* 3.2 3.5 + - - +
63A ILE* 3.0 29.0 + - - +
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Residues in contact with LEU 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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34A VAL* 5.2 1.6 - - + -
35A ASP 5.3 0.2 - - - +
36A LEU* 3.5 45.8 - - + +
39A LYS* 3.3 42.8 - - + -
56A PRO 3.2 8.9 + - - +
57A GLN* 3.2 18.9 + - - +
59A ALA* 1.3 79.1 - - - +
61A THR* 1.3 61.6 + - - +
63A ILE* 3.6 6.9 + - + +
64A ALA* 3.1 23.0 + - - +
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Residues in contact with THR 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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57A GLN* 3.1 30.2 + - - +
58A PHE* 3.8 8.6 - - - -
59A ALA 3.3 0.2 - - - -
60A LEU* 1.3 74.0 - - - +
62A ASN* 1.3 68.4 + - - +
64A ALA* 3.3 15.0 + - + +
65A VAL* 3.3 19.4 + - + +
7C LEU* 6.3 2.2 - - + -
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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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11A ASN* 2.9 28.8 + - - +
22A TYR* 4.2 2.1 - - + -
58A PHE 3.2 13.2 + - - +
59A ALA 3.6 7.6 - - - +
61A THR* 1.3 76.8 - - - +
63A ILE* 1.3 62.4 + - - +
65A VAL* 2.8 23.5 + - - +
66A LEU* 3.0 12.2 + - - +
11B PHE* 4.4 1.4 - - - -
5C LEU* 3.9 9.6 - - - +
6C TYR 3.1 24.2 + - - -
7C LEU* 3.8 16.3 - - - +
8C VAL* 3.6 32.5 + - + +
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 4.1 12.6 - - + -
12A LEU 3.5 30.1 - - - +
13A TYR* 4.1 23.4 - - + -
20A GLY* 5.2 0.2 - - - -
21A GLN 3.6 16.4 - - - +
22A TYR* 4.5 6.7 - - + -
36A LEU* 4.2 26.5 - - + -
59A ALA 3.0 23.1 + - - +
60A LEU* 3.8 8.3 - - + +
62A ASN* 1.3 74.9 - - - +
64A ALA* 1.3 62.7 + - - +
66A LEU* 3.2 8.1 + - + +
67A LYS* 3.2 20.4 + - - +
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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 LEU 3.1 15.2 + - - +
61A THR* 3.4 14.1 - - + +
62A ASN 3.0 0.8 - - - -
63A ILE* 1.3 77.9 - - - +
65A VAL* 1.3 61.9 + - + +
67A LYS* 3.4 11.6 + - + +
68A HIS* 3.2 19.2 + - - +
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Residues in contact with VAL 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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61A THR* 3.3 20.6 + - + +
62A ASN* 2.8 9.4 + - - +
64A ALA* 1.3 75.1 - - + +
66A LEU* 1.3 59.9 + - - +
68A HIS* 3.0 11.3 + - + +
69A ASN* 2.8 29.8 + - - +
8C VAL* 3.8 24.9 - - + +
9C CYS 4.1 1.6 - - - +
10C GLY* 3.5 31.6 - - - -
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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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11A ASN* 3.5 42.8 - - + +
12A LEU* 3.9 13.0 - - - +
13A TYR* 4.0 11.2 - - + +
62A ASN 3.0 12.6 + - - +
63A ILE* 3.2 12.5 + - + +
65A VAL* 1.3 78.1 - - - +
67A LYS* 1.3 52.2 + - - +
69A ASN* 3.2 5.0 + - - +
70A LEU* 2.7 36.3 + - - +
9B TYR* 3.7 26.2 - - + +
11B PHE* 3.7 11.9 - - + +
8C VAL* 3.5 38.1 - - + -
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Residues in contact with LYS 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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13A TYR* 3.0 51.5 + - + +
18A PRO* 5.0 5.7 - - - +
63A ILE 3.2 10.8 + - - +
64A ALA* 3.5 13.7 - - + +
65A VAL 3.2 0.2 - - - -
66A LEU* 1.3 75.8 - - - +
68A HIS* 1.3 63.1 + - - +
70A LEU* 3.4 1.6 + - - +
71A ASN* 3.2 42.3 + - - +
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Residues in contact with HIS 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 3.2 10.1 + - - +
65A VAL* 3.0 15.0 + - + +
67A LYS* 1.3 82.5 - - - +
69A ASN* 1.3 70.8 + - - -
71A ASN* 3.9 4.3 + - - +
72A ILE* 3.2 44.2 + - + +
10C GLY* 4.6 5.2 - - - -
11C GLU 2.9 29.6 + - - -
13C GLY* 4.0 12.6 + - - -
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Residues in contact with ASN 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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65A VAL 2.8 19.4 + - - +
66A LEU 3.6 2.9 - - - +
68A HIS* 1.3 80.5 - - - +
70A LEU* 1.3 65.1 + - - +
72A ILE* 3.1 4.7 + - - +
73A VAL* 2.9 25.3 + - - +
9B TYR* 3.2 38.2 + - + +
30B TYR* 4.4 1.0 - - - -
8C VAL* 4.2 8.7 - - - +
9C CYS 3.0 24.9 + - - -
10C GLY* 3.4 5.0 - - - -
11C GLU* 2.8 40.0 + - + +
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Residues in contact with LEU 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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13A TYR* 3.7 30.3 - - + +
15A SER* 4.1 10.8 - - - +
66A LEU 2.7 20.8 + - - +
67A LYS 3.8 4.7 - - - +
69A ASN* 1.3 72.5 - - - +
71A ASN* 1.3 60.7 + - - +
73A VAL* 3.1 2.2 + - - +
74A ILE* 2.8 45.8 + - + +
7B PHE* 3.5 26.0 - - + +
8B VAL 3.9 9.9 - - - -
9B TYR* 3.7 26.6 - - + -
32B TYR* 3.8 24.2 - - + -
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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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13A TYR* 6.0 1.6 - - - -
15A SER* 6.4 0.2 - - - -
67A LYS* 3.2 30.1 + - - +
68A HIS* 4.2 6.1 - - - +
70A LEU* 1.3 82.6 - - - +
72A ILE* 1.3 63.0 + - + +
74A ILE* 3.5 19.7 + - - +
75A LYS* 3.2 34.7 + - - +
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Residues in contact with ILE 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 HIS* 3.2 37.2 - - + +
69A ASN* 3.1 9.2 + - - +
71A ASN* 1.3 79.5 - - + +
73A VAL* 1.3 57.1 + - - +
75A LYS* 3.5 14.5 + - + +
76A ARG* 3.1 44.3 + - + +
11C GLU* 4.0 11.7 - - + +
12C ARG 3.8 12.1 - - - +
13C GLY* 3.6 30.7 - - - +
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Residues in contact with VAL 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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69A ASN 2.9 18.4 + - - +
70A LEU* 3.9 3.8 - - - +
72A ILE* 1.3 73.7 - - - +
74A ILE* 1.3 66.0 + - - +
75A LYS 3.2 1.1 - - - -
76A ARG* 3.7 15.5 - - - +
77A SER* 3.0 21.1 + - - -
9B TYR* 4.3 2.7 - - + -
32B TYR* 3.2 42.8 - - + -
37B TYR* 3.6 14.4 - - + +
53B LEU* 4.2 16.8 - - + -
11C GLU* 3.4 26.5 - - - +
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Residues in contact with ILE 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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15A SER* 5.1 3.1 - - - -
70A LEU* 2.8 37.6 + - + +
71A ASN* 3.7 20.6 - - - +
72A ILE 3.3 0.2 - - - -
73A VAL* 1.3 77.9 - - - +
75A LYS* 1.3 63.0 + - + +
77A SER* 3.4 1.9 + - - -
79A SER* 2.6 55.5 + - - +
7B PHE* 3.8 37.0 - - + -
32B TYR* 3.5 23.3 - - + +
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Residues in contact with LYS 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* 3.2 23.5 + - - +
72A ILE* 3.6 13.1 - - + +
74A ILE* 1.3 77.0 - - + +
76A ARG* 1.3 64.5 + - - +
78A ASN* 3.1 17.8 + - - +
79A SER* 4.8 2.2 - - - +
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Residues in contact with ARG 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 ILE* 3.1 27.4 + - + +
73A VAL* 3.4 17.7 + - - +
75A LYS* 1.3 80.6 - - - +
77A SER* 1.3 57.2 + - - +
78A ASN 3.3 2.1 + - - -
401A NAG 4.3 15.9 + - - +
37B TYR* 3.9 5.3 - - - -
52B PRO 5.5 0.9 - - - -
53B LEU* 2.7 52.3 + - + +
54B GLY* 4.6 1.0 - - - -
56B PRO* 3.7 34.4 - - + +
57B ALA* 4.7 0.8 - - - +
11C GLU* 2.7 44.5 + - - -
12C ARG 5.7 0.8 + - - -
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Residues in contact with SER 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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73A VAL 3.0 13.8 + - - -
74A ILE 3.4 1.9 + - - -
75A LYS 3.2 0.4 - - - -
76A ARG* 1.3 75.6 - - - +
78A ASN* 1.3 68.7 + - - +
80A THR* 2.7 48.3 + - - -
401A NAG 3.8 14.4 - - - +
32B TYR* 3.1 29.1 + - - -
53B LEU* 4.3 14.8 - - - -
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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
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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) + - + + + + + -
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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