Contacts of the helix formed by residues 12 - 42 (chain A) in PDB entry 4AL1
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 ALA 12 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER 3.1 1.0 + - - -
11A PRO* 1.3 79.7 - - + +
13A LEU* 1.3 64.7 + - - +
14A PRO 3.5 0.7 - - - -
15A ALA* 3.3 9.2 + - - +
16A PHE 3.0 18.0 + - - -
90A SER* 4.2 12.6 - - - +
94A PRO* 4.3 14.8 - - + +
96A PRO* 4.7 9.6 - - + +
99A ALA* 3.6 31.9 - - + -
100A TRP* 6.2 1.6 - - - -
103A PHE* 3.5 10.3 - - + -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 3.0 23.4 + - - +
12A ALA* 1.3 79.2 - - - +
14A PRO* 1.4 61.0 - - + +
16A PHE* 3.2 11.3 + - + +
17A LEU* 2.9 59.8 + - + +
87A PHE* 4.4 9.0 - - + -
90A SER* 4.0 17.7 - - - -
91A PHE* 3.7 39.9 - - + -
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Residues in contact with PRO 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER 3.7 5.8 - - - +
11A PRO* 3.6 13.7 - - + +
12A ALA 3.6 3.1 - - - -
13A LEU* 1.4 94.5 - - + +
15A ALA* 1.3 56.9 + - - +
17A LEU* 3.3 9.2 + - + +
18A LEU* 2.9 31.0 + - - +
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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 PRO 5.1 1.3 + - - +
12A ALA* 3.3 12.3 + - - +
13A LEU 3.3 0.4 - - - -
14A PRO* 1.3 78.1 - - - +
16A PHE* 1.3 63.9 + - - +
18A LEU* 3.3 4.0 + - - +
19A CYS* 3.0 28.2 + - - -
100A TRP* 3.4 53.4 - - + +
103A PHE* 3.9 12.1 - - + -
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Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA 3.0 7.0 + - - +
13A LEU* 3.5 12.3 - - + +
15A ALA* 1.3 76.8 - - - +
17A LEU* 1.3 76.5 + - + +
19A CYS* 3.8 1.3 - - - +
20A SER* 2.8 61.2 + - - -
82A PHE* 3.7 22.9 - + - -
83A LEU* 3.3 26.7 - - + -
86A GLY* 3.4 19.5 - - - -
87A PHE* 3.3 39.5 - + + -
90A SER* 3.3 21.5 - - - +
103A PHE* 3.6 17.1 - + + -
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 2.9 48.4 + - + +
14A PRO* 3.9 7.2 - - + +
16A PHE* 1.3 93.4 - - + +
18A LEU* 1.3 61.0 + - - +
20A SER* 4.1 4.0 - - - -
21A THR* 3.0 29.6 + - - +
87A PHE* 4.8 9.2 - - + -
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 2.9 17.0 + - - +
15A ALA* 3.7 4.0 - - - +
17A LEU* 1.3 78.5 - - - +
19A CYS* 1.3 65.9 + - - +
21A THR* 3.4 8.8 - - + +
22A LEU* 3.1 48.8 + - + +
100A TRP* 4.4 22.7 - - + -
107A LEU* 6.1 1.1 - - + -
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Residues in contact with CYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 3.0 20.5 + - - +
16A PHE 3.9 2.2 - - - +
18A LEU* 1.3 76.9 - - - +
20A SER* 1.3 66.1 + - - +
22A LEU* 3.4 6.6 + - - +
23A LEU* 3.0 29.8 + - + +
82A PHE* 4.8 7.2 - - + -
100A TRP* 4.3 17.9 - - - -
103A PHE* 3.7 39.5 - - + +
104A LEU* 4.5 1.6 - - - -
107A LEU* 4.0 25.9 - - + +
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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
----------------------------------------------------------
16A PHE* 2.8 56.2 + - - -
17A LEU* 4.1 5.2 - - - -
19A CYS* 1.3 76.8 - - - +
21A THR* 1.3 58.9 + - - +
23A LEU* 3.2 5.6 + - - +
24A VAL* 3.0 32.4 + - - +
82A PHE* 3.5 9.8 - - - -
83A LEU* 3.6 21.2 - - - +
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Residues in contact with THR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 3.0 26.2 + - - +
18A LEU* 3.4 14.6 - - + +
20A SER* 1.3 73.5 - - - +
22A LEU* 1.3 71.3 + - + +
24A VAL* 3.3 8.6 + - - +
25A ILE* 3.0 38.1 + - + +
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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
----------------------------------------------------------
18A LEU* 3.1 44.4 + - + +
19A CYS 3.6 4.3 - - - +
21A THR* 1.3 79.4 - - + +
23A LEU* 1.3 56.9 + - - +
25A ILE* 3.4 17.8 + - + +
26A LYS* 2.8 27.9 + - - +
107A LEU* 4.2 30.7 - - + -
111A VAL* 6.6 0.2 - - - -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A CYS 3.0 19.6 + - - +
20A SER* 3.2 6.5 + - - +
22A LEU* 1.3 74.4 - - - +
24A VAL* 1.3 60.3 + - - +
26A LYS* 3.3 19.3 + - + +
27A MET* 2.9 32.4 + - - +
79A ILE* 4.0 18.4 - - + -
82A PHE* 4.3 13.2 - - + -
106A PHE* 3.4 36.6 - - + -
107A LEU* 3.8 27.8 - - + +
110A ARG* 3.7 27.1 - - + -
111A VAL* 4.6 1.8 - - + -
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER 3.0 19.1 + - - +
21A THR* 3.7 11.4 - - - +
23A LEU* 1.3 73.5 - - - +
25A ILE* 1.3 61.0 + - + +
27A MET* 3.0 14.5 + - + +
28A TYR* 2.9 60.2 + - + +
79A ILE* 5.3 2.9 - - + -
80A TYR* 6.1 1.3 - - + -
83A LEU* 4.2 26.9 - - + -
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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 THR* 3.0 34.4 + - + +
22A LEU* 3.7 18.4 - - + +
24A VAL* 1.3 76.5 - - + +
26A LYS* 1.3 57.7 + - - +
28A TYR* 3.1 21.0 + - + +
29A VAL* 2.9 36.6 + - + +
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU 2.8 17.4 + - - +
23A LEU* 3.4 15.7 - - + +
24A VAL 3.2 0.2 - - - -
25A ILE* 1.3 76.8 - - - +
27A MET* 1.3 59.9 + - - +
29A VAL* 3.4 10.1 + - - +
30A VAL* 3.1 39.8 + - - +
75A ASP* 2.5 31.6 + - - -
79A ILE* 3.8 22.2 - - - -
110A ARG 4.2 11.9 - - - +
111A VAL* 4.2 20.2 - - + -
114A THR* 2.8 27.6 + - - +
202A PLM 3.6 20.1 - - + +
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Residues in contact with MET 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 2.9 16.5 + - - +
24A VAL* 3.0 13.2 + - + +
26A LYS* 1.3 73.5 - - - +
28A TYR* 1.3 68.0 + - + +
30A VAL* 3.2 6.1 + - - +
31A ALA* 3.0 20.4 + - - +
72A HIS* 3.9 20.0 + - + +
75A ASP* 3.5 37.0 - - + +
76A MET* 3.7 13.7 - - + +
79A ILE* 3.8 31.0 - - + -
80A TYR* 3.5 44.0 - - + +
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 2.9 41.6 + - + +
25A ILE* 3.1 21.5 + - + +
27A MET* 1.3 79.0 - - + +
29A VAL* 1.3 57.3 + - + +
31A ALA* 3.1 10.6 + - + +
32A ILE* 2.9 39.8 + - + +
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 2.9 28.3 + - + +
26A LYS* 3.5 10.1 - - - +
27A MET 3.2 0.4 - - - -
28A TYR* 1.3 76.2 - - + +
30A VAL* 1.3 58.3 + - - +
32A ILE* 3.3 14.2 + - + +
33A ILE* 2.8 45.5 + - + +
202A PLM 3.7 24.0 - - + -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 3.1 34.9 + - - +
27A MET* 3.2 9.8 + - - +
29A VAL* 1.3 75.8 - - - +
31A ALA* 1.3 56.5 + - - +
33A ILE* 3.4 8.3 + - + +
34A THR* 2.8 35.7 + - - +
68A CYS* 3.9 13.7 - - + +
71A ALA* 4.7 5.2 - - + -
72A HIS* 3.7 33.7 - - + +
75A ASP* 4.0 3.4 - - - +
114A THR* 3.7 20.2 - - + -
118A LEU* 4.6 8.7 - - + -
202A PLM 4.9 3.1 - - + -
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET 3.0 9.9 + - - +
28A TYR* 3.5 13.7 - - + +
30A VAL* 1.3 76.0 - - - +
32A ILE* 1.3 63.9 + - + +
34A THR* 3.3 7.7 + - - -
35A GLY* 3.1 19.4 + - - -
72A HIS* 3.8 23.9 - - + -
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Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 2.9 26.4 + - + +
29A VAL* 3.6 16.4 - - + +
31A ALA* 1.3 76.8 - - + +
33A ILE* 1.3 65.5 + - + +
35A GLY* 3.2 3.7 + - - -
36A GLN* 3.0 45.7 + - + +
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 2.8 43.6 + - + +
30A VAL* 3.4 6.0 + - - +
32A ILE* 1.3 72.7 - - + +
34A THR* 1.3 56.8 + - - +
36A GLN* 3.2 16.6 + - - +
37A VAL* 2.8 37.1 + - + +
68A CYS* 3.9 20.9 - - - -
118A LEU* 4.1 21.8 - - + -
202A PLM 4.2 12.8 - - + -
203A PLM 4.1 36.1 - - + -
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Residues in contact with THR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 2.8 27.3 + - - +
31A ALA* 3.5 8.4 - - - -
33A ILE* 1.3 75.1 - - - +
35A GLY* 1.3 64.5 + - - +
37A VAL* 3.3 3.0 + - - +
38A ARG* 3.0 37.8 + - - +
65A VAL* 4.6 6.2 - - + +
68A CYS* 3.3 35.2 + - + +
69A LEU* 4.2 24.7 - - + +
72A HIS* 4.8 4.0 + - - -
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Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA 3.1 14.0 + - - -
32A ILE* 3.2 4.0 + - - -
34A THR* 1.3 78.0 - - - +
36A GLN* 1.3 60.1 + - - +
38A ARG* 3.4 11.8 + - - +
39A LEU* 3.1 23.6 + - - +
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Residues in contact with GLN 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 3.0 34.7 + - + +
33A ILE* 3.2 21.5 + - + +
35A GLY* 1.3 75.5 - - - +
37A VAL* 1.3 59.0 + - + +
39A LEU 3.3 0.9 + - - -
40A ARG* 2.8 74.9 + - - +
203A PLM 5.9 2.6 - - - +
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 2.8 35.4 + - + +
34A THR* 3.7 4.7 - - - +
36A GLN* 1.3 75.0 - - + +
38A ARG* 1.3 59.2 + - - +
40A ARG* 4.5 4.7 - - - -
41A LYS* 2.8 39.7 + - + +
64A ASP* 3.9 26.2 - - + -
65A VAL* 3.7 22.9 - - + +
68A CYS* 4.1 8.7 - - - -
203A PLM 4.3 16.4 - - + -
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Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.0 25.8 + - - +
35A GLY* 3.6 12.1 - - - +
37A VAL* 1.3 75.0 - - - +
39A LEU* 1.3 57.8 + - - +
42A LYS* 2.9 24.9 + - - -
43A ALA 3.0 42.3 + - - +
44A PHE* 3.7 20.1 - - + +
45A ALA* 3.4 36.8 - - - +
49A ASP* 6.1 0.7 - - - -
60A ARG 5.1 2.0 + - - -
65A VAL* 3.6 34.7 - - + +
66A GLU* 5.4 0.6 + - - -
69A LEU* 3.8 22.6 - - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY 3.1 11.2 + - - +
36A GLN* 3.6 7.9 - - - +
38A ARG* 1.3 78.5 - - - +
40A ARG* 1.3 85.0 + - - +
42A LYS* 3.4 22.4 + - - +
44A PHE* 4.2 12.9 - - + -
53A HIS* 3.4 37.7 - - + +
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLN* 2.8 68.2 + - - +
37A VAL* 4.0 4.5 - - - +
39A LEU* 1.3 105.6 - - - +
41A LYS* 1.3 63.8 + - + +
42A LYS* 3.6 4.0 + - - +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 2.8 32.0 + - + +
40A ARG* 1.3 75.5 - - + +
42A LYS* 1.3 66.0 + - - +
43A ALA* 4.3 6.2 - - + +
60A ARG* 2.9 20.1 + - - -
62A ASP* 2.7 50.8 + - - +
63A PRO* 4.6 4.4 - - - +
64A ASP* 3.0 28.4 + - - +
65A VAL* 5.0 0.2 - - + -
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG 2.9 11.4 + - - -
39A LEU* 3.6 14.6 + - - +
40A ARG 3.3 4.4 - - - +
41A LYS* 1.3 77.7 - - - +
43A ALA* 1.3 56.9 + - - +
44A PHE* 3.7 14.6 - - + -
53A HIS* 2.9 37.2 + - - +
54A GLY* 4.7 0.9 - - - -
58A TYR* 3.4 49.5 - - + +
60A ARG* 2.9 22.6 + - - +
----------------------------------------------------------
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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