Contacts of the helix formed by residues 5 - 28 (chain A) in PDB entry 4CZ8
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 SER 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 1.3 73.7 - - - +
6A LEU* 1.3 62.9 + - - +
7A ALA* 3.3 6.9 + - - +
8A GLU* 2.4 42.0 + - - -
9A ALA* 3.0 26.3 + - - +
53A LEU* 6.0 0.4 - - - -
245B PHE* 5.8 0.7 - - - -
1425B TAM 2.3 31.7 + - - -
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Residues in contact with LEU 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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5A SER* 1.3 77.0 + - - +
7A ALA* 1.3 58.0 + - - +
9A ALA* 3.0 8.6 + - + +
10A LEU* 2.9 36.4 + - + +
53A LEU* 3.6 35.9 - - + -
57A ILE* 3.6 21.5 - - + -
1424A PTY 4.8 17.7 - - + -
1425B TAM 3.9 30.9 + - + -
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Residues in contact with ALA 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER* 3.3 9.0 + - - +
6A LEU* 1.3 81.9 - - - +
8A GLU* 1.3 56.8 + - - +
10A LEU* 3.4 10.7 + - - +
11A PHE* 2.9 30.5 + - - +
63B VAL* 6.3 1.3 - - + -
245B PHE* 3.4 26.6 - - + -
1425B TAM 3.9 20.5 + - + +
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Residues in contact with GLU 8 (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 GLU 4.7 0.2 - - - +
4A LEU* 3.2 30.0 - - + +
5A SER* 2.4 43.5 + - - +
6A LEU 3.3 0.4 - - - -
7A ALA* 1.3 76.0 - - - +
9A ALA* 1.3 57.4 + - - +
11A PHE* 3.8 8.9 - - + +
12A LEU* 2.9 29.1 + - - +
245B PHE* 3.8 30.5 - - + +
249B ARG* 2.3 42.0 + - - -
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.6 5.4 - - + +
5A SER 3.0 13.6 + - - +
6A LEU* 3.0 10.1 + - + +
8A GLU* 1.3 75.3 - - - +
10A LEU* 1.3 65.8 + - + +
12A LEU* 3.0 5.6 + - - +
13A ILE* 2.9 29.8 + - + +
48A LEU 5.1 2.2 - - - +
49A ILE* 3.6 27.1 - - + +
53A LEU* 3.8 23.3 - - + -
57A ILE* 6.3 0.4 - - + -
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 2.9 29.1 + - + +
7A ALA* 3.7 11.2 - - - +
9A ALA* 1.3 75.5 - - + +
11A PHE* 1.3 63.8 + - - +
13A ILE* 3.2 11.7 + - + +
14A LEU* 2.9 18.6 + - - +
57A ILE* 3.6 42.0 - - + -
304A PHE* 3.7 22.6 - - + -
1424A PTY 3.8 33.7 - - + -
60B PHE* 5.0 11.0 - - + -
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Residues in contact with PHE 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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7A ALA 2.9 17.4 + - - +
8A GLU* 3.8 8.3 - - + +
10A LEU* 1.3 76.2 - - - +
12A LEU* 1.3 69.9 + - + +
14A LEU* 3.2 10.2 + - + +
15A PHE* 2.8 49.7 + + + +
238B SER* 3.3 27.6 - - - -
241B PHE* 3.8 17.3 - - + -
242B LEU* 3.4 42.0 - - + -
245B PHE* 3.4 30.1 - + + -
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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
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4A LEU* 3.9 20.0 - - + -
8A GLU 2.9 19.8 + - - +
9A ALA 3.0 6.5 + - - +
11A PHE* 1.3 87.5 - - + +
13A ILE* 1.3 55.2 + - - +
15A PHE* 4.7 7.4 - - + -
16A THR* 2.4 55.3 + - + +
42A ILE* 4.8 10.1 - - + -
48A LEU* 3.8 34.8 - - + -
49A ILE* 4.6 7.9 - - + -
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Residues in contact with ILE 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 ALA* 2.9 21.5 + - + +
10A LEU* 3.3 15.7 - - + +
12A LEU* 1.3 76.5 - - - +
14A LEU* 1.3 57.0 - - - +
16A THR* 3.2 5.4 + - - -
17A GLY* 2.9 27.0 + - - -
42A ILE* 4.3 15.0 - - + +
49A ILE* 4.6 15.0 - - + -
57A ILE* 4.9 3.4 - - + -
303A ILE* 4.7 2.0 - - + +
304A PHE* 3.7 36.1 - - + +
307A VAL* 3.7 27.0 - - + +
308A LEU* 3.7 28.3 - - + -
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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 LEU 2.9 13.3 + - - +
11A PHE* 3.4 15.9 - - + +
13A ILE* 1.3 76.1 - - - +
15A PHE* 1.3 56.8 + - - +
17A GLY* 3.2 2.0 + - - -
18A VAL* 2.9 40.1 + - + +
300A LEU* 3.9 27.1 - - + -
303A ILE* 5.0 6.8 - - + +
304A PHE* 4.4 22.4 - - + -
234B ALA 4.9 0.9 - - - +
237B LEU* 3.7 29.4 - - + -
238B SER* 3.4 27.6 - - - +
241B PHE* 5.2 5.4 - - + -
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Residues in contact with PHE 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 PHE* 2.8 43.8 + + + +
12A LEU* 4.0 7.4 - - + +
14A LEU* 1.3 71.6 - - - +
16A THR* 1.3 71.0 + - + +
18A VAL* 3.1 5.4 + - + +
19A ILE* 2.9 51.7 + - + +
235B PHE* 5.5 10.1 - + - -
238B SER* 3.9 26.9 - - - -
239B LEU* 5.7 1.8 - - + -
242B LEU* 4.0 28.5 - - + -
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Residues in contact with THR 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* 2.4 46.8 + - + +
13A ILE* 3.2 7.8 + - - -
15A PHE* 1.3 78.8 - - + +
17A GLY* 1.3 58.2 + - - +
19A ILE* 3.4 9.5 + - - +
20A SER* 2.9 34.0 + - - -
38A THR* 3.7 17.1 - - + +
42A ILE* 3.9 28.0 - - + +
307A VAL* 5.0 0.7 - - - +
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Residues in contact with GLY 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 ILE 2.9 20.2 + - - -
14A LEU 3.6 0.9 - - - -
16A THR* 1.3 78.5 + - - +
18A VAL* 1.3 56.3 + - - +
20A SER* 3.3 4.5 + - - -
21A MSE 2.9 23.1 + - - +
35A PHE* 3.1 12.5 - - - -
38A THR* 5.0 0.4 - - - -
303A ILE* 3.7 20.9 - - - -
307A VAL* 4.3 11.0 - - - -
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Residues in contact with VAL 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 28.3 + - + +
15A PHE* 3.1 5.1 + - + +
17A GLY* 1.3 71.5 - - - +
19A ILE* 1.3 67.9 + - + +
21A MSE 3.0 12.3 + - + +
22A LEU* 2.9 33.4 + - + +
303A ILE* 4.6 7.9 - - + -
231B GLU 4.8 2.7 - - - +
234B ALA* 3.7 22.4 - - + -
235B PHE* 4.0 35.0 - - + +
238B SER* 3.5 19.3 - - - +
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Residues in contact with ILE 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 PHE* 2.9 50.1 + - + +
16A THR* 3.5 10.1 - - - +
18A VAL* 1.3 75.9 - - + +
20A SER* 1.3 59.0 + - - +
22A LEU* 3.2 20.5 + - + +
23A ILE* 2.9 50.0 + - + +
220B PHE* 5.0 11.9 - - + -
235B PHE* 5.4 6.3 - - + -
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Residues in contact with SER 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 THR 2.9 18.0 + - - -
17A GLY 3.6 5.6 - - - -
19A ILE* 1.3 77.9 - - - +
21A MSE 1.3 56.2 + - - +
23A ILE* 4.3 6.6 - - - +
24A SER* 2.9 28.1 + - - -
34A ILE* 3.4 22.4 - - - +
35A PHE* 3.9 12.1 - - - -
38A THR* 2.5 32.4 + - - +
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Residues in contact with MSE 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 GLY 2.9 13.5 + - - +
18A VAL* 3.0 15.0 + - - +
20A SER* 1.3 75.0 - - - +
22A LEU* 1.3 67.3 + - + +
24A SER* 3.1 6.5 + - - -
25A ARG* 2.9 24.2 + - + +
31A TYR* 5.7 0.4 - - - -
35A PHE* 3.6 15.7 - - + -
299A ALA* 4.8 6.1 - - + -
303A ILE* 3.7 31.2 - - + -
1426A TAM 3.3 29.9 - - + +
230B PRO* 3.9 30.3 - - + +
231B GLU* 4.3 27.6 - - + +
234B ALA* 5.1 5.6 - - - -
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Residues in contact with LEU 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 VAL* 2.9 25.1 + - + +
19A ILE* 3.4 16.2 - - + +
21A MSE 1.3 76.0 - - + +
23A ILE* 1.3 65.4 + - + +
25A ARG* 3.1 2.9 + - - -
26A ARG* 2.9 39.4 + - - +
220B PHE* 3.9 31.4 - - + -
224B THR* 4.8 7.9 - - + -
226B ILE* 4.1 17.5 - - + -
231B GLU* 3.4 42.8 - - + +
235B PHE* 4.5 10.3 - - + -
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Residues in contact with ILE 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 ILE* 2.9 37.9 + - + +
20A SER* 3.9 8.1 - - - +
22A LEU* 1.3 76.2 - - + +
24A SER* 1.3 57.0 + - - +
26A ARG* 4.5 4.3 - - - -
27A THR* 2.6 47.4 + - - +
29A ILE* 6.1 1.8 - - + -
34A ILE* 5.0 12.3 - - + -
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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 SER 2.9 20.3 + - - -
21A MSE 3.3 7.0 - - - -
23A ILE* 1.3 76.9 - - - +
25A ARG* 1.3 57.5 + - - +
28A GLY* 3.0 25.3 + - - -
29A ILE* 2.8 30.7 + - - +
31A TYR* 3.2 32.5 + - - +
34A ILE* 4.4 11.7 - - - -
1426A TAM 4.4 8.4 + - - +
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Residues in contact with ARG 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 MSE 2.9 13.2 + - + +
22A LEU 3.1 1.3 + - - +
24A SER* 1.3 77.7 + - - +
26A ARG* 1.3 71.4 + - - +
28A GLY* 3.7 7.3 + - - -
1426A TAM 3.2 61.8 + - + +
228B ASP* 2.4 43.7 + - - +
229B PHE 3.4 21.0 + - - -
230B PRO* 3.7 10.9 - - - +
231B GLU* 3.3 32.8 + - - +
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Residues in contact with ARG 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 LEU* 2.9 31.8 + - - +
23A ILE* 3.9 5.6 - - - +
25A ARG* 1.3 87.9 - - - +
27A THR* 1.3 63.0 + - - +
28A GLY* 3.4 0.9 + - - -
224B THR* 2.3 48.7 + - + +
225B GLY* 2.3 26.1 + - - -
226B ILE* 4.3 1.8 - - - +
231B GLU* 2.4 38.0 + - - -
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Residues in contact with THR 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 ILE* 2.6 35.7 + - - +
26A ARG* 1.3 77.0 - - - +
28A GLY* 1.3 58.7 + - - +
29A ILE* 3.2 33.9 + - + +
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Residues in contact with GLY 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 3.0 9.0 + - - -
25A ARG 3.7 5.8 + - - -
26A ARG 3.2 3.8 - - - -
27A THR* 1.3 78.0 - - - +
29A ILE* 1.3 63.0 + - - +
30A SER 3.9 0.9 + - - -
137A LEU* 5.9 2.4 - - - +
1426A TAM 5.5 1.7 + - - -
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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
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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