Contacts of the helix formed by residues 21 - 59 (chain A) in PDB entry 5AJI
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 GLN 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.1 22.8 - - - +
19A ALA 2.8 9.7 + - - +
20A ASN* 1.3 71.7 - - - +
22A ALA* 1.3 63.9 + - - +
23A LEU 3.4 1.1 - - - -
24A LEU* 3.6 31.2 - - + +
25A LEU* 3.7 37.4 + - + +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA 4.7 0.8 + - - -
20A ASN 3.6 0.8 - - - -
21A GLN* 1.3 79.3 - - - +
23A LEU* 1.3 58.3 + - + +
25A LEU* 5.0 0.7 - - - +
26A SER* 3.3 22.5 + - - -
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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
----------------------------------------------------------
20A ASN* 4.2 23.8 - - + +
22A ALA* 1.3 77.3 - - + +
24A LEU* 1.3 68.8 + - + +
26A SER* 3.5 17.3 - - - +
27A TYR* 3.8 33.5 + - + +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASN 4.1 5.6 - - - +
21A GLN* 3.6 42.5 + - + +
22A ALA 3.3 0.8 - - - -
23A LEU* 1.3 81.9 - - + +
25A LEU* 1.3 66.7 + - + +
26A SER 3.1 0.9 - - - -
27A TYR* 3.0 31.6 + - + +
28A ALA* 3.6 3.1 + - - +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 3.7 38.5 + - + +
22A ALA 5.0 0.9 - - - +
24A LEU* 1.3 82.6 - - + +
26A SER* 1.3 65.5 + - - +
28A ALA* 3.1 31.4 + - + +
29A VAL* 3.4 12.4 + - - +
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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 ALA 3.3 21.7 + - - -
23A LEU* 3.5 16.2 - - - +
25A LEU* 1.3 77.6 - - - +
27A TYR* 1.3 64.1 + - - +
29A VAL* 3.9 17.2 + - - +
30A ASN* 4.2 5.5 + - - +
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Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.8 34.3 - - + +
24A LEU* 3.0 18.2 + - + +
26A SER* 1.3 75.9 - - - +
28A ALA* 1.3 67.6 + - - +
29A VAL 3.1 2.5 - - - -
30A ASN* 2.6 40.6 + - - +
31A ILE* 3.0 15.7 + - + +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU 3.6 3.1 + - - +
25A LEU* 3.2 30.7 - - + +
27A TYR* 1.3 78.6 - - - +
29A VAL* 1.3 54.7 + - + +
31A ILE* 3.3 11.4 + - - +
32A VAL* 2.9 38.0 + - + +
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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 LEU 3.7 12.8 - - - +
26A SER* 4.1 12.1 - - - +
27A TYR 3.1 1.0 - - - -
28A ALA* 1.3 77.5 - - + +
30A ASN* 1.3 58.3 + - - +
32A VAL* 3.2 11.8 - - + +
33A ALA* 2.9 31.9 + - + +
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Residues in contact with ASN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 4.2 4.0 + - - +
27A TYR* 2.6 42.1 + - - +
29A VAL* 1.3 78.9 - - - +
31A ILE* 1.3 72.4 + - - +
33A ALA* 3.6 6.3 - - - +
34A ALA* 2.7 36.3 + - - +
88A ARG* 3.1 30.0 + - + +
89A VAL* 4.0 17.6 - - - +
90A GLY 5.2 0.2 - - - +
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Residues in contact with ILE 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 TYR* 3.0 23.0 + - + +
28A ALA* 3.6 12.1 - - - +
30A ASN* 1.3 92.4 + - - +
32A VAL* 1.3 64.7 + - + +
34A ALA* 3.5 6.7 + - - +
35A LEU* 3.2 32.4 + - + +
89A VAL* 4.3 15.5 - - + -
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 2.9 21.1 + - + +
29A VAL* 3.2 20.9 - - + +
31A ILE* 1.3 75.6 - - + +
33A ALA* 1.3 57.9 + - - +
35A LEU* 3.1 13.2 + - + +
36A ALA* 2.7 35.5 + - - +
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Residues in contact with ALA 33 (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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29A VAL* 2.9 24.2 + - + +
30A ASN* 3.6 8.1 - - - +
32A VAL* 1.3 77.4 - - + +
34A ALA* 1.3 54.9 + - - +
36A ALA* 3.1 8.5 + - - +
37A ILE* 2.8 48.2 + - + +
88A ARG* 5.3 6.3 - - + -
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Residues in contact with ALA 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 ASN 2.7 21.9 + - - +
31A ILE* 3.5 6.7 - - - +
33A ALA* 1.3 73.3 - - - +
35A LEU* 1.3 62.5 + - + +
37A ILE* 3.5 6.4 + - - +
38A ILE* 3.1 31.5 + - + +
85A ALA* 3.4 19.9 - - + +
88A ARG* 5.1 1.3 - - + +
89A VAL* 3.3 27.4 - - + +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 3.2 23.7 + - + +
32A VAL* 3.1 16.2 + - + +
34A ALA* 1.3 74.1 - - + +
36A ALA* 1.3 61.2 + - - +
38A ILE* 3.1 19.5 + - + +
39A ILE* 2.8 44.3 + - + +
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL 2.7 17.6 + - - +
33A ALA* 3.4 13.0 - - - +
35A LEU* 1.3 73.5 - - - +
37A ILE* 1.3 52.7 + - + +
39A ILE* 3.3 9.4 + - - +
40A VAL* 2.8 45.9 + - + +
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA* 2.8 34.0 + - + +
34A ALA* 3.8 8.5 - - - +
36A ALA* 1.3 73.1 - - + +
38A ILE* 1.3 53.0 + - - +
40A VAL* 4.0 4.8 - - - +
41A GLY 2.7 31.2 + - - -
81A THR* 3.2 33.4 - - + +
84A ALA* 4.4 15.9 - - + +
85A ALA* 3.9 14.6 - - + +
88A ARG* 4.4 17.9 - - + +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 3.1 25.7 + - + +
35A LEU* 3.1 21.7 + - + +
37A ILE* 1.3 74.7 - - - +
39A ILE* 1.3 61.8 + - + +
41A GLY* 3.8 0.3 - - - -
42A LEU* 2.8 56.6 + - + +
81A THR* 3.6 10.8 - - + +
82A LEU* 5.1 17.7 - - + -
85A ALA* 3.6 17.9 - - + -
86A LEU* 6.2 2.2 - - + -
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Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 2.8 35.8 + - + +
36A ALA* 3.7 7.4 - - - +
38A ILE* 1.3 79.6 - - + +
40A VAL* 1.3 65.2 + - + +
42A LEU* 3.2 8.7 + - + +
43A ILE* 3.0 46.4 + - + +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 2.8 28.8 + - + +
37A ILE* 4.0 4.9 - - - +
39A ILE* 1.3 74.7 - - + +
41A GLY* 1.3 57.9 + - - +
43A ILE* 3.5 9.4 + - + +
44A ILE* 2.9 38.1 + - + +
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE 2.7 22.3 + - - -
40A VAL* 1.3 73.5 - - - +
42A LEU* 1.3 57.9 + - - +
44A ILE* 3.3 11.2 - - - +
45A ALA* 2.9 31.2 + - - +
77A ILE* 4.0 2.6 - - - +
78A ILE* 5.7 0.9 - - - -
81A THR* 3.5 23.6 - - - -
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 2.8 45.4 + - + +
39A ILE* 3.2 8.3 + - + +
41A GLY* 1.3 74.4 - - - +
43A ILE* 1.3 59.6 + - + +
45A ALA* 3.4 5.3 + - - +
46A ARG* 3.1 26.0 + - - +
74A ARG* 4.6 10.6 + - - +
78A ILE* 3.7 31.6 - - + -
81A THR* 4.6 1.3 - - + +
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 3.0 38.6 + - + +
40A VAL* 3.8 8.5 - - + +
42A LEU* 1.3 75.0 - - + +
44A ILE* 1.3 64.8 + - - +
45A ALA 3.1 1.6 - - - -
46A ARG* 3.2 22.6 - - + +
47A MET* 3.3 25.9 + - + +
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Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 2.9 26.4 + - + +
41A GLY* 3.3 19.7 - - - +
43A ILE* 1.3 76.0 - - - +
45A ALA* 1.3 58.6 + - - +
47A MET* 4.0 20.1 - - + +
48A ILE* 3.3 42.2 + - + +
77A ILE* 4.3 11.7 - - + -
81A THR* 5.5 0.2 - - - +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLY 2.9 19.3 + - - +
42A LEU* 3.5 7.2 - - - +
43A ILE 3.1 0.2 - - - -
44A ILE* 1.3 75.4 - - - +
46A ARG* 1.3 58.4 + - - +
48A ILE* 3.4 1.0 + - - +
49A SER* 2.5 38.2 + - - -
74A ARG* 4.1 5.6 - - + +
77A ILE* 3.7 26.4 - - + +
78A ILE* 3.9 26.7 - - + -
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU 3.1 10.8 + - - +
43A ILE* 3.2 15.5 - - + +
45A ALA* 1.3 77.1 - - - +
47A MET* 1.3 63.6 + - + +
49A SER* 3.0 11.4 + - - -
50A ASN* 3.0 44.4 + - - +
67A R1A 4.0 17.8 + - - +
74A ARG* 3.2 40.5 - - - +
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Residues in contact with MET 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.3 24.1 + - + +
44A ILE* 4.0 29.6 - - + +
45A ALA 3.2 0.6 - - - -
46A ARG* 1.3 83.3 - - + +
48A ILE* 1.3 63.0 + - + +
49A SER 3.2 0.2 - - - -
50A ASN* 3.3 5.0 + - - +
51A ALA* 2.8 32.7 + - - +
54A ARG* 4.5 7.4 + - - +
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Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.3 41.2 + - + +
47A MET* 1.3 82.1 - - + +
49A SER* 1.3 56.9 + - - +
51A ALA* 3.6 6.8 + - - +
52A VAL* 3.1 31.2 + - + +
73A VAL* 4.0 11.2 - - + -
77A ILE* 3.6 29.2 - - + -
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 2.5 23.9 + - - -
46A ARG* 3.0 11.4 + - - -
48A ILE* 1.3 77.2 - - - +
50A ASN* 1.3 61.2 + - - +
52A VAL* 3.1 21.2 - - - +
53A ASN* 3.4 12.3 + - - +
67A R1A 5.0 5.1 - - - +
70A SER* 3.6 26.9 - - - -
73A VAL* 4.2 3.4 - - - -
74A ARG* 3.4 31.7 + - - +
----------------------------------------------------------
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Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 3.0 52.8 + - - +
47A MET* 3.8 2.8 - - - +
49A SER* 1.3 77.4 + - - +
51A ALA* 1.3 59.2 + - - +
52A VAL 3.3 0.2 - - - -
53A ASN* 2.9 7.0 + - - +
54A ARG* 2.9 58.9 + - + +
67A R1A 4.1 24.4 - - - +
74A ARG* 5.4 1.0 + - - -
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A MET 2.8 18.6 + - - +
48A ILE* 3.6 8.3 - - - +
50A ASN* 1.3 75.7 - - - +
52A VAL* 1.3 62.2 + - + +
54A ARG* 3.5 22.9 + - - +
55A LEU* 3.1 24.4 + - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.1 19.9 + - + +
49A SER* 3.1 26.5 - - - +
51A ALA* 1.3 78.6 - - + +
53A ASN* 1.3 60.6 + - - +
55A LEU* 3.4 13.5 + - + +
56A MET* 3.1 35.6 + - + +
70A SER* 4.0 7.9 - - - +
73A VAL* 4.1 29.6 - - + -
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER 3.4 8.7 - - - +
50A ASN* 2.9 15.0 + - - +
52A VAL* 1.3 77.8 - - - +
54A ARG* 1.3 64.8 + - + +
56A MET* 3.4 3.4 + - - +
57A ILE* 3.0 42.1 + - - +
66A ALA* 3.7 12.9 - - - +
67A R1A 3.8 40.1 + - - +
70A SER* 3.2 20.2 + - - +
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A MET* 4.5 6.9 + - - +
50A ASN* 2.9 42.5 + - + +
51A ALA* 3.5 24.8 - - - +
53A ASN* 1.3 76.3 - - + +
55A LEU* 1.3 57.8 + - - +
57A ILE* 4.0 7.2 - - - +
58A SER* 2.8 35.3 + - - -
----------------------------------------------------------
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA 3.1 18.8 + - - +
52A VAL* 3.5 15.3 - - + +
53A ASN 3.2 0.2 - - - -
54A ARG* 1.3 76.3 - - - +
56A MET* 1.3 59.0 + - + +
58A SER* 2.9 21.2 + - - +
59A ARG* 3.1 31.0 + - + +
----------------------------------------------------------
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Residues in contact with MET 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.1 27.7 + - + +
53A ASN* 3.8 0.9 - - - +
54A ARG 3.2 0.2 - - - -
55A LEU* 1.3 76.9 - - + +
57A ILE* 1.3 65.6 + - - +
59A ARG* 3.0 12.1 + - - -
60A LYS 3.3 0.2 + - - -
61A ILE* 3.1 47.3 + - + +
66A ALA* 3.4 32.5 - - + +
69A LEU* 4.0 29.8 - - + -
70A SER* 3.2 29.4 - - - +
73A VAL* 5.9 1.1 - - + -
----------------------------------------------------------
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASN* 3.0 40.0 + - - +
54A ARG* 4.0 5.6 - - - +
56A MET* 1.3 75.7 - - - +
58A SER* 1.3 59.5 - - - +
60A LYS* 3.1 22.2 + - - +
61A ILE 4.0 10.4 - - - +
63A ALA* 4.6 17.5 - - + +
66A ALA* 4.0 11.9 - - + -
----------------------------------------------------------
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ARG 2.8 15.6 + - - -
55A LEU* 2.9 24.6 + - - +
57A ILE* 1.3 79.9 - - - +
59A ARG* 1.3 55.7 + - - +
60A LYS* 3.2 16.4 + - - +
----------------------------------------------------------
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.1 28.2 + - + +
56A MET* 3.0 8.9 + - - +
58A SER* 1.3 79.8 + - - +
60A LYS* 1.3 69.0 + - - +
61A ILE* 3.2 16.8 + - + +
46B ARG* 4.5 17.2 - - - +
----------------------------------------------------------
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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