Contacts of the helix formed by residues 10 - 33 (chain A) in PDB entry 1QAP
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 ARG 10 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASP* 3.6 10.0 - - + +
9A ASP* 1.3 76.7 - - - +
11A ARG* 1.3 53.5 + - - +
13A ALA* 3.6 9.3 - - + +
14A LEU* 2.7 55.6 + - + +
173A ASN* 4.4 9.7 + - + +
174A HIS* 3.6 26.1 + - - +
175A ARG* 4.0 17.2 - - - +
176A LEU* 4.6 7.0 - - + +
180A ASP* 3.4 42.8 + - - +
181A ALA* 4.8 1.8 - - - +
210A PRO* 4.2 19.8 - - - +
231A ILE* 6.4 0.4 - - - +
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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
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8A ASP* 4.9 13.2 + - - +
9A ASP 2.8 1.7 + - - +
10A ARG* 1.3 77.0 - - - +
12A ASP* 1.3 69.9 + - - +
14A LEU* 3.6 8.5 - - - +
15A LEU* 2.8 49.7 + - + +
167A LEU* 4.9 20.0 - - + +
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Residues in contact with ASP 12 (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 ASP 4.5 2.6 - - - +
9A ASP* 2.6 39.5 + - - +
11A ARG* 1.3 83.7 - - - +
13A ALA* 1.3 58.2 + - - +
15A LEU* 3.9 12.0 - - - +
16A GLU* 3.2 27.4 + - - +
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Residues in contact with ALA 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 ASP* 2.7 20.4 + - + +
10A ARG* 3.6 14.1 - - + +
12A ASP* 1.3 72.7 - - - +
14A LEU* 1.3 63.0 + - - +
16A GLU* 3.7 3.8 + - - +
17A ARG* 3.3 23.4 + - - +
176A LEU* 5.2 8.5 - - + +
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Residues in contact with LEU 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 ARG* 2.7 34.7 + - + +
11A ARG* 3.6 6.5 - - - +
13A ALA* 1.3 72.7 - - - +
15A LEU* 1.3 64.4 + - + +
16A GLU 3.0 0.9 + - - -
17A ARG* 3.0 6.1 + - - +
18A ILE* 2.9 35.2 + - + +
160A THR* 5.2 6.2 - - - +
163A LYS* 3.7 33.4 - - + -
167A LEU* 4.1 13.5 - - + -
173A ASN* 3.1 35.9 - - + +
176A LEU* 3.4 29.4 - - + -
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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* 2.8 40.1 + - + +
12A ASP* 4.0 13.2 - - - +
13A ALA 3.5 0.2 - - - -
14A LEU* 1.3 77.6 - - + +
16A GLU* 1.3 57.6 + - - +
18A ILE* 3.9 16.8 - - + +
19A ASN* 2.7 37.0 + - - +
164A TYR* 4.6 15.0 - - + -
167A LEU* 5.8 6.1 - - + -
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Residues in contact with GLU 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 ASP 3.2 18.3 + - - +
13A ALA* 4.1 4.3 - - - +
14A LEU 3.1 0.4 - - - -
15A LEU* 1.3 74.1 - - - +
17A ARG* 1.3 75.6 + - - +
19A ASN* 3.0 23.9 + - - +
20A LEU* 3.2 32.8 + - - +
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Residues in contact with ARG 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 ALA 3.3 15.2 + - - +
14A LEU* 3.0 6.1 + - + +
16A GLU* 1.3 88.6 + - - +
18A ILE* 1.3 56.7 + - - +
20A LEU* 3.3 12.8 + - - +
21A ASP* 2.9 63.5 + - - +
160A THR* 3.9 14.6 - - + -
176A LEU* 4.7 20.5 - - + +
31B ARG* 3.9 9.3 + - - +
32B GLU* 3.5 37.5 + - - +
35B GLY* 4.5 11.5 - - - -
36B GLY* 4.0 11.4 - - - +
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Residues in contact with ILE 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 LEU* 2.9 29.7 + - + +
15A LEU* 3.9 15.3 - - + +
17A ARG* 1.3 71.2 - - - +
19A ASN* 1.3 61.6 + - - +
21A ASP* 4.0 0.7 - - + -
22A ILE* 2.6 44.3 + - + +
72A TRP* 3.7 28.7 - - + -
160A THR* 3.2 38.5 + - - +
161A ALA* 4.1 0.4 - - + -
164A TYR* 3.6 37.7 - - + -
167A LEU* 6.2 0.7 - - + -
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Residues in contact with ASN 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* 2.7 29.5 + - - +
16A GLU* 3.0 13.6 + - - +
18A ILE* 1.3 80.2 - - - +
20A LEU* 1.3 57.8 + - - +
22A ILE* 4.3 10.1 - - - +
23A PRO* 3.2 25.5 - - - +
71A ARG* 5.2 9.9 + - - +
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Residues in contact with LEU 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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16A GLU* 3.2 32.6 + - - +
17A ARG* 3.6 13.5 - - - +
18A ILE 3.2 0.6 - - - -
19A ASN* 1.3 79.9 - - - +
21A ASP* 1.3 68.8 + - - +
23A PRO* 4.0 11.8 - - - +
24A ALA* 4.2 8.3 - - - +
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Residues in contact with ASP 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 ARG* 2.9 43.6 + - - +
18A ILE* 3.6 3.4 - - + +
20A LEU* 1.3 88.7 - - - +
22A ILE* 1.3 67.7 + - - +
23A PRO 3.4 0.7 - - - -
24A ALA* 3.2 9.8 + - - +
25A ALA* 3.1 22.1 + - - +
160A THR* 3.0 38.6 - - - +
28B GLN* 5.6 1.6 - - - +
32B GLU* 5.8 0.7 - - - +
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Residues in contact with ILE 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 ILE* 2.6 35.8 + - + +
19A ASN* 4.3 6.7 - - - +
21A ASP* 1.3 72.3 - - - +
23A PRO* 1.3 72.8 - - + +
25A ALA* 3.1 1.3 + - - +
26A VAL* 2.9 35.3 + - + +
71A ARG* 3.5 43.3 - - + +
72A TRP* 3.7 54.7 - - + +
75A GLU* 3.9 17.5 - - + +
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Residues in contact with PRO 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 ASN 3.2 20.2 - - - +
20A LEU* 4.0 8.7 - - - +
21A ASP 3.8 0.2 - - - -
22A ILE* 1.3 91.9 - - + +
24A ALA* 1.3 56.6 + - - +
26A VAL* 4.4 0.2 - - + -
27A ALA* 2.8 38.0 + - - +
71A ARG* 6.1 2.0 - - - +
75A GLU* 3.2 32.1 - - + +
79A GLN* 3.6 4.0 + - - +
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Residues in contact with ALA 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 LEU 4.2 10.8 - - - +
21A ASP* 3.2 13.8 + - + +
23A PRO* 1.3 80.8 - - - +
25A ALA* 1.3 58.8 + - - +
27A ALA* 3.8 6.5 - - - +
28A GLN* 3.8 17.5 + - - +
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Residues in contact with ALA 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 ASP 3.1 14.8 + - - +
22A ILE* 3.9 3.4 - - - +
24A ALA* 1.3 73.5 - - - +
26A VAL* 1.3 68.6 + - + +
27A ALA 3.1 1.1 - - - -
28A GLN* 2.9 9.8 + - - +
29A ALA* 2.9 22.2 + - - +
72A TRP* 5.5 3.4 - - - +
123A PHE* 4.1 15.8 - - + -
157A GLY 5.8 3.4 - - - +
158A LEU* 5.4 9.4 - - + -
156B PRO* 5.8 0.8 - - + +
157B GLY 5.8 0.5 + - - -
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Residues in contact with VAL 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 ILE* 2.9 37.5 + - + +
23A PRO 3.9 1.1 - - - +
25A ALA* 1.3 74.8 - - - +
27A ALA* 1.3 65.1 + - - +
29A ALA* 3.1 2.3 + - - +
30A LEU* 3.0 33.7 + - + +
72A TRP* 4.0 13.0 - - + +
75A GLU* 3.8 14.4 - - + -
76A VAL* 3.5 35.9 - - + +
79A GLN* 4.0 3.6 - - - +
123A PHE* 3.7 27.8 - - + -
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Residues in contact with ALA 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 PRO 2.8 21.4 + - - +
24A ALA* 3.8 8.3 - - - +
26A VAL* 1.3 75.9 - - - +
28A GLN* 1.3 56.7 + - - +
30A LEU* 3.5 1.3 + - - +
31A ARG* 2.9 36.3 + - + +
38A VAL* 3.6 12.1 - - + +
79A GLN* 3.0 20.6 - - - +
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Residues in contact with GLN 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 ALA 3.9 11.1 - - - +
25A ALA* 2.9 12.2 + - - +
27A ALA* 1.3 78.7 - - - +
29A ALA* 1.3 60.6 + - - +
31A ARG* 3.1 12.4 + - + +
32A GLU* 2.9 38.1 + - - +
24B ALA* 6.1 2.6 - - - +
25B ALA* 6.0 1.6 - - - +
28B GLN* 4.9 16.1 + - - +
157B GLY* 3.7 33.8 + - - -
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Residues in contact with ALA 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 ALA 2.9 11.7 + - - +
26A VAL 3.6 7.6 - - - +
28A GLN* 1.3 76.0 - - - +
30A LEU* 1.3 60.0 + - - +
32A GLU* 2.9 31.9 - - - +
33A ASP* 3.5 9.0 + - - +
119A THR* 3.8 15.0 + - + +
123A PHE* 3.7 27.1 - - + -
156B PRO* 4.4 14.6 - - + -
157B GLY 4.7 2.4 - - - +
159B ARG* 5.3 1.6 + - - -
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Residues in contact with LEU 30 (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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26A VAL* 3.0 28.2 + - + +
27A ALA 3.7 2.9 - - - +
29A ALA* 1.3 74.5 - - - +
31A ARG* 1.3 61.2 + - - +
33A ASP* 3.0 6.6 + - + +
34A LEU* 2.8 39.7 + - + +
37A GLU 4.6 0.9 - - - -
38A VAL* 4.4 12.8 - - + -
76A VAL* 3.4 32.5 - - + +
79A GLN* 3.7 34.1 - - + +
80A LEU* 4.2 21.5 - - + -
115A THR* 5.8 2.2 - - + +
116A GLY* 5.3 2.2 - - - -
119A THR* 3.8 18.2 - - + +
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Residues in contact with ARG 31 (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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27A ALA* 2.9 34.4 + - - +
28A GLN* 3.1 12.8 + - + +
30A LEU* 1.3 76.5 - - - +
32A GLU* 1.3 58.9 + - - +
33A ASP 3.3 0.3 + - - -
34A LEU 3.5 0.2 + - - -
35A GLY 3.3 5.4 + - - -
36A GLY* 2.7 54.3 + - - +
37A GLU* 3.7 20.0 - - - +
38A VAL* 3.2 22.4 - - + +
17B ARG* 4.6 0.4 - - - -
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Residues in contact with GLU 32 (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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28A GLN* 2.9 18.6 + - - +
29A ALA* 2.9 30.2 - - - +
31A ARG* 1.3 76.5 - - - +
33A ASP* 1.3 59.1 + - - +
35A GLY 4.0 2.8 + - - -
17B ARG* 3.3 35.1 + - - +
154B THR* 4.5 2.1 + - - +
155B LEU 4.5 1.0 - - - +
156B PRO* 4.4 3.8 - - - +
157B GLY* 3.1 45.2 + - - +
159B ARG* 3.2 46.1 + - + +
176B LEU 3.5 10.0 - - - +
177B GLY* 4.3 0.5 - - - -
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Residues in contact with ASP 33 (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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29A ALA 3.5 10.8 + - - +
30A LEU* 3.0 10.9 + - + +
32A GLU* 1.3 80.3 - - - +
34A LEU* 1.3 61.2 + - + +
35A GLY 3.3 4.3 + - - -
115A THR 4.6 3.5 - - - +
118A ARG* 4.3 3.5 - - - +
119A THR* 4.0 12.3 + - - +
152B ARG* 2.7 41.3 + - - -
159B ARG* 3.1 24.4 + - - +
177B GLY* 3.4 8.7 - - - -
178B LEU* 2.8 44.6 + - + +
179B THR 3.9 2.1 + - - -
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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