Contacts of the helix formed by residues 4 - 29 (chain B) in PDB entry 3QIR
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 CYS 4 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B ASP* 1.3 70.5 - - - +
5B VAL* 1.4 64.3 - - - +
6B LEU* 3.8 9.0 - - - -
7B ASP* 3.0 40.9 + - - +
8B VAL* 3.1 13.8 + - - +
110C PRO 3.6 11.7 - - - -
111C GLU* 3.5 31.6 - - - -
113C SER 3.5 7.4 - - - -
114C PHE* 3.6 20.5 - - + -
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Residues in contact with VAL 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ASP 3.5 1.0 + - - -
4B CYS* 1.4 68.4 - - - +
6B LEU* 1.3 58.2 + - - +
8B VAL* 3.2 10.5 + - + +
9B MET* 2.9 47.3 + - + +
28C LEU* 3.6 33.2 - - + -
33C VAL* 4.8 2.7 - - + -
87C LEU* 4.1 6.5 - - + -
110C PRO* 3.5 17.7 + - + +
113C SER* 2.9 36.7 + - - +
114C PHE* 4.1 2.9 - - - +
115C MET* 4.2 21.8 - - + -
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Residues in contact with LEU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B CYS* 3.3 3.9 - - - -
5B VAL* 1.3 74.2 - - - +
7B ASP* 1.3 58.0 + - - +
9B MET* 3.3 15.3 + - + +
10B HIS* 2.8 60.8 + - + +
81C GLU* 3.6 30.3 - - + -
84C GLN* 3.7 32.5 - - + +
85C PRO* 4.6 3.4 - - + -
110C PRO* 3.2 23.1 + - + +
111C GLU* 3.9 20.4 - - + +
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Residues in contact with ASP 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP* 5.6 3.1 - - + -
4B CYS* 3.0 31.7 + - + +
6B LEU* 1.3 74.5 - - - +
8B VAL* 1.3 66.0 + - + +
10B HIS* 3.3 17.3 + - - +
11B ALA* 3.1 23.0 + - - +
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Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP* 4.0 20.9 - - + -
4B CYS 3.1 15.1 + - - +
5B VAL* 3.2 10.5 + - + +
7B ASP* 1.3 73.5 - - - +
9B MET* 1.4 61.2 + - + +
11B ALA* 3.3 9.1 + - - +
12B ILE* 3.1 29.8 + - + +
27C LEU* 3.7 29.6 - - + -
28C LEU* 6.0 1.6 - - + -
115C MET* 4.4 18.2 - - + -
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Residues in contact with MET 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 2.9 21.3 + - + +
6B LEU* 3.4 15.0 - - + +
8B VAL* 1.4 74.2 - - + +
10B HIS* 1.4 59.5 + - - +
12B ILE* 3.3 2.1 + - - +
13B TYR* 2.9 28.6 + - - +
20C PHE* 3.6 10.8 - - + -
24C CYS* 4.0 21.8 - - + -
28C LEU* 3.6 27.8 - - + -
47C VAL* 5.1 4.7 - - + -
49C TRP* 4.6 14.6 - - + -
85C PRO* 4.1 27.4 - - + -
87C LEU* 3.9 22.0 - - + -
110C PRO* 4.2 14.4 - - + -
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Residues in contact with HIS 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 2.8 56.9 + - + +
7B ASP* 3.3 19.3 + - - +
9B MET* 1.4 72.8 - - - +
11B ALA* 1.4 56.9 + - - +
13B TYR* 3.3 13.2 + - - +
14B GLN* 3.0 29.9 + - - +
81C GLU* 5.6 3.1 - - + +
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASP 3.1 12.4 + - - +
8B VAL* 3.5 11.4 - - - +
10B HIS* 1.4 73.6 - - - +
12B ILE* 1.4 63.5 + - + +
14B GLN* 3.5 8.0 + - - +
15B GLN* 3.2 22.2 + - - +
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 3.1 26.2 + - + +
9B MET* 3.7 7.0 - - - +
11B ALA* 1.4 72.7 - - + +
13B TYR* 1.4 64.6 + - - +
15B GLN* 3.3 6.2 + - + +
16B ASN* 2.8 45.0 + - - +
20C PHE* 4.0 10.8 - - + -
23C GLU* 3.7 32.1 - - + +
24C CYS* 4.2 13.5 - - - +
27C LEU* 5.0 9.2 - - + -
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Residues in contact with TYR 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET 2.9 14.7 + - - +
10B HIS* 3.3 17.0 + - - +
12B ILE* 1.4 76.6 - - - +
14B GLN* 1.4 58.3 + - + +
16B ASN* 3.2 5.0 + - + +
17B LYS* 2.9 63.0 + - + +
13C TYR* 4.3 21.3 + + - -
20C PHE* 3.6 38.3 - + + -
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Residues in contact with GLN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B HIS 3.0 16.9 + - - +
11B ALA* 3.6 9.0 - - - +
12B ILE 3.3 0.2 - - - -
13B TYR* 1.4 81.1 - - + +
15B GLN* 1.3 61.6 + - - +
17B LYS* 3.4 12.8 + - + +
18B GLU* 3.2 23.9 + - - +
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA 3.2 13.6 + - - +
12B ILE* 3.7 10.8 - - + +
14B GLN* 1.3 76.4 - - - +
16B ASN* 1.3 60.0 + - - +
18B GLU* 3.6 6.3 + - + +
19B HIS* 3.2 25.6 + - - +
23C GLU* 5.8 2.7 - - - +
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Residues in contact with ASN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 2.8 35.7 + - - +
13B TYR* 3.6 4.7 - - + +
15B GLN* 1.3 76.1 - - - +
17B LYS* 1.4 60.2 + - - +
19B HIS* 3.4 6.3 + - - +
20B PHE* 3.0 24.3 + - - +
16C ASN* 3.5 23.4 - - - +
19C HIS* 2.8 28.0 + - - +
20C PHE* 3.4 29.0 + - + +
23C GLU* 2.9 23.0 + - - -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TYR* 2.9 46.8 + - + +
14B GLN* 3.6 13.2 - - + +
15B GLN 3.4 0.2 - - - -
16B ASN* 1.4 72.6 - - - +
18B GLU* 1.4 58.1 + - - +
20B PHE* 3.2 13.6 + - + +
21B GLN* 3.0 59.0 + - + +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLN 3.2 16.8 + - - +
15B GLN* 3.8 7.9 - - + +
17B LYS* 1.4 72.2 - - - +
19B HIS* 1.3 60.0 + - - +
21B GLN* 3.3 10.4 + - - +
22B ASP* 2.9 42.5 + - - +
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Residues in contact with HIS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLN 3.2 14.9 + - - +
16B ASN* 3.6 12.3 - - - +
17B LYS 3.3 0.2 - - - -
18B GLU* 1.3 76.6 - - - +
20B PHE* 1.3 54.8 + - - +
22B ASP* 3.8 7.3 - - + +
23B GLU* 2.9 48.5 + - + +
16C ASN* 2.8 22.8 + - - +
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASN 3.0 14.2 + - - +
17B LYS* 3.4 18.6 - - + +
19B HIS* 1.3 74.3 - - - +
21B GLN* 1.3 72.7 + - + +
23B GLU* 3.3 3.4 + - - +
24B CYS* 3.1 40.9 + - - -
49B TRP* 3.8 30.7 - + - -
9C MET* 3.5 26.9 - - + -
12C ILE* 4.1 3.8 - - + -
13C TYR* 3.7 45.8 - + + -
16C ASN* 3.4 22.4 + - + +
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Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS* 3.0 48.7 + - - +
18B GLU* 3.7 9.2 - - - +
20B PHE* 1.3 83.1 - - + +
22B ASP* 1.3 59.5 + - - +
24B CYS 3.3 0.9 + - - -
25B THR* 2.7 37.6 + - - -
49B TRP* 3.6 66.0 + - + +
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Residues in contact with ASP 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU* 2.9 26.8 + - - +
19B HIS* 3.9 6.9 + - + +
21B GLN* 1.3 77.7 - - - +
23B GLU* 1.3 57.0 + - - +
25B THR* 4.0 5.4 - - - -
26B LYS* 2.9 32.4 + - - +
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B HIS* 2.9 35.7 + - + +
20B PHE* 3.5 7.2 - - - +
21B GLN 3.3 0.4 - - - -
22B ASP* 1.3 77.1 - - - +
24B CYS* 1.3 57.6 + - - +
26B LYS* 3.7 6.0 + - - +
27B LEU* 3.2 27.4 + - - +
12C ILE* 5.0 11.7 - - + -
15C GLN* 6.5 0.2 - - - -
16C ASN* 3.9 20.9 - - - +
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Residues in contact with CYS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.1 46.9 + - - +
23B GLU* 1.3 73.3 - - - +
25B THR* 1.3 61.4 + - - +
27B LEU* 3.4 9.4 + - - +
28B LEU* 3.0 38.8 + - + +
47B VAL* 5.0 0.7 - - + -
49B TRP* 3.7 21.1 - - + -
9C MET* 4.0 24.9 - - + -
12C ILE* 4.1 15.5 - - - -
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLN 2.7 21.7 + - - -
22B ASP* 4.0 6.1 - - - -
24B CYS* 1.3 72.9 - - - +
26B LYS* 1.4 64.7 + - - +
28B LEU 3.3 0.3 + - - -
29B VAL* 3.0 48.3 + - + +
46B ASP* 3.9 17.3 - - - +
47B VAL* 3.9 16.4 - - + +
49B TRP* 2.9 22.6 + - + +
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ASP 2.9 19.8 + - - +
23B GLU* 3.8 7.0 - - - +
25B THR* 1.4 75.8 - - - +
27B LEU* 1.3 61.2 + - - +
28B LEU 3.6 0.3 + - - -
29B VAL* 4.1 10.8 - - - +
31B ASN* 5.0 0.2 + - - -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU 3.2 15.9 + - - +
24B CYS* 3.4 11.7 - - - +
26B LYS* 1.3 79.6 - - - +
28B LEU* 1.4 65.2 + - + +
31B ASN* 2.6 26.4 + - - -
115B MET* 5.2 9.7 - - - +
8C VAL* 3.7 29.4 - - + -
9C MET* 6.2 1.3 - - + -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B CYS* 3.0 25.3 + - + +
25B THR 3.3 0.9 + - - +
27B LEU* 1.4 87.1 - - + +
29B VAL* 1.3 66.2 + - - +
30B GLY 3.3 0.3 + - - -
31B ASN* 3.0 26.1 + - - +
33B VAL* 4.4 7.4 - - + -
44B ILE* 3.6 22.5 - - + +
47B VAL* 4.6 9.6 - - + -
87B LEU* 4.3 17.3 - - + -
115B MET* 4.2 17.3 - - + -
5C VAL* 3.7 44.0 - - + -
8C VAL* 6.4 0.2 - - + -
9C MET* 4.5 15.5 - - + -
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 3.0 41.5 + - + +
26B LYS* 4.1 8.6 - - - +
27B LEU 3.9 0.2 - - - -
28B LEU* 1.3 73.3 - - - +
30B GLY* 1.3 63.2 + - - +
31B ASN* 3.6 6.2 + - - -
44B ILE* 3.5 7.4 - - + +
45B ASP* 4.0 15.0 - - - +
46B ASP* 3.9 26.0 - - - +
47B VAL* 5.1 0.7 - - + -
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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
------------------------------------------------------------
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