Contacts of the helix formed by residues 7 - 34 (chain A) in PDB entry 3RFM
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 7 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 1.3 61.5 + - - +
9A TYR 3.6 1.1 - - - -
10A ILE* 3.9 30.5 - - - +
11A THR* 2.7 34.9 + - - -
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Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER* 1.3 80.4 - - - +
9A TYR* 1.3 68.6 + - - +
10A ILE 3.1 1.1 - - - -
11A THR* 3.0 8.2 + - - -
12A VAL* 2.9 33.4 + - + +
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Residues in contact with TYR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER 3.6 0.2 - - - -
8A VAL* 1.3 79.5 - - - +
10A ILE* 1.3 68.0 - - + +
12A VAL* 3.4 5.8 + - + +
13A GLU* 2.9 59.2 + - + +
63A ALA* 4.5 12.8 + - - +
64A ILE* 4.8 10.3 - - + -
67A SER* 4.6 21.7 - - - -
271A TYR* 3.4 54.4 - + + +
274A ILE* 4.3 18.0 - - - +
275A VAL* 3.6 14.8 - - + -
330A CFF 5.9 0.3 - - - -
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Residues in contact with ILE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER* 3.9 31.4 - - - +
8A VAL 3.1 0.2 - - - -
9A TYR* 1.3 87.0 - - + +
11A THR* 1.3 63.8 + - - +
13A GLU* 3.2 4.8 + - - +
14A LEU* 3.0 49.6 + - + +
64A ILE* 4.4 21.3 - - + -
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Residues in contact with THR 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER* 2.7 19.3 + - - -
8A VAL* 3.0 12.4 + - - -
10A ILE* 1.3 78.5 - - - +
12A VAL* 1.3 60.5 + - + +
14A LEU* 3.2 9.5 + - - +
15A ALA* 2.9 29.3 + - + +
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 2.9 29.3 + - + +
9A TYR* 3.8 6.3 - - - +
11A THR* 1.3 78.3 - - + +
13A GLU* 1.3 62.6 + - - +
15A ALA* 3.2 9.2 + - + +
16A ILE* 3.0 28.5 + - + +
271A TYR* 6.5 0.7 - - + -
275A VAL* 4.4 26.2 - - + -
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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
----------------------------------------------------------
9A TYR* 2.9 51.8 + - + +
10A ILE 3.2 2.4 + - - +
12A VAL* 1.3 77.5 - - + +
14A LEU* 1.3 62.6 + - - +
16A ILE* 3.6 3.8 + - - +
17A ALA* 3.1 17.2 + - - +
60A ILE* 3.4 34.7 - - - +
63A ALA* 5.8 0.7 - - - -
64A ILE* 3.6 23.6 - - + -
275A VAL* 3.1 32.8 - - + +
278A HIS* 3.6 26.4 + - - +
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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 ILE* 3.0 39.4 + - + +
11A THR* 3.6 11.4 - - - +
13A GLU* 1.3 73.0 - - - +
15A ALA* 1.3 66.2 + - - +
17A ALA* 3.2 8.4 + - + +
18A VAL* 3.1 30.4 + - + +
60A ILE* 5.5 0.2 - - + -
64A ILE* 3.5 25.4 - - + -
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 2.9 16.7 + - + +
12A VAL* 3.4 13.9 - - + +
14A LEU* 1.3 77.7 - - - +
16A ILE* 1.3 63.1 + - + +
18A VAL* 3.5 5.7 + - - +
19A LEU* 3.1 32.5 + - + +
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Residues in contact with ILE 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 VAL* 3.0 21.9 + - + +
13A GLU* 3.8 9.2 - - - +
15A ALA* 1.3 75.3 - - + +
17A ALA* 1.3 57.7 + - - +
19A LEU* 3.0 9.6 + - + +
20A ALA* 2.8 33.3 + - + +
60A ILE* 3.7 12.6 - - + -
275A VAL* 3.8 25.4 - - + +
278A HIS* 3.4 26.7 - - + +
279A THR* 3.5 26.9 - - + +
282A VAL* 3.8 15.0 - - + -
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU 3.1 12.8 + - - +
14A LEU* 3.2 13.6 + - + +
16A ILE* 1.3 78.0 - - - +
18A VAL* 1.3 62.6 + - + +
20A ALA* 3.8 0.7 - - - +
21A ILE* 3.1 33.0 + - + +
56A GLY* 3.4 26.5 - - - +
60A ILE* 3.6 17.7 - - + +
61A PRO* 5.5 0.9 - - + -
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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* 3.1 17.2 + - + +
15A ALA* 3.6 9.4 - - - +
16A ILE 3.1 0.4 - - - -
17A ALA* 1.3 77.2 - - + +
19A LEU* 1.3 64.4 + - + +
21A ILE* 3.3 7.3 + - - +
22A LEU* 2.9 56.8 + - + +
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Residues in contact with LEU 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 ALA* 3.1 20.6 - - + +
16A ILE* 3.0 8.0 + - + +
18A VAL* 1.3 85.9 - - + +
20A ALA* 1.3 59.2 + - - +
22A LEU* 4.6 6.7 - - + -
23A GLY* 2.7 34.1 + - - -
282A VAL* 3.9 30.2 - - + +
285A PRO* 5.2 0.9 - - - +
286A PHE* 4.9 14.7 - - + -
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 2.8 22.8 + - + +
17A ALA 3.8 4.5 - - - +
19A LEU* 1.3 73.1 - - - +
21A ILE* 1.3 63.9 + - - +
24A ASN* 3.1 27.4 + - - +
52A ASP 3.9 12.8 - - - +
53A ILE* 4.4 0.9 - - - +
55A VAL* 5.2 0.4 - - + -
56A GLY* 4.2 13.5 - - - +
281A SER* 3.6 28.7 - - - +
282A VAL* 3.6 11.7 - - + +
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Residues in contact with ILE 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 ALA* 3.1 20.5 + - + +
18A VAL* 3.6 6.3 - - - +
19A LEU 3.1 0.2 - - - -
20A ALA* 1.3 74.1 - - - +
22A LEU* 1.3 76.6 + - + +
23A GLY 3.1 0.3 + - - -
24A ASN* 4.4 0.2 - - - +
25A VAL* 2.8 44.6 + - + +
53A ILE* 4.3 9.9 - - + +
56A GLY 3.7 20.0 - - - +
57A VAL* 3.8 25.1 - - + -
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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 44.7 + - + +
19A LEU* 4.0 6.7 - - + +
21A ILE* 1.3 79.8 - - + +
23A GLY* 1.3 57.0 + - - +
25A VAL* 3.9 4.2 - - - +
26A LEU* 2.9 31.8 + - - +
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Residues in contact with GLY 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 LEU 2.7 21.0 + - - -
22A LEU* 1.3 74.0 - - - +
24A ASN* 1.3 61.0 + - - +
26A LEU* 3.0 12.6 + - - +
27A VAL* 3.0 22.7 + - - +
285A PRO* 3.4 24.2 - - - +
286A PHE* 5.9 3.4 - - - -
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Residues in contact with ASN 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 3.1 17.8 + - - +
23A GLY* 1.3 74.4 - - - +
25A VAL* 1.3 57.3 + - - +
27A VAL* 3.2 10.2 + - - +
28A CYS* 3.0 32.2 + - - -
48A LEU* 5.6 0.2 - - - +
49A ALA* 3.7 23.8 - - + +
52A ASP* 3.2 22.8 + - - +
53A ILE* 3.3 22.7 - - + -
281A SER 2.9 25.6 + - - +
284A ASN* 4.3 7.8 + - - +
285A PRO* 3.5 16.5 - - - +
288A TYR* 5.5 1.2 - - - -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 2.8 43.8 + - + +
22A LEU* 3.9 4.5 - - + +
24A ASN* 1.3 73.6 - - - +
26A LEU* 1.3 65.8 + - - +
28A CYS* 3.3 5.6 + - - +
29A TRP* 3.0 29.9 + - + +
53A ILE* 3.7 23.6 - - + -
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Residues in contact with LEU 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 20.0 + - - +
23A GLY* 3.2 10.3 - - - +
25A VAL* 1.3 77.3 - - - +
27A VAL* 1.3 55.3 + - - +
29A TRP* 3.5 10.1 + - + +
30A ALA* 2.9 30.1 + - - +
285A PRO* 6.4 0.7 - - + -
299A PHE* 3.3 35.4 - - + -
302A ILE* 4.2 30.1 - - + -
303A ILE* 4.8 18.6 - - + -
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Residues in contact with VAL 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 GLY 3.0 14.4 + - - +
24A ASN* 3.3 14.6 - - - +
25A VAL 3.2 0.2 - - - -
26A LEU* 1.3 75.8 - - - +
28A CYS* 1.3 66.5 + - - +
30A ALA* 3.3 2.3 + - - +
31A VAL* 3.1 27.8 + - + +
45A VAL* 4.5 20.4 - - + -
46A VAL* 6.2 1.1 - - + -
49A ALA* 4.8 8.7 - - + -
285A PRO* 4.0 24.9 - - + -
288A TYR* 4.3 10.5 - - + -
295A PHE* 4.2 17.9 - - + -
299A PHE* 3.8 20.2 - - + -
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Residues in contact with CYS 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 ASN 3.0 20.3 + - - +
25A VAL* 3.3 6.7 + - - +
27A VAL* 1.3 77.1 - - - +
29A TRP* 1.3 58.0 + - - +
31A VAL* 3.4 7.8 + - - +
32A TRP* 3.1 27.9 + - - +
46A VAL* 4.5 22.7 - - + -
49A ALA* 3.4 23.8 - - - -
50A ALA* 4.6 2.9 - - - -
53A ILE* 4.3 12.6 - - - -
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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 VAL* 3.0 24.4 + - + +
26A LEU* 3.8 13.2 - - + +
28A CYS* 1.3 75.4 - - - +
30A ALA* 1.3 58.8 + - - +
32A TRP* 3.2 26.3 + + - +
33A LEU* 2.9 38.8 + - + +
302A ILE* 3.8 36.6 - - + -
305A SER 6.5 0.4 - - - -
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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
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26A LEU 2.9 19.0 + - - +
27A VAL 3.6 3.6 - - - +
29A TRP* 1.3 76.9 - - - +
31A VAL* 1.3 56.8 + - - +
33A LEU* 4.5 0.7 - - - -
34A ASN* 3.0 32.4 + - - +
37A LEU* 3.9 7.1 - - + +
295A PHE* 5.0 0.9 - - + -
298A THR* 3.4 22.8 - - + +
299A PHE* 3.5 24.0 - - + -
302A ILE* 3.7 12.7 - - + +
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Residues in contact with VAL 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 VAL* 3.1 21.4 + - + +
28A CYS* 3.7 7.2 - - - +
29A TRP 3.2 0.2 - - - -
30A ALA* 1.3 74.8 - - - +
32A TRP* 1.3 58.4 - - - +
33A LEU 3.1 4.7 - - - -
34A ASN 3.1 16.0 - - - +
37A LEU* 3.8 28.0 - - + +
38A GLN* 2.9 30.3 + - + +
42A ASN* 4.7 7.2 - - + +
45A VAL* 6.0 2.2 - - + -
46A VAL* 4.6 21.8 - - + -
295A PHE* 4.3 21.5 - - + -
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Residues in contact with TRP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A CYS 3.1 17.8 + - - +
29A TRP* 3.2 25.3 + + - +
31A VAL* 1.3 77.8 - - - +
33A LEU* 1.3 60.0 + - + +
38A GLN* 3.7 14.1 + - - +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TRP* 2.9 28.8 + - + +
30A ALA 3.9 3.8 - - - +
32A TRP* 1.3 82.5 - - + +
34A ASN* 1.3 62.6 + - - +
35A SER* 3.5 3.8 + - - -
38A GLN* 4.9 0.9 + - - -
301A LYS* 3.2 34.3 - - + +
302A ILE* 4.0 22.0 - - + -
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Residues in contact with ASN 34 (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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30A ALA 3.0 15.0 + - - +
31A VAL 3.1 15.9 - - - +
33A LEU* 1.3 75.4 - - - +
35A SER* 1.3 63.2 + - - +
36A ASN* 2.8 37.3 + - - +
37A LEU* 3.2 18.3 + - + +
38A GLN* 3.7 0.9 - - - +
294A GLU* 2.8 26.8 + - - -
298A THR* 3.5 25.2 + - + +
301A LYS* 4.7 7.8 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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