Contacts of the helix formed by residues 1 - 27 (chain A) in PDB entry 5JXL
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 MET 1 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG* 1.3 68.9 + - - +
3A SER* 3.4 11.4 + - - +
4A LEU* 3.3 25.9 + - - +
5A TRP* 3.2 39.2 - - + +
839A SER* 5.4 4.8 + - - +
843A LEU* 4.8 34.9 - - + +
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Residues in contact with ARG 2 (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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1A MET* 1.3 77.0 - - - +
3A SER* 1.3 66.6 + - - +
5A TRP* 3.0 24.9 + - - +
6A SER* 3.1 12.7 + - - -
46A GLN* 3.2 26.8 + - - +
66A ILE* 4.4 21.4 - - + +
68A LEU* 3.8 35.7 - - + +
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Residues in contact with SER 3 (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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1A MET 4.4 5.7 + - - -
2A ARG* 1.3 79.9 - - - +
4A LEU* 1.3 57.1 + - - +
6A SER* 3.0 11.7 + - - -
7A GLY* 2.9 25.6 + - - -
835A THR* 3.8 14.0 - - - +
839A SER* 2.8 27.7 + - - -
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Residues in contact with LEU 4 (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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1A MET* 3.3 22.3 + - - +
2A ARG 3.1 0.4 - - - -
3A SER* 1.3 82.8 + - - +
5A TRP* 1.3 79.1 + - + +
7A GLY* 3.3 1.1 + - - -
8A VAL* 2.9 32.0 + - + +
836A ILE* 4.4 18.1 - - + +
839A SER* 4.1 17.7 - - - -
840A ASP* 3.3 26.9 - - - +
843A LEU* 4.4 17.7 - - + -
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Residues in contact with TRP 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.2 44.1 + - + +
2A ARG* 3.0 15.2 + - - +
4A LEU* 1.3 87.1 - - + +
6A SER* 1.3 66.4 + - - +
8A VAL* 3.1 21.6 - - + +
9A SER* 3.0 22.6 + - - -
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Residues in contact with SER 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ARG* 3.1 10.5 + - - -
3A SER* 3.0 23.4 + - - -
5A TRP* 1.3 77.5 - - - +
7A GLY* 1.3 56.8 + - - +
9A SER* 3.1 9.3 - - - -
10A GLY* 3.0 24.3 + - - -
68A LEU* 4.5 7.2 - - - -
69A GLY* 3.7 28.9 - - - -
70A VAL 5.1 0.2 + - - -
835A THR* 5.3 1.4 - - - +
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Residues in contact with GLY 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER 2.9 18.6 + - - -
4A LEU 3.7 0.9 - - - -
5A TRP 3.1 0.4 - - - -
6A SER* 1.3 76.0 + - - +
8A VAL* 1.3 64.7 + - - +
10A GLY 3.5 1.0 + - - -
11A LEU* 3.3 19.4 + - - +
832A ASN* 3.7 14.3 - - - +
835A THR* 4.3 14.1 - - - -
836A ILE* 3.9 15.1 - - - +
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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
----------------------------------------------------------
4A LEU* 2.9 20.6 + - + +
5A TRP* 3.1 37.0 - - + +
7A GLY* 1.3 74.1 - - - +
9A SER* 1.3 66.7 + - - +
11A LEU* 3.1 10.3 + - + +
12A GLN* 3.0 27.3 + - + +
836A ILE* 3.7 18.5 - - + +
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Residues in contact with SER 9 (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 TRP 3.0 14.3 + - - -
6A SER* 3.1 14.4 - - - -
7A GLY 3.1 0.2 - - - -
8A VAL* 1.3 79.8 - - - +
10A GLY* 1.3 63.8 + - - +
11A LEU 3.1 0.2 + - - -
12A GLN* 3.3 17.3 + - - +
13A ALA* 3.0 21.3 + - - +
43A MET* 5.1 2.3 - - - +
69A GLY* 4.2 3.0 - - - -
70A VAL 2.5 38.6 + - - +
71A SER* 5.2 0.3 - - - -
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Residues in contact with GLY 10 (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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6A SER 3.0 10.1 + - - -
7A GLY 3.5 1.3 + - - -
8A VAL 3.4 0.2 - - - -
9A SER* 1.3 80.4 - - - +
11A LEU* 1.3 55.2 + - - +
13A ALA* 3.4 6.3 - - - +
14A HIS* 2.5 41.1 + - - -
70A VAL* 4.8 11.6 - - - +
832A ASN* 3.2 20.4 - - - -
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Residues in contact with LEU 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 GLY 3.3 12.6 + - - +
8A VAL* 3.2 16.6 - - + +
9A SER 3.0 0.4 - - - -
10A GLY* 1.3 80.5 - - - +
12A GLN* 1.3 63.8 + - - +
14A HIS* 3.3 4.2 + - - +
15A GLN* 3.0 19.8 + - - +
829A TYR* 3.3 63.3 - - + +
832A ASN* 3.6 4.9 - - + +
833A SER* 4.4 13.2 - - - +
836A ILE* 3.7 23.1 - - + -
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Residues in contact with GLN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.0 18.7 + - + +
9A SER* 3.3 18.7 + - - +
11A LEU* 1.3 77.0 - - - +
13A ALA* 1.3 66.2 + - + +
15A GLN* 3.1 11.1 + - + +
16A VAL* 3.0 30.1 + - + +
70A VAL 5.8 0.6 + - - -
71A SER* 6.1 2.6 - - - -
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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 SER 3.0 13.7 + - - +
10A GLY* 3.4 13.0 - - - +
11A LEU 3.2 0.2 - - - -
12A GLN* 1.3 79.2 - - + +
14A HIS* 1.3 65.1 + - + +
16A VAL* 3.0 15.3 + - - +
17A ALA 3.0 9.9 + - - -
40A PHE* 3.7 26.9 - - + -
70A VAL* 4.4 15.9 - - + +
71A SER* 4.8 4.7 - - - -
72A VAL* 4.5 12.3 - - + -
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Residues in contact with HIS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY* 2.5 35.1 + - - +
11A LEU 3.8 3.6 - - - +
13A ALA* 1.3 76.5 - - + +
15A GLN* 1.3 62.4 + - - +
17A ALA* 3.7 5.3 - - - +
18A MET* 2.9 19.1 + - - +
40A PHE* 4.5 20.8 - + - -
70A VAL* 6.3 2.0 - - + -
824A ILE* 5.2 1.6 - - + -
825A ILE* 3.4 43.1 - - + +
828A GLY* 4.1 12.6 - - - -
829A TYR* 4.2 23.3 - - + -
832A ASN* 3.3 24.0 + - - -
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Residues in contact with GLN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 3.0 14.0 + - - +
12A GLN* 3.2 16.4 - - + +
13A ALA 3.1 0.2 - - - -
14A HIS* 1.3 77.4 - - - +
16A VAL* 1.3 64.4 + - + +
18A MET* 3.0 21.9 + - - +
19A ASP* 3.0 34.0 + - - +
829A TYR* 4.5 22.8 + - + -
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Residues in contact with VAL 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 GLN* 3.0 24.0 + - + +
13A ALA* 3.0 7.2 + - - +
15A GLN* 1.3 77.0 - - + +
17A ALA* 1.3 62.6 + - - +
19A ASP* 3.3 19.0 + - + +
20A VAL* 3.5 21.0 + - + +
38A ALA* 5.4 2.9 - - + -
72A VAL* 4.1 27.4 - - + -
75A THR* 6.0 3.6 - - + -
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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
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13A ALA 3.0 5.5 + - - -
14A HIS* 3.7 7.2 - - - +
15A GLN 3.2 0.2 - - - -
16A VAL* 1.3 77.2 - - - +
18A MET* 1.3 64.7 + - - +
20A VAL* 3.3 3.9 + - - +
21A GLU* 3.0 23.1 + - - +
38A ALA* 4.0 20.3 - - + +
40A PHE* 3.9 24.4 - - + -
825A ILE* 3.7 23.1 - - + +
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Residues in contact with MET 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 HIS 2.9 13.7 + - - +
15A GLN* 3.0 20.6 + - - +
17A ALA* 1.3 78.6 - - - +
19A ASP* 1.3 58.4 - - - +
21A GLU* 3.4 3.7 + - - +
22A GLY* 2.9 27.3 + - - -
822A LEU* 3.7 37.2 - - + +
825A ILE* 3.6 29.6 - - + +
826A GLN* 4.6 9.2 - - + +
829A TYR* 6.6 0.2 - - + -
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Residues in contact with ASP 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 GLN* 3.0 36.3 + - - +
16A VAL* 3.7 12.7 - - + +
17A ALA 3.2 0.4 - - - -
18A MET* 1.3 78.9 - - - +
20A VAL* 1.3 64.6 + - + +
22A GLY* 3.1 2.7 + - - -
23A ASN* 3.0 21.8 + - - +
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Residues in contact with VAL 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 VAL* 3.6 17.9 - - + +
17A ALA* 3.3 7.3 + - - +
19A ASP* 1.3 77.4 - - + +
21A GLU* 1.3 63.2 + - - +
23A ASN* 3.1 9.8 + - + +
24A ASN* 3.0 23.4 + - - +
36A SER* 4.0 37.5 - - - +
37A ARG* 4.4 7.4 - - - +
38A ALA* 4.7 9.0 - - + +
75A THR* 4.5 20.6 - - + -
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Residues in contact with GLU 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 3.0 16.8 + - - +
18A MET* 3.8 8.1 - - - +
20A VAL* 1.3 79.7 - - - +
22A GLY* 1.3 61.0 + - - +
24A ASN* 3.3 14.7 + - - +
25A ILE* 3.0 27.8 + - + +
36A SER 5.4 0.2 - - - +
818A SER* 2.8 46.4 - - - +
821A GLU* 2.8 32.2 - - + +
822A LEU* 3.8 24.5 - - + +
825A ILE* 5.5 4.0 - - + -
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Residues in contact with GLY 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 MET* 2.9 17.6 + - - -
19A ASP* 3.1 5.1 + - - -
21A GLU* 1.3 76.9 - - - +
23A ASN* 1.3 57.3 + - - +
25A ILE* 3.6 5.6 + - - +
26A SER* 2.9 30.1 + - - -
822A LEU* 5.6 3.6 - - - -
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Residues in contact with ASN 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 ASP 3.0 13.4 + - - +
20A VAL* 3.4 11.6 - - + +
22A GLY* 1.3 74.8 - - - +
24A ASN* 1.3 62.5 + - - +
26A SER* 2.9 17.2 + - - -
27A ASN* 2.7 38.1 + - - +
33A PHE* 4.6 15.8 - - - -
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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 VAL* 3.0 18.9 + - - +
21A GLU* 3.3 23.6 + - - +
23A ASN* 1.3 81.5 + - - +
25A ILE* 1.3 64.6 + - + +
27A ASN* 3.5 12.7 + - - +
28A VAL* 3.8 10.7 + - - +
33A PHE* 3.4 12.5 - - - -
35A TYR* 3.3 30.2 - - + +
36A SER* 2.7 37.3 + - - +
813A VAL* 4.1 14.9 - - + +
818A SER* 5.7 1.8 - - - -
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.0 29.1 + - + +
22A GLY* 4.1 4.5 - - - +
24A ASN* 1.3 74.3 - - - +
26A SER* 1.3 65.4 + - - +
27A ASN 3.2 0.5 + - - -
28A VAL* 3.4 20.3 + - + +
813A VAL* 5.5 0.7 - - - -
815A LEU* 4.8 11.2 - - + -
818A SER* 3.6 29.6 - - - +
819A LEU* 4.3 7.6 - - + -
822A LEU* 3.5 34.8 - - + -
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Residues in contact with SER 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY 2.9 19.7 + - - -
23A ASN* 2.9 14.6 + - - -
25A ILE* 1.3 79.1 - - - +
27A ASN* 1.3 60.1 + - - +
28A VAL 3.8 2.3 + - - +
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Residues in contact with ASN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASN* 2.7 35.4 + - - +
24A ASN 3.5 4.4 - - - +
25A ILE 3.2 0.2 - - - -
26A SER* 1.3 79.6 - - - +
28A VAL* 1.3 62.6 + - - +
29A ASN 4.0 0.3 + - - -
30A THR* 3.1 28.5 - - + +
33A PHE* 3.2 52.0 - - - +
811A SER* 4.6 0.3 + - - -
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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