Contacts of the helix formed by residues 5 - 28 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B GLU 3.6 2.0 + - - -
4B LEU* 1.3 76.5 - - - +
6B LEU* 1.3 60.3 + - - +
7B ALA* 3.9 7.1 + - - +
8B GLU* 2.6 41.0 + - - +
9B ALA* 2.9 27.1 + - - +
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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
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1424A PTY 5.5 20.4 - - + +
5B SER* 1.3 74.6 - - - +
7B ALA* 1.3 58.6 + - - +
9B ALA* 3.1 5.9 + - + +
10B LEU* 2.9 48.8 + - + +
53B LEU* 3.7 37.9 - - + -
57B ILE* 4.3 8.3 - - + -
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Residues in contact with ALA 7 (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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63A VAL* 5.9 1.3 - - + -
245A PHE* 3.5 26.5 - - + -
1424A PTY 3.9 40.0 + - + +
5B SER* 3.3 7.1 + - - +
6B LEU* 1.3 80.1 - - - +
8B GLU* 1.3 57.4 + - - +
9B ALA 3.2 0.2 + - - -
10B LEU* 3.3 4.8 + - - +
11B PHE* 2.9 29.8 + - - +
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Residues in contact with GLU 8 (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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245A PHE* 3.9 27.8 - - + +
249A ARG* 3.7 34.2 + - - +
3B GLU 4.1 2.8 - - - +
4B LEU* 3.5 29.5 - - + +
5B SER* 2.6 45.6 + - - +
7B ALA* 1.3 74.5 - - - +
9B ALA* 1.3 58.1 + - - +
11B PHE* 3.9 12.0 - - + +
12B LEU* 2.9 28.5 + - - +
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Residues in contact with ALA 9 (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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4B LEU* 4.4 10.5 - - + +
5B SER 2.9 14.6 + - - +
6B LEU* 3.2 14.4 - - + +
7B ALA 3.1 0.2 - - - -
8B GLU* 1.3 75.4 - - - +
10B LEU* 1.3 66.3 + - - +
12B LEU* 3.0 9.2 + - - +
13B ILE* 2.9 27.8 + - - +
48B LEU 5.6 1.1 - - - +
49B ILE* 3.9 15.0 - - + +
50B PRO* 6.2 0.4 - - + -
53B LEU* 4.4 20.6 - - + -
57B ILE* 5.3 1.8 - - + -
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Residues in contact with LEU 10 (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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60A PHE* 5.3 6.3 - - + -
1424A PTY 4.1 41.7 - - + -
6B LEU* 2.9 34.5 + - + +
7B ALA* 3.7 3.1 - - - +
9B ALA* 1.3 74.7 - - - +
11B PHE* 1.3 58.8 + - - +
13B ILE* 3.1 10.4 + - + +
14B LEU 2.9 23.2 + - - -
57B ILE* 3.7 42.2 - - + -
304B PHE* 3.3 22.3 - - + -
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Residues in contact with PHE 11 (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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238A SER* 3.1 32.3 - - - -
241A PHE* 3.8 16.4 - - + -
242A LEU* 3.4 44.4 - - + -
245A PHE* 3.3 33.7 - + + -
1424A PTY 4.4 8.4 - - + +
7B ALA 2.9 10.5 + - - +
8B GLU* 3.9 7.9 - - + +
10B LEU* 1.3 73.7 - - - +
12B LEU* 1.3 69.9 + - + +
14B LEU* 3.5 10.0 - - + +
15B PHE* 2.9 48.6 + + + +
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Residues in contact with LEU 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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4B LEU* 3.6 26.7 - - + -
8B GLU 2.9 20.9 + - - +
9B ALA* 3.0 5.6 + - - +
11B PHE* 1.3 82.5 - - + +
13B ILE* 1.3 53.1 + - - +
15B PHE* 4.8 4.7 - - + -
16B THR* 2.4 56.6 + - + +
42B ILE* 4.4 9.6 - - + -
48B LEU* 4.1 23.8 - - + -
49B ILE* 3.8 23.8 - - + -
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Residues in contact with ILE 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 ALA 2.9 19.0 + - - +
10B LEU* 3.1 8.7 + - - +
12B LEU* 1.3 76.1 - - - +
14B LEU* 1.3 57.7 + - - +
16B THR* 3.0 5.6 + - - -
17B GLY* 2.9 26.9 + - - -
42B ILE* 4.6 6.7 - - + -
49B ILE* 3.6 21.3 - - + -
57B ILE* 4.1 16.6 - - + -
303B ILE* 4.4 2.1 - - + +
304B PHE* 3.6 39.0 - - + +
307B VAL* 3.9 23.7 - - + +
308B LEU* 3.6 28.9 - - + -
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Residues in contact with LEU 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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234A ALA 5.0 1.1 - - - +
237A LEU* 4.0 28.9 - - + -
238A SER* 3.5 26.0 - - - +
241A PHE* 5.5 0.9 - - + -
1424A PTY 4.1 20.9 - - + -
10B LEU 2.9 10.4 + - - +
11B PHE* 3.2 13.4 + - + +
13B ILE* 1.3 76.9 - - - +
15B PHE* 1.3 55.4 + - - +
17B GLY* 3.3 2.1 + - - -
18B VAL* 2.9 37.4 + - + +
300B LEU* 3.9 29.2 - - + -
303B ILE* 4.8 6.5 - - + +
304B PHE* 3.7 26.9 - - + -
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Residues in contact with PHE 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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235A PHE* 5.2 11.4 - + - -
238A SER* 4.0 27.3 + - - -
239A LEU* 5.9 0.7 - - - -
242A LEU* 4.2 22.2 - - + -
11B PHE* 2.9 44.6 + + + +
12B LEU* 4.0 5.2 - - + +
14B LEU* 1.3 69.2 - - - +
16B THR* 1.3 74.3 + - + +
18B VAL* 2.9 6.2 + - + +
19B ILE* 2.9 56.5 + - + +
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Residues in contact with THR 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 LEU* 2.4 46.9 + - + +
13B ILE* 3.0 14.4 + - - -
15B PHE* 1.3 82.3 - - + +
17B GLY* 1.3 52.3 + - - +
19B ILE* 3.4 5.5 + - - +
20B SER* 2.6 38.4 + - - -
38B THR* 3.8 17.0 - - + +
42B ILE* 4.0 27.9 - - + +
307B VAL* 4.8 0.9 - - - +
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Residues in contact with GLY 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 ILE 2.9 19.3 + - - -
14B LEU 3.7 0.2 - - - -
16B THR* 1.3 79.5 + - - +
18B VAL* 1.3 55.7 + - - +
20B SER* 4.2 5.2 - - - -
21B MSE 2.9 26.0 + - - +
35B PHE* 3.3 10.4 - - - -
38B THR* 4.9 0.2 - - - +
303B ILE* 3.6 24.3 - - - +
307B VAL* 4.4 9.2 - - - +
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Residues in contact with VAL 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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231A GLU* 5.1 1.6 - - - +
234A ALA* 3.7 26.5 - - + +
235A PHE* 4.0 34.5 - - + +
238A SER* 3.2 20.6 - - - +
14B LEU* 2.9 23.9 + - + +
15B PHE* 2.9 9.6 + - + +
17B GLY* 1.3 74.3 - - - +
19B ILE* 1.3 63.1 + - + +
21B MSE 3.1 10.1 + - - +
22B LEU* 2.9 39.0 + - + +
303B ILE* 4.9 3.8 - - + -
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Residues in contact with ILE 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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220A PHE* 5.2 11.9 - - + -
235A PHE* 5.4 5.2 - - + -
15B PHE* 2.9 50.6 + - + +
16B THR* 3.8 7.0 - - - +
18B VAL* 1.3 79.5 - - + +
20B SER* 1.3 58.8 + - - +
22B LEU* 3.1 20.4 + - + +
23B ILE* 2.9 41.1 + - + +
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Residues in contact with SER 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 THR 2.6 23.1 + - - -
17B GLY* 3.7 0.9 - - - -
19B ILE* 1.3 76.3 - - - +
21B MSE 1.3 57.2 - - - +
23B ILE* 3.2 12.3 - - - +
24B SER* 2.9 30.0 + - - -
34B ILE* 3.6 8.3 - - - +
35B PHE* 3.6 22.4 - - - -
38B THR* 2.7 33.4 + - - +
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Residues in contact with MSE 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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230A PRO* 4.4 20.6 - - + +
231A GLU* 4.1 32.3 - - + -
234A ALA* 5.1 7.2 - - + -
17B GLY 2.9 16.0 + - - +
18B VAL* 3.1 12.8 + - - +
20B SER* 1.3 73.3 - - - +
22B LEU* 1.3 67.9 + - + +
24B SER* 3.2 6.0 + - - -
25B ARG* 2.9 38.8 + - - +
31B TYR* 5.8 0.4 - - - -
35B PHE* 3.5 17.2 - - + -
299B ALA* 5.0 7.2 - - + +
303B ILE* 3.7 30.1 - - + -
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Residues in contact with LEU 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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220A PHE* 4.3 18.4 - - + -
224A THR* 4.9 4.3 - - + +
226A ILE* 4.1 26.2 - - + -
231A GLU* 3.5 44.4 - - + +
235A PHE* 4.8 2.2 - - + -
18B VAL* 2.9 32.9 + - + +
19B ILE* 3.1 18.1 + - + +
21B MSE 1.3 77.2 - - + +
23B ILE* 1.3 59.9 + - + +
25B ARG* 3.1 4.5 + - - +
26B ARG* 2.9 42.7 + - + +
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Residues in contact with ILE 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 ILE* 2.9 30.5 + - + +
20B SER* 3.2 19.5 - - - +
22B LEU* 1.3 77.5 - - + +
24B SER* 1.3 59.3 + - - +
26B ARG* 4.4 7.0 - - + -
27B THR* 2.5 41.8 + - - +
29B ILE* 6.3 1.3 - - + -
34B ILE* 3.7 27.1 - - + -
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Residues in contact with SER 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 SER 2.9 20.8 + - - -
21B MSE 3.3 9.2 - - - -
23B ILE* 1.3 81.2 - - - +
25B ARG* 1.3 56.6 + - - +
27B THR* 4.9 0.4 - - - -
28B GLY* 2.8 26.2 + - - -
29B ILE* 2.6 35.8 + - - +
30B SER 3.6 0.2 - - - -
31B TYR* 3.4 26.9 + - - +
34B ILE* 4.3 9.9 - - - -
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Residues in contact with ARG 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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228A ASP* 5.3 12.5 + - - +
229A PHE 4.5 13.3 + - - -
230A PRO* 4.6 7.5 - - - +
231A GLU* 2.7 50.7 + - - +
21B MSE 2.9 24.6 + - - +
22B LEU 3.7 5.8 - - - +
24B SER* 1.3 76.3 + - - +
26B ARG* 1.3 78.4 + - - +
27B THR 3.4 0.2 + - - -
28B GLY* 3.5 8.9 + - - -
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Residues in contact with ARG 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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224A THR* 2.4 47.9 + - - +
225A GLY 3.7 8.4 + - - -
226A ILE* 3.9 6.1 - - - +
231A GLU* 2.8 41.4 + - - -
22B LEU* 2.9 31.2 + - + +
23B ILE* 4.0 6.3 - - - +
25B ARG* 1.3 95.0 - - - +
27B THR* 1.3 62.8 + - - +
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Residues in contact with THR 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 ILE* 2.5 30.9 + - - +
26B ARG* 1.3 78.2 - - - +
28B GLY* 1.3 58.5 + - - +
29B ILE* 3.6 32.9 - - + +
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Residues in contact with GLY 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 SER 2.8 9.1 + - - -
25B ARG 4.0 6.3 - - - -
26B ARG 3.4 2.0 - - - -
27B THR* 1.3 77.8 - - - +
29B ILE* 1.3 64.0 + - - +
30B SER 3.8 1.4 + - - -
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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