Contacts of the helix formed by residues 5 - 30 (chain A) in PDB entry 1QUU
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 GLU 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GLY 3.4 28.9 - - - +
2A SER* 2.9 8.4 + - - +
4A ASN* 1.3 75.9 - - - +
6A ILE* 1.3 62.9 - - + +
8A ARG* 2.3 48.9 + - - +
9A LEU* 3.0 43.5 + - + +
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Residues in contact with ILE 6 (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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2A SER* 3.4 18.8 - - - +
3A SER* 2.6 31.3 + - - +
5A GLU* 1.3 77.1 - - + +
7A ARG* 1.3 61.4 + - + +
9A LEU* 2.8 14.2 + - + +
10A GLU* 2.8 50.6 + - + +
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Residues in contact with ARG 7 (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* 2.6 37.0 + - - +
4A ASN* 2.9 40.1 + - - +
6A ILE* 1.3 74.1 - - + +
8A ARG* 1.3 56.8 + - - +
10A GLU* 3.3 18.2 + - - +
11A ARG* 3.0 27.0 + - - +
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Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASN 3.6 14.0 + - - +
5A GLU* 2.3 52.0 + - - +
6A ILE 3.1 0.4 - - - -
7A ARG* 1.3 81.3 - - - +
9A LEU* 1.3 76.5 + - - +
11A ARG* 3.5 24.3 + - + +
12A LEU* 3.7 22.1 + - - +
84A LEU* 4.9 13.8 + - - +
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Residues in contact with LEU 9 (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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5A GLU* 3.0 39.7 + - + +
6A ILE* 2.8 13.0 + - + +
8A ARG* 1.3 88.5 - - - +
10A GLU* 1.3 64.4 + - + +
11A ARG 3.3 0.4 - - - -
12A LEU* 3.4 26.1 - - + +
13A GLU* 3.4 20.0 + - - +
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Residues in contact with GLU 10 (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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6A ILE* 2.8 33.0 + - + +
7A ARG* 3.7 22.0 - - - +
9A LEU* 1.3 75.1 - - + +
11A ARG* 1.3 54.6 + - - +
13A GLU* 2.9 13.8 + - + +
14A HIS* 2.7 54.6 + - + +
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Residues in contact with ARG 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG 3.0 13.3 + - - +
8A ARG* 3.5 20.2 + - - +
10A GLU* 1.3 75.3 - - - +
12A LEU* 1.3 55.1 + - - +
14A HIS* 2.7 18.9 + - + +
15A LEU* 2.7 50.8 + - + +
80A GLU* 2.9 36.4 + - - -
84A LEU* 3.6 18.2 - - - +
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 3.8 18.8 - - - +
9A LEU* 3.4 28.0 + - + +
11A ARG* 1.3 86.6 - - - +
13A GLU* 1.3 64.2 + - - +
15A LEU* 3.1 11.2 + - + +
16A ALA* 3.0 20.6 + - - +
80A GLU* 5.2 0.7 - - + -
81A LEU* 3.6 17.2 - - + +
84A LEU* 3.4 57.9 - - + +
85A ASP 5.0 0.2 - - - -
86A TYR* 4.0 27.1 - - + -
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Residues in contact with GLU 13 (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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9A LEU 3.4 9.3 + - - +
10A GLU* 2.9 16.8 + - + +
12A LEU* 1.3 78.6 - - - +
14A HIS* 1.3 67.7 - - + +
16A ALA* 3.4 1.2 + - - +
17A GLU* 2.9 33.8 + - - +
20A ARG* 4.3 6.9 + - - -
86A TYR* 3.0 22.3 + - + -
87A HIS* 2.9 30.0 + - + -
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Residues in contact with HIS 14 (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 GLU* 2.7 35.2 + - + +
11A ARG* 2.7 21.9 + - + +
13A GLU* 1.3 73.9 - - + +
15A LEU* 1.3 48.9 + - - +
17A GLU* 3.0 26.7 + - - +
18A LYS* 2.7 33.7 + - - +
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Residues in contact with LEU 15 (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 ARG* 2.7 38.8 + - + +
12A LEU* 3.1 15.7 + - + +
14A HIS* 1.3 72.7 - - - +
16A ALA* 1.3 51.5 + - - +
18A LYS* 2.8 29.1 + - + +
19A PHE* 2.6 31.4 + - - +
77A ILE* 3.8 24.1 - - + +
80A GLU* 3.1 37.5 - - + +
81A LEU* 4.4 7.4 - - + -
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Residues in contact with ALA 16 (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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12A LEU 3.0 6.9 + - - +
13A GLU 3.8 4.7 - - - +
15A LEU* 1.3 71.6 - - - +
17A GLU* 1.3 56.1 + - - +
19A PHE* 2.4 30.7 + - - +
20A ARG* 2.7 32.6 + - - +
81A LEU* 3.7 16.5 - - + +
86A TYR* 3.5 36.1 - - + +
92A VAL* 4.6 2.9 - - + -
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Residues in contact with GLU 17 (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 GLU* 2.9 28.5 + - - +
14A HIS* 3.1 37.6 - - - +
16A ALA* 1.3 75.8 - - - +
18A LYS* 1.3 61.9 + - - +
20A ARG* 3.4 20.8 + - - +
21A GLN* 3.3 20.1 + - - +
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Residues in contact with LYS 18 (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 HIS 2.7 12.5 + - - +
15A LEU* 2.9 27.2 - - + +
17A GLU* 1.3 76.7 - - - +
19A PHE* 1.3 61.8 + - - +
21A GLN* 3.7 9.6 + - - +
22A LYS* 3.5 35.6 + - + +
73A GLN* 5.7 2.1 + - - -
77A ILE* 4.0 21.4 - - + +
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Residues in contact with PHE 19 (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 LEU 2.6 10.4 + - - +
16A ALA* 2.4 29.0 + - - +
18A LYS* 1.3 75.1 - - - +
20A ARG* 1.3 64.1 + - + -
22A LYS* 3.5 2.6 + - - +
23A ALA* 2.9 34.8 + - + +
74A ILE* 3.5 44.4 - - + -
77A ILE* 4.0 16.8 - - + -
78A ALA* 3.9 20.2 - - + -
81A LEU* 4.7 1.8 - - + -
92A VAL* 3.4 48.2 - - + -
95A ARG* 4.1 21.5 - - + -
96A CYS* 3.8 12.3 - - + -
99A ILE* 5.6 0.2 - - + -
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Residues in contact with ARG 20 (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 GLU* 4.3 6.9 + - - -
16A ALA* 2.7 32.8 + - - +
17A GLU* 3.4 18.5 + - - +
19A PHE* 1.3 74.8 - - + +
21A GLN* 1.3 60.8 + - - +
23A ALA* 4.3 0.2 - - - -
24A SER* 2.8 36.2 + - - +
86A TYR* 3.3 27.6 + - - -
88A ASP* 3.2 26.9 + - - -
92A VAL* 4.4 8.3 - - - +
95A ARG* 3.5 25.0 + - - +
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Residues in contact with GLN 21 (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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17A GLU 3.3 11.8 + - - +
18A LYS* 3.8 15.6 - - - +
19A PHE 3.2 0.4 - - - -
20A ARG* 1.3 80.2 - - - +
22A LYS* 1.3 76.5 + - - +
24A SER* 3.2 4.7 - - - -
25A THR* 2.9 28.8 + - - +
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Residues in contact with LYS 22 (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 LYS* 3.5 30.1 + - + +
19A PHE* 3.5 2.4 + - - +
21A GLN* 1.3 91.7 + - - +
23A ALA* 1.3 64.6 + - - +
25A THR* 3.1 9.3 + - - -
26A HIS* 3.0 24.3 + - - +
70A ARG* 4.8 21.0 - - + +
73A GLN* 2.8 42.6 + - + +
74A ILE* 3.8 16.4 - - + +
77A ILE* 4.2 20.6 - - + -
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Residues in contact with ALA 23 (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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19A PHE* 2.9 33.0 + - + +
22A LYS* 1.3 75.1 - - - +
24A SER* 1.3 66.8 + - - +
26A HIS* 3.2 1.2 + - - +
27A GLU* 2.8 28.4 + - - +
74A ILE* 3.8 14.0 - - + +
95A ARG* 3.1 28.3 - - + +
99A ILE* 4.1 14.1 - - + -
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Residues in contact with SER 24 (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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20A ARG* 2.8 25.1 + - - +
21A GLN* 3.2 5.4 - - - -
23A ALA* 1.3 76.0 - - - +
25A THR* 1.3 68.0 + - - +
27A GLU* 2.9 12.3 + - - +
28A THR* 3.1 26.0 + - - +
95A ARG* 4.1 8.7 + - - -
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Residues in contact with THR 25 (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 GLN* 2.9 19.0 + - - +
22A LYS* 3.3 12.5 - - - -
24A SER* 1.3 74.9 - - - +
26A HIS* 1.3 67.2 + - - +
28A THR* 2.7 29.7 + - - +
29A TRP* 3.1 8.2 + - + +
67A HIS* 6.5 0.7 - - + -
70A ARG* 6.1 5.4 - - + -
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Residues in contact with HIS 26 (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 LYS 3.0 14.4 + - - +
23A ALA 3.8 2.5 - - - +
25A THR* 1.3 78.1 - - - +
27A GLU* 1.3 67.7 + - - +
29A TRP* 3.0 24.6 + + - +
30A ALA* 2.9 23.5 + - + +
67A HIS* 4.6 11.2 + - + +
70A ARG* 4.7 10.8 - - + +
71A VAL* 3.3 31.8 - - + +
74A ILE* 4.0 15.0 - - + +
99A ILE* 3.9 24.5 + - + +
102A GLN* 4.3 12.8 + - - +
103A TRP* 3.7 24.3 - + - +
106A LEU* 5.4 0.6 - - - +
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Residues in contact with GLU 27 (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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23A ALA* 2.8 27.1 + - - +
24A SER* 2.9 13.8 + - - +
26A HIS* 1.3 75.6 - - - +
28A THR* 1.3 64.0 + - + +
30A ALA* 3.4 4.2 + - - +
31A TYR* 3.4 18.0 + - - +
95A ARG* 2.4 48.7 + - - +
98A LYS* 4.5 14.4 + - - +
99A ILE* 4.1 17.8 - - + +
102A GLN* 5.4 3.4 - - - +
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Residues in contact with THR 28 (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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24A SER* 3.1 17.4 + - - +
25A THR* 2.7 25.9 + - - +
27A GLU* 1.3 71.0 - - + +
29A TRP* 1.3 62.8 + - - +
31A TYR* 3.4 18.8 + - - +
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Residues in contact with TRP 29 (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 THR* 3.1 12.2 + - + +
26A HIS* 3.0 23.1 + + - +
28A THR* 1.3 79.0 + - - +
30A ALA* 1.3 97.7 + - + +
31A TYR 3.2 2.5 + - - +
33A LYS* 3.5 39.1 - - + +
60A PHE* 5.8 1.3 - + - -
63A ASP* 2.4 35.2 + - - -
64A LEU* 3.5 31.9 - - + -
67A HIS* 2.8 40.4 + + + +
103A TRP* 3.8 13.9 - + - -
106A LEU* 3.8 12.6 - - + -
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 2.9 15.8 + - - +
27A GLU 3.4 4.2 + - - +
28A THR 3.3 0.4 - - - -
29A TRP* 1.3 100.9 - - + +
31A TYR* 1.3 65.6 + - - +
32A GLY 3.4 1.7 + - - -
33A LYS* 3.5 14.6 + - - +
34A GLU* 4.4 4.5 - - - +
102A GLN* 3.4 38.9 + - - +
106A LEU* 4.3 5.3 - - + +
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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