Contacts of the helix formed by residues 67 - 91 (chain A) in PDB entry 2DA6
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A SER* 3.4 36.0 + - - +
4A GLY* 5.6 0.7 - - - -
40A VAL* 3.4 11.9 - - - -
65A LEU* 3.9 21.8 - - + +
66A VAL* 1.3 84.9 - - - +
68A GLU* 1.3 70.9 + - - +
69A VAL* 3.7 12.1 + - - +
70A ARG* 2.6 35.0 + - - +
71A VAL* 3.2 8.0 + - - +
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Residues in contact with GLU 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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3A SER* 4.1 11.7 + - - +
33A LYS* 3.3 37.5 - - + +
36A ARG* 3.7 34.1 + - + +
37A GLU* 5.3 10.3 - - + -
40A VAL* 3.2 19.0 - - + +
67A THR* 1.3 72.5 - - - +
69A VAL* 1.3 60.2 + - + +
71A VAL* 3.4 1.9 + - - +
72A TYR* 2.9 28.8 + - + +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER 4.9 5.6 + - - +
4A GLY* 5.5 7.0 - - - -
67A THR* 2.6 13.8 + - - +
68A GLU* 1.3 75.7 - - + +
70A ARG* 1.3 76.4 + - - +
72A TYR* 2.6 30.7 + - + +
73A ASN* 2.8 36.9 + - - +
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Residues in contact with ARG 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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8A ARG* 5.6 8.7 - - - +
9A ASN* 4.5 23.7 + - - +
11A PHE* 3.4 50.3 - - - +
13A TRP* 3.3 27.5 + - + -
65A LEU 3.9 8.9 + - - +
66A VAL* 3.9 1.3 - - + -
67A THR* 2.6 38.2 + - - +
69A VAL* 1.3 87.1 - - - +
71A VAL* 1.3 62.0 + - - +
73A ASN* 3.3 26.4 + - - +
74A TRP 3.1 18.5 + - - -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TRP* 4.2 8.3 - - + -
21A LEU* 4.3 4.7 - - + -
36A ARG* 4.1 18.2 - - + +
39A LEU* 3.3 40.8 - - + -
40A VAL* 3.6 30.7 - - + -
66A VAL* 3.9 14.4 - - + -
67A THR 3.7 3.1 - - - +
68A GLU 3.8 4.0 - - - +
69A VAL 3.1 0.4 - - - -
70A ARG* 1.3 72.2 - - - +
72A TYR* 1.3 65.1 + - - +
74A TRP* 3.8 1.3 - - - +
75A PHE* 3.0 44.3 + - + -
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Residues in contact with TYR 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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36A ARG* 3.8 36.3 - - - +
68A GLU* 2.9 15.2 + - + +
69A VAL* 2.6 18.9 + - + +
71A VAL* 1.3 73.0 - - - +
73A ASN* 1.3 78.6 + - - -
75A PHE* 4.1 2.9 - - - +
76A ALA* 3.1 34.2 + - + +
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Residues in contact with ASN 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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8A ARG* 5.7 4.7 + - - -
69A VAL* 2.8 44.7 + - - +
70A ARG* 3.6 19.7 - - - +
72A TYR* 1.3 90.6 - - - +
74A TRP* 1.3 65.0 + - - +
76A ALA* 3.0 6.5 + - - +
77A ASN* 2.9 24.8 + - - +
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Residues in contact with TRP 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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13A TRP* 3.3 37.3 - + + +
18A GLN* 5.0 4.6 + - - +
21A LEU* 3.5 35.5 - - + +
22A TYR* 3.6 33.9 + + - -
25A TYR* 3.6 29.8 - + + -
70A ARG 3.1 16.5 + - - +
71A VAL* 3.8 3.4 - - - +
73A ASN* 1.3 76.0 - - - +
75A PHE* 1.3 88.0 - + - +
77A ASN* 3.2 6.7 + - + +
78A ARG* 2.9 86.0 + - + +
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Residues in contact with PHE 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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21A LEU* 3.8 6.3 - - + -
24A ALA* 4.2 1.6 - - + -
25A TYR* 3.1 46.2 - + + -
28A GLN 3.5 11.4 - - - -
29A LYS 3.4 5.6 - - - +
31A PRO* 3.1 39.0 - - + -
36A ARG* 5.6 2.7 - - - +
39A LEU* 3.3 35.7 - - + -
71A VAL* 3.0 34.8 + - + +
72A TYR* 4.1 4.3 - - - +
74A TRP* 1.3 98.0 - + - +
76A ALA* 1.3 61.9 + - - +
78A ARG* 3.4 1.7 + - - +
79A ARG* 3.2 29.4 + - - +
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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 TYR* 3.1 32.4 + - + +
73A ASN* 3.0 9.1 + - - +
75A PHE* 1.3 77.9 - - - +
77A ASN* 1.3 56.6 + - - +
79A ARG* 3.4 6.0 + - - +
80A LYS* 3.0 39.8 + - + +
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Residues in contact with ASN 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 ASN 2.9 14.7 + - - +
74A TRP* 3.7 6.3 - - - +
76A ALA* 1.3 72.2 - - - +
78A ARG* 1.3 62.8 + - + +
79A ARG 3.1 2.0 - - - -
80A LYS* 4.2 16.6 - - - +
81A GLU* 2.9 45.7 + - - +
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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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18A GLN* 4.7 4.2 + - - -
22A TYR* 3.0 37.5 + - - -
25A TYR* 3.6 25.5 - - + -
74A TRP* 2.9 75.7 + - + +
75A PHE 3.7 0.7 - - - +
76A ALA 3.3 0.2 - - - -
77A ASN* 1.3 77.9 + - + +
79A ARG* 1.3 56.6 + - - +
81A GLU* 3.5 37.0 + - - +
82A GLU* 3.4 22.3 - - - +
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Residues in contact with ARG 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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25A TYR* 2.8 24.0 - - + +
29A LYS* 4.0 22.9 - - + +
30A ASN* 4.7 20.2 - - - +
75A PHE 3.2 17.1 + - - +
76A ALA* 3.4 6.3 + - - +
77A ASN 3.1 0.4 - - - -
78A ARG* 1.3 77.9 - - - +
80A LYS* 1.3 61.9 + - + +
81A GLU 3.4 0.4 - - - -
82A GLU* 3.2 29.1 + - - +
83A ALA* 3.4 13.2 - - - +
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Residues in contact with LYS 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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76A ALA* 3.0 28.8 + - + +
77A ASN* 3.2 18.4 + - - +
79A ARG* 1.3 78.6 - - + +
81A GLU* 1.3 59.2 + - - +
83A ALA* 3.6 4.1 + - - +
84A PHE* 3.0 28.2 + - - +
87A LYS* 6.1 0.8 - - - +
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Residues in contact with GLU 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 ASN* 2.9 28.7 + - - +
78A ARG* 3.5 42.6 + - - +
80A LYS* 1.3 74.4 - - - +
82A GLU* 1.3 74.0 + - + +
83A ALA 3.1 1.8 - - - -
84A PHE* 2.8 35.3 + - - +
85A ARG* 3.7 6.1 + - - +
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Residues in contact with GLU 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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25A TYR* 3.1 32.5 + - - -
29A LYS* 5.0 5.9 - - - +
78A ARG 3.4 9.8 - - - +
79A ARG* 3.2 26.7 + - - +
81A GLU* 1.3 84.6 - - + +
83A ALA* 1.3 65.2 + - + +
84A PHE 3.6 0.2 + - - -
85A ARG* 4.2 10.7 + - - +
86A GLN* 4.3 11.1 + - - +
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Residues in contact with ALA 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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79A ARG 3.4 17.6 + - - +
80A LYS* 3.8 4.9 - - - +
81A GLU 3.1 0.4 - - - -
82A GLU* 1.3 81.4 - - + +
84A PHE* 1.3 53.4 + - - +
85A ARG 3.5 0.2 - - - -
86A GLN* 3.0 13.9 + - + +
87A LYS* 2.6 37.0 + - + +
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Residues in contact with PHE 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 LYS 3.0 14.9 + - - +
81A GLU* 2.8 21.1 + - - +
83A ALA* 1.3 72.1 - - - +
85A ARG* 1.3 55.7 + - + +
86A GLN 2.5 6.8 + - - -
87A LYS* 2.5 53.8 + - - +
88A LEU* 2.8 43.2 + - + +
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Residues in contact with ARG 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 GLU 3.7 4.8 + - - +
82A GLU* 4.5 9.4 - - - +
83A ALA 3.5 0.4 - - - -
84A PHE* 1.3 79.9 - - + +
86A GLN* 1.3 59.7 + - + +
88A LEU* 2.8 34.7 - - + +
89A ALA* 4.0 4.2 - - - +
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Residues in contact with GLN 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 GLU 4.3 12.4 + - - +
83A ALA* 3.0 12.5 + - + +
84A PHE 2.5 5.4 + - - -
85A ARG* 1.3 78.7 - - + +
87A LYS* 1.3 63.2 + - - +
88A LEU 3.3 1.1 - - - -
89A ALA* 3.2 18.1 + - - +
90A MET* 3.3 28.9 - - + +
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Residues in contact with LYS 87 (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 LYS* 6.1 0.8 - - - +
83A ALA* 2.6 16.9 + - + +
84A PHE* 2.5 45.6 + - - +
86A GLN* 1.3 67.4 - - - +
88A LEU* 1.3 63.1 + - - +
89A ALA 3.0 6.1 + - - -
90A MET* 3.3 25.6 + - + +
91A ASP* 4.0 3.5 + - - +
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Residues in contact with LEU 88 (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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84A PHE* 2.8 45.8 + - + +
85A ARG* 2.8 33.9 - - + +
87A LYS* 1.3 81.4 - - + +
89A ALA* 1.3 64.9 + - + +
90A MET 3.5 0.4 - - - -
91A ASP* 4.0 15.2 - - - +
94A SER* 5.3 1.6 - - - -
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Residues in contact with ALA 89 (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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85A ARG 4.0 5.4 - - - +
86A GLN* 3.4 12.3 - - - +
87A LYS 3.0 0.4 - - - -
88A LEU* 1.3 91.0 - - + +
90A MET* 1.3 56.0 + - - +
91A ASP 3.0 2.7 - - - -
94A SER* 2.6 28.0 + - - +
95A SER* 5.5 2.9 - - - +
96A ASN* 2.4 33.0 - - - +
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Residues in contact with MET 90 (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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86A GLN* 3.3 31.4 - - + +
87A LYS* 3.3 16.5 + - + +
89A ALA* 1.3 71.9 - - - +
91A ASP* 1.3 68.3 + - - +
96A ASN* 3.2 19.5 - - - +
97A SER 3.4 20.4 - - - +
98A GLY* 3.7 5.5 - - - -
99A PRO* 5.0 1.0 - - - +
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Residues in contact with ASP 91 (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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87A LYS 4.0 3.9 + - - +
88A LEU* 4.0 16.8 - - - +
89A ALA 3.0 9.8 - - - +
90A MET* 1.3 85.6 - - - +
92A ALA* 1.3 80.6 + - - +
94A SER* 3.4 4.7 - - - -
96A ASN* 3.5 5.7 - - - +
98A GLY* 4.7 2.0 - - - -
99A PRO* 3.0 17.1 - - - +
101A SER* 2.7 32.2 + - - +
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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