Contacts of the helix formed by residues 38 - 66 (chain I) in PDB entry 1S3Q
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 LEU 38 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I PHE* 2.9 19.3 + - + +
36I ILE* 3.9 22.0 - - + +
37I GLY* 1.3 79.7 - - - +
39I LYS* 1.3 59.7 + - - +
41I PHE* 3.3 22.3 + - + +
42I SER* 3.0 25.8 + - - -
85I PRO* 3.7 30.1 - - + -
153I LEU* 4.4 19.3 - - + -
154I LEU* 4.3 20.2 - - + -
157I ASP* 3.3 28.3 - - + +
142K LYS* 4.9 0.7 - - - -
145K LEU* 4.9 5.6 - - + -
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Residues in contact with LYS 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I ASP* 2.8 50.2 + - - +
37I GLY* 3.4 14.6 + - - +
38I LEU* 1.3 71.1 - - - +
40I GLY* 1.3 60.3 + - - +
42I SER* 3.5 11.9 + - - -
43I ASN* 3.0 27.4 + - - +
46I ARG* 5.9 2.0 - - - +
157I ASP* 3.4 3.4 + - - +
161I SER* 4.6 1.6 - - - -
61J ASP* 5.7 2.0 + - - -
138K ASP* 4.9 18.6 - - - +
142K LYS* 5.6 4.2 - - - +
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Residues in contact with GLY 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I LYS* 1.3 76.6 - - - +
41I PHE* 1.3 63.3 + - - -
43I ASN* 3.4 1.6 + - - +
44I TRP 3.1 16.8 + - - -
157I ASP* 2.8 31.0 + - - -
160I LEU* 3.4 20.0 - - - +
161I SER* 3.4 20.6 + - - -
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Residues in contact with PHE 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I PHE* 3.5 37.5 - + + -
38I LEU* 3.3 12.8 + - + +
40I GLY* 1.3 71.3 - - - +
42I SER* 1.3 66.4 + - - +
44I TRP* 3.2 5.3 + - - +
45I MSE 3.0 25.5 + - - +
85I PRO* 4.3 6.1 - - + -
89I PHE* 3.7 29.2 - + - -
139I ILE* 4.8 0.2 - - + -
143I LEU* 4.1 11.9 - - + -
153I LEU* 4.0 23.6 - - + -
156I LEU* 3.7 24.7 - - + -
157I ASP* 3.1 44.7 + - + -
160I LEU* 3.7 19.1 - - + -
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Residues in contact with SER 42 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ALA* 2.7 33.1 + - - +
33I PHE* 3.8 5.5 - - - +
34I ASP* 3.2 17.5 + - - +
38I LEU 3.0 13.2 + - - -
39I LYS* 3.5 24.0 - - - -
41I PHE* 1.3 77.8 - - - +
43I ASN* 1.3 58.6 + - - +
45I MSE 3.1 4.9 + - - +
46I ARG* 2.9 34.4 + - - +
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Residues in contact with ASN 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I LYS 3.0 15.6 + - - +
40I GLY* 3.5 7.4 - - - +
42I SER* 1.3 79.6 - - - +
44I TRP* 1.3 55.2 + - - +
46I ARG* 3.1 9.2 + - - +
47I VAL* 2.9 39.9 + - - +
160I LEU 3.1 18.2 - - - +
161I SER* 3.4 13.9 + - - +
163I ARG* 3.1 25.8 + - - +
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Residues in contact with TRP 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I TYR* 5.6 0.4 - + - -
40I GLY 3.1 13.2 + - - +
41I PHE* 3.4 9.6 - - - +
43I ASN* 1.3 80.6 + - - +
45I MSE 1.3 90.6 + - + +
47I VAL* 3.4 0.5 + - - +
48I GLN* 2.9 47.5 + - + -
89I PHE* 3.7 15.3 - + + -
92I VAL* 4.6 14.4 - - + -
135I SER* 4.7 17.6 - - - -
136I ALA* 5.2 3.4 - - + -
139I ILE* 3.5 26.4 - - + +
160I LEU* 3.7 33.6 - - + +
163I ARG* 3.3 50.2 + - + +
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Residues in contact with MSE 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I TYR* 3.5 31.6 - - - +
29I MSE 3.7 34.8 - - + +
30I ALA* 3.7 11.4 - - + +
33I PHE* 3.9 14.4 - - + -
41I PHE 3.0 15.3 + - - +
42I SER 3.1 8.3 + - - +
44I TRP* 1.3 102.3 - - + +
46I ARG* 1.3 60.3 + - - +
48I GLN* 3.2 2.1 + - - +
49I TRP* 2.8 30.4 + - - +
89I PHE* 3.7 23.6 - - + -
92I VAL* 3.8 15.5 - - + -
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Residues in contact with ARG 46 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I LEU* 3.8 21.5 - - - -
30I ALA* 3.9 11.9 - - + +
34I ASP* 5.4 3.4 + - - -
39I LYS* 5.9 2.2 - - - +
42I SER* 2.9 21.2 + - - +
43I ASN* 3.1 11.2 + - - +
45I MSE 1.3 75.5 - - - +
47I VAL* 1.3 57.5 + - + +
49I TRP* 3.3 13.3 - - - -
50I GLN* 3.0 38.4 + - - +
57J MSE 4.0 31.6 + - - +
60J PHE* 3.5 19.0 - - - -
61J ASP* 2.7 42.0 + - - -
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Residues in contact with VAL 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I ASN* 2.9 28.4 + - - +
44I TRP 3.6 6.3 - - - +
46I ARG* 1.3 76.3 - - + +
48I GLN* 1.3 56.1 + - - +
50I GLN* 3.2 16.7 + - - +
51I GLU* 2.9 38.4 + - + +
163I ARG* 3.4 52.3 - - - +
164I GLN* 3.6 24.9 - - - +
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Residues in contact with GLN 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I TYR* 3.3 31.6 - - + -
44I TRP* 2.9 38.3 + - + +
45I MSE 3.6 5.2 - - - +
47I VAL* 1.3 74.7 - - - +
49I TRP* 1.3 66.4 + - - +
51I GLU* 3.2 10.0 + - - +
52I GLU* 2.8 55.7 + - - +
55I HIS* 4.8 0.6 - - - -
92I VAL* 6.2 0.2 - - + -
132I GLU* 3.0 27.6 + - - +
163I ARG* 2.8 36.6 + - - +
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Residues in contact with TRP 49 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ILE* 5.5 1.3 - - + -
23I ALA* 3.4 53.2 - - + +
24I TYR* 4.3 13.5 - + - -
26I TYR* 4.2 1.7 - - - +
27I LEU* 3.9 35.9 - - + +
45I MSE 2.8 19.1 + - - +
46I ARG* 3.3 27.8 - - - +
48I GLN* 1.3 73.4 - - - +
50I GLN* 1.3 78.0 + - + +
52I GLU 3.4 0.2 + - - -
53I LEU* 3.1 51.7 + - + +
20J ILE* 4.9 8.7 - - + -
53J LEU* 4.6 22.2 - - + -
57J MSE 3.7 41.5 - - + +
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Residues in contact with GLN 50 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I ARG* 3.0 30.1 + - - +
47I VAL* 3.6 19.0 + - - +
49I TRP* 1.3 92.0 - - + +
51I GLU* 1.3 62.5 + - + +
53I LEU* 3.3 10.8 + - + +
54I MSE 3.1 20.8 + - - +
164I GLN 5.0 6.1 + - - -
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Residues in contact with GLU 51 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I VAL* 2.9 30.2 + - + +
48I GLN* 3.2 15.9 + - - +
50I GLN* 1.3 75.4 - - + +
52I GLU* 1.3 61.5 + - - +
54I MSE 3.2 17.4 + - + +
55I HIS* 2.9 39.0 + - - +
128I GLU* 4.4 11.3 - - - +
132I GLU* 4.5 0.5 - - - +
163I ARG* 3.0 29.2 + - - -
164I GLN 5.0 4.2 - - - +
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Residues in contact with GLU 52 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I GLU* 3.1 12.2 - - - +
22I SER* 3.8 11.2 - - - -
23I ALA* 3.5 33.2 - - + +
26I TYR* 3.5 12.7 - - + -
48I GLN* 2.8 38.7 + - - +
51I GLU* 1.3 72.1 - - - +
53I LEU* 1.3 64.1 + - - +
55I HIS* 3.2 6.8 + - - +
56I ALA* 3.0 22.7 + - - +
96I GLU* 3.3 3.5 - - - +
132I GLU* 3.3 0.2 - - - +
917I ZN 2.1 30.5 - - - -
918I ZN 2.2 30.0 - - - -
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Residues in contact with LEU 53 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ILE* 4.5 24.5 - - + -
23I ALA* 3.3 22.4 - - + -
49I TRP* 3.1 55.9 + - + +
50I GLN* 3.5 11.2 - - + +
52I GLU* 1.3 77.8 - - - +
54I MSE 1.3 57.4 + - - +
56I ALA* 3.2 5.4 + - + +
57I MSE 2.9 35.1 + - + +
49J TRP* 4.6 20.9 - - + -
53J LEU* 4.5 12.8 - - + -
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Residues in contact with MSE 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I GLN 3.1 13.1 + - - +
51I GLU* 3.2 21.5 + - + +
53I LEU* 1.3 72.8 - - - +
55I HIS* 1.3 85.7 + - + +
57I MSE 3.3 6.0 + - - +
58I LYS* 2.9 40.1 + - + +
124I TRP* 4.1 20.2 - - + -
128I GLU* 6.2 0.2 - - - -
----------------------------------------------------------
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Residues in contact with HIS 55 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I GLU* 3.4 15.6 - - - +
48I GLN* 4.8 1.3 - - - -
51I GLU* 2.9 31.5 + - - +
52I GLU* 3.1 15.6 + - - +
54I MSE 1.3 93.7 - - + +
56I ALA* 1.3 63.0 + - - +
58I LYS* 4.6 0.7 - - - -
59I MSE 3.3 6.8 + - - +
124I TRP* 3.7 17.8 - + - -
125I TYR* 2.7 36.4 + + + -
128I GLU* 3.7 36.0 + - + +
129I GLN* 4.9 0.9 + - - -
132I GLU* 4.2 2.5 - - - -
917I ZN 2.0 33.6 - - - -
918I ZN 3.8 9.0 - - - -
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Residues in contact with ALA 56 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I ILE* 3.9 11.0 - - + +
19I GLU* 3.8 16.8 - - + +
20I ILE* 3.7 30.3 - - + -
52I GLU 3.0 9.2 + - - +
53I LEU* 3.2 11.0 + - - +
55I HIS* 1.3 79.1 - - - +
57I MSE 1.3 67.2 + - + +
59I MSE 3.3 6.0 + - - +
60I PHE* 2.8 27.2 + - - +
----------------------------------------------------------
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Residues in contact with MSE 57 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I ILE* 5.1 1.1 - - + -
20I ILE* 4.6 5.8 - - + -
53I LEU* 2.9 19.9 + - + +
54I MSE 3.3 6.3 + - - +
56I ALA* 1.3 89.5 - - + +
58I LYS* 1.3 61.0 + - - +
60I PHE* 3.4 13.2 - - + +
61I ASP* 2.9 36.5 + - - +
27J LEU* 3.8 35.4 - - + -
46J ARG* 3.9 24.2 + - - +
49J TRP* 3.7 38.4 - - + +
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Residues in contact with LYS 58 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I MSE 2.9 24.5 + - - +
55I HIS 3.7 0.2 - - - +
56I ALA 3.3 0.2 - - - -
57I MSE 1.3 78.3 - - - +
59I MSE 1.3 56.2 + - - +
61I ASP* 3.5 6.0 + - - +
62I PHE* 3.0 26.0 + - - +
121I PHE* 3.6 24.6 + - + -
124I TRP* 3.6 57.2 - - + +
125I TYR* 3.4 18.8 - - + +
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Residues in contact with MSE 59 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I LEU* 3.6 36.6 - - + +
15I GLN* 3.6 31.2 - - + +
16I ILE* 3.7 18.2 - - + -
19I GLU* 5.2 1.6 - - - +
55I HIS 3.3 3.3 + - - +
56I ALA* 3.3 8.4 + - - +
58I LYS* 1.3 76.1 - - - +
60I PHE* 1.3 64.0 + - - +
62I PHE* 3.2 1.4 + - + +
63I VAL* 3.0 29.5 + - + +
103I ILE* 4.8 0.9 - - + -
106I LEU* 4.8 0.2 - - + -
121I PHE* 3.8 19.5 - - + -
122I LEU* 4.2 15.3 - - + -
125I TYR* 3.3 39.4 + - + +
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Residues in contact with PHE 60 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I ILE* 3.7 13.5 - - + +
56I ALA 2.8 17.4 + - - +
57I MSE 3.4 22.7 - - + +
59I MSE 1.3 71.3 - - - +
61I ASP* 1.3 65.6 + - - +
63I VAL 3.5 0.3 + - - -
64I SER* 3.3 20.4 + - - -
70I VAL* 3.6 36.6 - - + +
72I LEU* 4.5 5.4 - - + -
27J LEU* 3.7 48.5 - - + -
30J ALA* 4.6 2.0 - - + -
31J SER* 4.0 18.2 - - - -
34J ASP* 4.1 17.0 - - - -
46J ARG* 3.7 29.2 - - - -
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Residues in contact with ASP 61 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I MSE 2.9 18.0 + - - +
58I LYS* 3.8 6.9 - - - +
60I PHE* 1.3 80.7 - - - +
62I PHE* 1.3 56.3 + - - +
64I SER* 3.6 5.2 + - - -
65I GLU* 2.9 30.7 + - - +
34J ASP* 5.5 1.0 - - - +
39J LYS* 5.6 3.1 + - - -
46J ARG* 2.7 43.0 + - - -
----------------------------------------------------------
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Residues in contact with PHE 62 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ILE* 4.7 0.9 - - + -
12I LEU* 4.1 17.9 - - + -
58I LYS 3.0 8.8 + - - +
59I MSE 3.2 3.8 + - + +
61I ASP* 1.3 73.5 - - - +
63I VAL* 1.3 69.2 + - + +
65I GLU* 3.1 13.4 + - + +
66I ARG* 2.9 56.8 + - + +
117I ALA* 3.7 17.9 - - + -
118I THR* 3.4 28.9 - - - -
121I PHE* 3.5 64.8 - + + -
----------------------------------------------------------
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Residues in contact with VAL 63 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ILE* 5.2 2.0 - - + +
9I VAL* 4.2 11.4 - - + +
12I LEU* 3.7 39.5 - - + -
13I ASN* 4.2 11.0 - - - +
16I ILE* 4.3 4.7 - - + -
59I MSE 3.0 22.0 + - + +
62I PHE* 1.3 79.3 - - + +
64I SER* 1.3 55.7 + - - +
66I ARG* 3.3 9.3 + - - +
68I GLY* 2.8 51.4 + - - -
69I ARG 4.0 6.3 - - - +
70I VAL* 3.7 20.4 - - + -
----------------------------------------------------------
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Residues in contact with SER 64 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I PHE* 3.3 17.1 + - - -
61I ASP* 3.7 7.2 - - - -
62I PHE 3.2 0.6 - - - -
63I VAL* 1.3 77.0 - - - +
65I GLU* 1.3 64.4 + - - +
67I GLY* 3.0 15.2 + - - -
68I GLY 3.6 11.8 + - - +
70I VAL* 4.6 5.1 - - - +
34J ASP* 3.2 37.2 + - - +
39J LYS* 5.1 4.2 + - - -
----------------------------------------------------------
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Residues in contact with GLU 65 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I ASP 2.9 21.2 + - - +
62I PHE* 3.1 13.3 + - + +
64I SER* 1.3 72.9 - - - +
66I ARG* 1.3 62.6 + - - +
67I GLY 3.1 3.6 + - - -
----------------------------------------------------------
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Residues in contact with ARG 66 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I SER* 4.2 14.3 + - - +
4I ILE* 3.5 54.0 + - + +
62I PHE* 2.9 46.0 + - + +
63I VAL 3.3 5.6 + - - +
64I SER 3.2 0.6 - - - -
65I GLU* 1.3 79.7 - - - +
67I GLY* 1.3 60.3 + - - +
68I GLY 3.5 0.3 + - - -
115I ASP* 2.9 21.4 + - - -
117I ALA* 3.6 21.4 - - - +
118I THR* 2.9 28.1 + - - -
----------------------------------------------------------
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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