Contacts of the helix formed by residues 38 - 69 (chain R) in PDB entry 1Q90
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 ASP 38 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R VAL 3.1 7.0 + - - +
37R PRO* 1.3 73.4 - - - +
39R MET* 1.3 67.6 + - - +
40R ASN* 3.3 21.0 + - - +
41R LYS* 2.7 52.2 + - - +
42R ARG* 3.1 7.4 + - - +
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Residues in contact with MET 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R PRO 3.8 1.2 + - - -
38R ASP* 1.3 72.8 + - - +
40R ASN* 1.3 54.8 + - - +
42R ARG* 2.8 65.7 + - - +
43R ASN* 2.9 33.7 + - - +
950R SQD 5.0 1.6 - - - -
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Residues in contact with ASN 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L LEU* 6.0 0.2 - - - +
38R ASP* 2.9 20.9 + - - +
39R MET* 1.3 71.9 - - - +
41R LYS* 1.3 64.9 + - - +
42R ARG 2.8 9.6 + - - -
43R ASN* 2.9 24.3 + - - +
44R ILE* 2.9 36.6 + - - +
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Residues in contact with LYS 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLN* 2.7 23.0 + - - -
30L LYS* 3.0 33.9 + - - +
31L LEU* 3.7 35.3 - - + +
32L ILE* 4.8 6.9 + - - -
35R GLU* 4.3 22.1 + - - +
36R VAL 5.0 0.4 - - - -
37R PRO* 3.9 10.7 - - + +
38R ASP* 2.7 44.6 + - - +
40R ASN* 1.3 77.6 - - - +
42R ARG* 1.3 54.4 + - - +
44R ILE* 4.0 1.8 - - - -
45R MET 3.6 10.4 + - - -
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Residues in contact with ARG 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 3.1 11.0 + - - +
275A GLN* 3.5 14.1 - - - +
276A PHE* 3.0 24.8 - - - -
279A VAL* 3.5 34.1 - - - +
37R PRO* 3.9 13.4 + - + +
38R ASP 3.5 9.4 - - - +
39R MET* 2.8 54.5 + - - +
41R LYS* 1.3 79.0 - - - +
43R ASN* 1.3 61.9 + - - +
44R ILE 3.2 0.2 - - - -
45R MET 3.4 0.9 + - - -
46R ASN* 2.9 28.6 + - - +
950R SQD 2.8 33.8 + - - +
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Residues in contact with ASN 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R MET* 2.9 46.6 + - - +
40R ASN* 2.9 14.6 + - - +
42R ARG* 1.3 73.1 - - - +
44R ILE* 1.3 68.8 + - + +
46R ASN* 3.4 14.7 + - - +
47R LEU* 3.1 29.0 + - + +
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Residues in contact with ILE 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L VAL* 6.2 0.2 - - + -
31L LEU* 3.2 40.4 - - + -
40R ASN* 2.9 39.2 + - - +
41R LYS* 3.9 1.1 - - - +
43R ASN* 1.3 79.3 - - + +
45R MET* 1.3 64.2 + - - +
47R LEU* 2.9 23.5 + - + +
48R ILE* 3.0 22.3 + - + +
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Residues in contact with MET 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 4.8 8.5 - - + +
271A LEU* 5.0 1.8 - - - -
272A LYS* 3.9 34.8 - - + -
275A GLN* 3.4 28.3 - - + +
25L LEU* 3.8 25.8 - - + -
31L LEU* 4.4 10.5 - - + +
32L ILE* 4.8 8.3 - - + -
41R LYS 3.6 3.2 + - - +
42R ARG 3.4 8.9 + - - +
43R ASN 3.3 0.2 - - - -
44R ILE* 1.3 79.2 - - - +
46R ASN* 1.3 64.7 + - - +
48R ILE* 2.9 44.1 + - + +
49R LEU* 2.7 29.3 + - + +
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Residues in contact with ASN 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 3.1 22.0 - - - +
38D TYR* 4.5 2.9 + - - -
42R ARG 2.9 23.9 + - - -
43R ASN* 3.6 16.9 + - - +
44R ILE 3.3 0.2 - - - -
45R MET* 1.3 77.7 - - - +
47R LEU* 1.3 60.4 + - + +
49R LEU* 3.5 8.2 + - - +
50R ALA* 2.8 30.7 + - - +
950R SQD 3.2 62.2 + - - +
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Residues in contact with LEU 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R ASN* 3.1 19.2 + - + +
44R ILE* 2.9 16.6 + - + +
46R ASN* 1.3 75.8 - - + +
48R ILE* 1.3 66.5 + - + +
50R ALA* 3.2 9.5 + - + +
51R GLY* 2.9 21.1 + - - -
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Residues in contact with ILE 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 3.5 24.4 - - + +
25L LEU* 4.8 11.2 - - + -
31L LEU* 3.8 22.0 - - + -
44R ILE* 3.0 16.0 + - + +
45R MET* 2.9 32.2 + - + +
47R LEU* 1.3 74.9 - - + +
49R LEU* 1.3 54.4 + - - +
51R GLY* 3.1 3.5 + - - -
52R GLY* 2.7 34.1 + - - -
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Residues in contact with LEU 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A THR* 4.3 2.9 - - + +
268A LEU* 3.7 30.5 - - + +
269A LEU* 3.7 38.1 - - + +
272A LYS* 3.8 32.5 - - + -
38D TYR* 4.4 5.4 - - + -
45R MET* 2.7 21.7 + - + +
46R ASN* 3.6 7.6 - - - +
48R ILE* 1.3 73.1 - - - +
50R ALA* 1.3 63.2 + - - +
53R ALA* 2.9 29.3 + - + +
950R SQD 4.1 23.3 - - + -
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Residues in contact with ALA 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46R ASN 2.8 21.8 + - - +
47R LEU* 3.4 13.2 - - + +
49R LEU* 1.3 75.4 - - - +
51R GLY* 1.3 64.8 + - - +
53R ALA* 3.2 4.4 + - - +
54R GLY* 2.9 20.3 + - - -
950R SQD 4.6 16.8 - - + +
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Residues in contact with GLY 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R LEU 2.9 14.4 + - - -
48R ILE 3.5 2.7 - - - -
50R ALA* 1.3 74.8 - - - +
52R GLY* 1.3 65.2 + - - +
54R GLY* 3.2 11.9 + - - -
55R LEU* 3.6 10.5 + - - +
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Residues in contact with GLY 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 4.4 14.8 - - - -
265A THR* 3.4 7.6 + - - -
268A LEU* 4.0 15.5 - - - -
48R ILE 2.7 19.7 + - - -
49R LEU 3.7 1.3 - - - -
51R GLY* 1.3 71.2 - - - +
53R ALA* 1.3 56.7 + - - +
55R LEU* 2.8 29.0 + - - +
56R PRO* 3.2 9.2 - - - +
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Residues in contact with ALA 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A THR* 3.5 24.5 + - + +
49R LEU* 2.9 20.9 + - + +
50R ALA* 3.7 4.3 - - - +
52R GLY* 1.3 69.9 - - - -
54R GLY* 1.3 62.3 + - - +
56R PRO* 3.3 2.8 - - - +
57R ILE* 3.2 32.4 + - + +
950R SQD 3.7 36.6 - - + -
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Residues in contact with GLY 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50R ALA 2.9 12.3 + - - -
51R GLY* 3.6 7.2 - - - -
52R GLY 2.8 2.6 + - - -
53R ALA* 1.3 78.7 - - - +
55R LEU* 1.3 55.4 + - - +
57R ILE* 4.5 5.2 - - - -
58R THR* 2.5 41.4 + - - -
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Residues in contact with LEU 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PHE* 3.6 41.5 - - + -
264A LEU* 3.7 30.1 - - + -
51R GLY 3.6 7.1 + - - +
52R GLY* 2.8 12.6 + - - +
54R GLY* 1.3 80.2 - - - +
56R PRO* 1.4 69.9 - - + +
58R THR* 3.6 3.3 - - - -
59R THR* 3.0 25.4 + - - -
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Residues in contact with PRO 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PHE* 4.1 16.8 - - + -
261A PHE* 3.7 26.0 - - + +
262A VAL* 4.3 8.3 - - + -
265A THR* 3.2 24.9 - - + +
45D LEU* 4.5 14.1 - - + -
52R GLY 3.2 9.4 - - - +
53R ALA* 3.3 7.4 - - - +
55R LEU* 1.4 94.3 - - + +
57R ILE* 1.3 59.3 + - + +
59R THR* 3.3 3.4 + - - +
60R LEU* 3.0 36.7 + - + +
950R SQD 6.5 0.2 - - + -
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Residues in contact with ILE 57 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LEU* 5.9 4.3 - - + -
53R ALA* 3.2 23.5 + - + +
54R GLY* 4.0 4.7 - - - +
56R PRO* 1.3 81.4 - - + +
58R THR* 1.3 61.1 + - - +
60R LEU* 3.8 10.5 - - + +
61R ALA* 2.9 29.4 + - + +
950R SQD 4.0 28.7 - - + -
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Residues in contact with THR 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R GLY* 2.5 33.4 + - - -
55R LEU* 3.6 3.1 - - - -
57R ILE* 1.3 72.9 - - - +
59R THR* 1.3 67.3 + - - +
61R ALA* 3.4 5.7 - - + +
62R LEU* 2.9 45.4 + - + +
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Residues in contact with THR 59 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PHE* 3.8 25.1 - - + -
261A PHE* 3.6 22.4 - - + -
960B LFA 4.2 18.6 - - + +
55R LEU 3.0 14.3 + - - -
56R PRO 3.5 7.4 - - - -
58R THR* 1.3 77.9 - - - +
60R LEU* 1.3 65.6 + - - +
62R LEU* 3.7 6.2 - - - +
63R GLY* 2.9 21.5 + - - -
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Residues in contact with LEU 60 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PHE* 3.9 25.1 - - + -
960B LFA 3.7 45.2 - - + +
45D LEU* 5.3 6.3 - - + -
48D PHE* 3.8 26.9 - - + -
52D ILE* 4.0 15.3 - - + -
56R PRO* 3.0 23.7 + - + +
57R ILE* 3.8 9.2 - - + +
59R THR* 1.3 78.7 - - - +
61R ALA* 1.3 65.5 - - - +
63R GLY* 3.2 0.3 + - - -
64R TYR* 2.9 26.8 + - - +
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Residues in contact with ALA 61 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57R ILE* 2.9 23.0 + - + +
58R THR* 3.4 9.0 - - + +
60R LEU* 1.3 77.2 - - - +
62R LEU* 1.3 60.0 + - + +
64R TYR* 3.4 6.1 - - - +
65R GLY* 2.9 26.3 + - - -
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Residues in contact with LEU 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58R THR* 2.9 42.2 + - + +
59R THR* 3.7 4.9 - - - +
61R ALA* 1.3 71.9 - - + +
63R GLY* 1.3 65.9 + - - +
65R GLY* 3.8 1.3 - - - +
66R ALA* 2.9 25.9 + - - +
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Residues in contact with GLY 63 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 3.9 25.4 - - - -
82B ILE* 6.1 0.4 - - - -
960B LFA 3.6 22.2 - - - -
59R THR 2.9 12.8 + - - -
62R LEU* 1.3 75.1 - - - +
64R TYR* 1.3 65.6 + - - +
66R ALA* 3.0 18.5 + - - +
67R PHE* 3.1 6.9 + - - +
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Residues in contact with TYR 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 2.8 46.5 + - + +
50B THR* 4.6 3.1 - - - -
52B PHE* 3.5 19.5 - + - -
53B ALA* 3.8 13.4 - - + +
82B ILE* 4.5 8.7 - - + -
960B LFA 3.7 33.7 - - + +
60R LEU 2.9 17.4 + - - +
61R ALA* 3.4 6.1 - - - +
63R GLY* 1.3 73.9 - - - +
65R GLY* 1.3 65.0 + - - +
67R PHE* 3.2 21.4 - - + +
68R PHE* 3.3 29.1 - + - -
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Residues in contact with GLY 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61R ALA 2.9 16.0 + - - -
62R LEU* 3.8 2.0 - - - -
63R GLY 3.2 0.2 - - - -
64R TYR* 1.3 78.0 - - - +
66R ALA* 1.3 64.4 + - - +
68R PHE* 2.8 28.0 + - - +
69R VAL* 3.6 8.4 + - - +
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Residues in contact with ALA 66 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 3.0 28.0 + - + +
78B PHE* 4.0 20.4 - - + -
62R LEU 2.9 13.7 + - - +
63R GLY 3.1 11.2 - - - +
65R GLY* 1.3 74.6 - - - +
67R PHE* 1.3 61.8 + - - +
69R VAL* 3.0 19.5 + - - +
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Residues in contact with PHE 67 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA* 3.0 42.8 - - + -
54B MET* 4.1 7.4 - - + -
57B TYR* 2.9 45.2 + + - -
72B ILE* 4.4 6.1 - - + -
76B VAL* 3.4 21.5 - - + +
77B ASN* 3.1 30.0 + - - +
78B PHE* 5.0 0.4 - - + -
79B GLY* 3.8 10.1 - - - -
82B ILE* 3.3 37.0 - - + -
63R GLY 3.1 6.2 + - - +
64R TYR* 3.2 15.0 - + + +
66R ALA* 1.3 79.0 - - - +
68R PHE* 1.3 74.2 + + - +
69R VAL 3.5 2.8 + - - +
----------------------------------------------------------
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Residues in contact with PHE 68 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 3.5 33.9 - + - -
53B ALA* 3.8 20.4 - - + -
56B PHE* 3.6 48.7 - + + -
57B TYR* 3.5 8.0 + - - -
64R TYR* 3.3 43.7 - + - -
65R GLY* 2.8 18.4 + - - +
67R PHE* 1.3 81.0 - + - +
69R VAL* 1.3 63.2 + - + +
70R PRO* 3.0 11.1 - - - +
----------------------------------------------------------
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Residues in contact with VAL 69 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 4.1 0.4 - - - -
77B ASN* 3.2 21.2 + - - +
65R GLY 3.9 9.0 - - - +
66R ALA* 3.0 18.3 + - - +
67R PHE 3.9 1.6 - - - +
68R PHE* 1.3 74.7 - - + +
70R PRO* 1.3 83.7 - - + +
71R PRO* 3.3 3.5 - - - +
----------------------------------------------------------
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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