Contacts of the helix formed by residues 64 - 86 (chain A) in PDB entry 1HUL
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 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 5.3 2.1 - - - +
21A HIS* 3.1 29.5 + - - -
63A GLY* 1.3 70.8 - - - -
65A VAL* 1.4 58.9 + - - +
66A GLU 3.2 1.1 + - - -
67A ARG* 3.4 18.6 + - - +
68A LEU 4.4 0.9 + - - -
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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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21A HIS* 3.7 17.0 - - + -
24A LEU* 3.7 29.8 - - + +
25A LEU* 4.2 9.2 - - + -
59A THR* 4.2 2.0 - - + -
60A VAL 3.5 16.6 - - - +
61A GLN* 3.5 24.0 - - - +
63A GLY* 3.2 6.0 + - - +
64A THR* 1.4 74.9 + - - +
66A GLU* 1.3 63.9 + - - +
67A ARG 3.2 0.2 - - - -
68A LEU* 3.2 28.1 + - + +
69A PHE* 3.3 28.8 + - + -
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN* 3.3 34.9 - - - +
62A GLY* 3.4 24.8 + - - +
63A GLY 3.3 15.1 + - - +
64A THR 3.2 1.0 - - - -
65A VAL* 1.3 76.8 - - - +
67A ARG* 1.3 62.7 + - - +
69A PHE* 3.9 2.9 - - + +
70A LYS* 3.1 27.3 + - + +
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Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 3.9 18.4 + - - +
17A LEU* 3.9 22.4 - - + -
63A GLY 4.8 0.2 + - - -
64A THR 3.4 12.3 + - - +
65A VAL 3.2 1.0 - - - -
66A GLU* 1.3 75.3 - - - +
68A LEU* 1.3 57.4 + - - +
70A LYS* 3.1 37.3 + - - +
71A ASN* 2.9 32.3 + - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR* 3.7 26.5 - - + +
17A LEU* 3.9 18.7 - - + +
18A LEU* 3.5 50.5 - - + +
21A HIS* 4.9 5.2 - - + -
25A LEU* 4.2 19.5 - - + -
64A THR 4.4 0.4 + - - -
65A VAL* 3.2 25.6 + - + +
67A ARG* 1.3 77.0 - - - +
69A PHE* 1.3 70.2 + - + +
71A ASN* 3.6 4.2 - - - +
72A LEU* 3.1 37.5 + - + +
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.8 24.7 - - + -
52A ILE* 4.3 21.0 - - + +
55A LEU* 4.3 13.0 - - + -
56A GLU* 4.0 50.4 - - + +
59A THR* 4.1 9.0 - - + -
61A GLN* 3.3 39.3 - - - +
65A VAL* 3.3 33.1 + - + +
66A GLU* 4.4 2.5 - - + +
67A ARG 3.3 0.4 - - - -
68A LEU* 1.3 89.1 - - + +
70A LYS* 1.3 61.9 + - - +
72A LEU* 4.0 7.9 - - + +
73A SER* 3.3 20.1 + - - -
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Residues in contact with LYS 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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10A LEU* 4.3 10.9 - - - +
13A GLU* 4.6 1.4 + - - -
66A GLU* 3.1 18.0 + - + +
67A ARG* 3.1 39.0 + - - +
69A PHE* 1.3 75.9 - - - +
71A ASN* 1.3 98.1 + - - +
73A SER* 3.3 8.7 - - - -
74A LEU* 3.2 43.1 + - + +
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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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10A LEU* 3.9 12.7 + - + +
13A GLU* 3.0 26.5 + - - +
14A THR* 2.9 37.9 + - - +
17A LEU* 3.7 8.9 - - - +
67A ARG* 2.9 16.4 + - - +
68A LEU 3.6 4.9 - - - +
70A LYS* 1.3 110.9 + - - +
72A LEU* 1.3 53.3 + - - +
74A LEU* 2.7 28.6 + - - +
75A ILE* 2.8 20.9 + - + +
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Residues in contact with LEU 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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14A THR* 3.7 23.6 - - + -
18A LEU* 5.0 1.3 - - + -
49A PHE* 3.6 13.8 - - + -
52A ILE* 3.7 48.0 - - + -
68A LEU* 3.1 34.3 + - + +
69A PHE* 4.0 13.2 - - + +
70A LYS 3.4 0.2 - - - -
71A ASN* 1.3 74.2 - - - +
73A SER* 1.3 62.9 + - - +
75A ILE* 3.5 8.2 + - + +
76A LYS* 3.2 23.4 + - - +
100B LEU* 4.6 12.1 - - + -
104B LEU* 4.7 15.7 - - + -
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Residues in contact with SER 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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56A GLU* 6.2 0.2 - - - -
69A PHE 3.3 15.9 + - - -
70A LYS* 3.3 13.7 - - - -
71A ASN 3.1 0.8 - - - -
72A LEU* 1.3 75.8 - - - +
74A LEU* 1.3 66.5 + - - +
76A LYS* 3.5 7.8 + - - +
77A LYS* 3.2 21.8 + - - +
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Residues in contact with LEU 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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10A LEU* 4.2 20.4 - - + -
70A LYS* 3.2 43.1 + - + +
71A ASN* 2.7 17.2 + - - +
73A SER* 1.3 78.8 - - - +
75A ILE* 1.3 59.5 + - - +
77A LYS* 3.0 19.4 + - + +
78A TYR* 3.0 20.1 + - - +
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR* 5.1 7.0 - - + -
10A LEU* 4.5 12.8 - - + +
11A VAL* 3.8 29.8 - - + +
14A THR* 4.1 18.2 - - - +
49A PHE* 4.4 14.8 - - + -
71A ASN 2.8 16.4 + - - +
72A LEU* 4.0 11.2 - - + +
73A SER 3.4 0.4 - - - -
74A LEU* 1.3 76.5 - - + +
76A LYS* 1.3 56.6 + - - +
78A TYR* 3.3 9.7 + - + +
79A ILE* 3.1 29.1 + - + +
103B PHE* 5.7 0.9 - - + -
104B LEU* 3.9 20.0 - - + -
107B MET* 4.1 26.2 - - + -
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU* 4.2 13.9 - - - +
49A PHE* 3.5 49.6 - - + -
72A LEU 3.2 10.5 + - - +
73A SER* 3.6 8.3 - - - +
74A LEU 3.1 0.4 - - - -
75A ILE* 1.3 76.0 - - - +
77A LYS* 1.3 64.6 + - - +
78A TYR 3.1 0.3 + - - -
79A ILE* 3.3 3.4 + - + +
80A ASP* 2.9 54.4 + - - +
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Residues in contact with LYS 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 SER 3.2 11.9 + - - +
74A LEU* 3.0 21.1 + - + +
76A LYS* 1.3 76.3 - - - +
78A TYR* 1.3 61.3 + - - +
80A ASP* 3.7 11.7 + - + +
81A GLY* 3.2 15.6 + - - -
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Residues in contact with TYR 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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7A THR* 3.8 36.6 - - + +
74A LEU 3.0 11.8 + - - +
75A ILE* 3.3 12.1 - - - +
76A LYS 3.1 0.2 - - - -
77A LYS* 1.3 73.4 - - - +
79A ILE* 1.4 61.4 + - + +
81A GLY* 2.8 21.7 + - - -
82A GLN* 3.1 41.6 + - + +
107B MET* 4.1 16.6 - - + -
111B TRP* 4.0 25.8 - + - -
112B ILE* 4.2 22.9 - - + +
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Residues in contact with ILE 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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45A THR* 4.4 11.7 - - + +
46A GLU* 4.2 11.7 - - - +
49A PHE* 3.9 25.1 - - + -
75A ILE* 3.1 21.4 + - + +
76A LYS* 3.3 6.0 + - + +
78A TYR* 1.4 76.2 - - + +
80A ASP* 1.3 63.3 + - - +
81A GLY 2.9 1.4 + - - -
82A GLN* 3.0 7.5 + - - +
83A LYS* 2.9 44.7 + - + +
43B LEU* 4.9 7.9 - - + -
103B PHE* 4.0 21.3 - - + -
107B MET* 4.5 3.8 - - + -
111B TRP* 4.3 20.9 - - + -
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Residues in contact with ASP 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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46A GLU* 2.9 25.6 - - - +
76A LYS* 2.9 52.9 + - - +
77A LYS* 3.9 10.2 - - + +
79A ILE* 1.3 69.6 - - - +
81A GLY* 1.3 59.6 + - - +
83A LYS* 4.0 12.2 - - - +
84A LYS* 3.1 34.0 + - - +
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Residues in contact with GLY 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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77A LYS 3.2 9.4 + - - -
78A TYR 2.8 11.8 + - - -
80A ASP* 1.3 77.0 - - - +
82A GLN* 1.3 62.4 + - - -
84A LYS* 3.3 11.3 + - - +
85A LYS* 3.1 28.0 + - - +
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Residues in contact with GLN 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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78A TYR* 3.1 50.5 + - + +
79A ILE* 3.0 8.5 + - - +
81A GLY* 1.3 74.3 - - - +
83A LYS* 1.3 63.6 + - - +
85A LYS* 3.1 21.6 + - - +
86A CYS 3.4 0.2 + - - -
38B HIS* 2.7 42.1 + - - +
40B ASN* 3.0 30.2 - - - +
43B LEU* 3.9 18.2 - - + -
111B TRP* 4.8 1.6 - - + -
112B ILE* 5.8 1.6 - - - +
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Residues in contact with LYS 83 (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 THR* 3.8 10.7 + - - -
46A GLU* 3.1 38.2 + - - +
79A ILE* 2.9 20.8 + - + +
80A ASP* 4.2 12.1 - - - +
81A GLY 3.2 0.2 - - - -
82A GLN* 1.3 77.1 - - - +
84A LYS* 1.3 57.4 + - - +
86A CYS* 3.0 29.9 + - - +
87A GLY 4.7 0.2 + - - -
43B LEU* 4.4 32.4 - - + +
47B GLU* 5.0 4.5 - - - +
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Residues in contact with LYS 84 (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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80A ASP* 3.1 27.2 + - - +
81A GLY* 3.3 15.3 + - - +
83A LYS* 1.3 75.3 - - - +
85A LYS* 1.3 60.6 + - + +
86A CYS 3.1 2.5 + - - -
87A GLY 3.6 9.6 + - - +
88A GLU* 3.8 19.4 + - - +
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Residues in contact with LYS 85 (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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81A GLY 3.1 25.3 + - - +
82A GLN* 3.1 22.3 + - - +
84A LYS* 1.3 78.7 - - + +
86A CYS* 1.3 58.9 + - - +
87A GLY 3.3 1.8 + - - -
88A GLU* 3.6 36.0 + - - +
36B PRO* 3.6 0.3 - - - +
37B VAL* 3.2 40.4 + - + +
38B HIS* 3.9 11.7 - - + -
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Residues in contact with CYS 86 (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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82A GLN 3.4 1.5 + - - -
83A LYS* 3.0 25.9 + - - +
85A LYS* 1.3 76.3 - - - +
87A GLY* 1.3 56.6 + - - +
34B PRO 4.6 1.7 - - - +
35B VAL 4.1 1.0 - - - -
36B PRO* 3.6 25.1 - - - +
38B HIS* 3.7 8.3 - - - -
43B LEU 4.0 4.7 - - - -
44B CYS* 2.0 55.4 - - + -
47B GLU* 3.6 30.1 - - - +
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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