Contacts of the helix formed by residues 37 - 66 (chain A) in PDB entry 2QQY
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 TYR 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 4.7 0.4 - - + -
34A SER* 2.6 30.3 + - - -
35A GLY* 4.1 6.1 - - - -
36A ILE* 1.3 76.0 - - - +
38A ARG* 1.3 58.7 + - - +
39A GLN 3.0 1.8 - - - -
40A VAL* 2.6 34.6 + - + +
41A LEU* 2.6 36.1 + - + +
83A VAL* 3.1 35.4 - - + +
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Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 2.8 24.9 + - - -
31A ALA* 3.2 18.6 + - - +
33A VAL* 2.8 54.7 + - + +
34A SER* 4.0 7.2 - - - +
35A GLY 3.0 17.4 + - - +
37A TYR* 1.3 79.5 - - - +
39A GLN* 1.3 68.2 - - + +
41A LEU 4.3 0.2 - - - +
42A LYS* 3.0 59.6 + - + +
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY 5.8 0.2 - - - +
36A ILE* 3.2 18.4 + - + +
37A TYR 3.0 0.4 - - - -
38A ARG* 1.3 83.2 - - + +
40A VAL* 1.3 57.2 + - + +
42A LYS* 5.5 0.2 - - - -
43A PRO* 3.3 21.8 - - - +
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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 ILE 4.4 0.2 + - - -
37A TYR* 2.6 27.3 + - + +
39A GLN* 1.3 75.6 - - + +
41A LEU* 1.3 81.6 + - + +
42A LYS 3.6 0.2 - - - -
43A PRO* 3.3 12.0 - - - +
44A PHE* 3.7 10.4 + - + +
137A LEU* 6.2 3.4 - - + -
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 4.0 13.2 - - + -
37A TYR* 2.6 31.4 + - + +
40A VAL* 1.3 88.3 - - + +
42A LYS* 1.3 66.8 + - - +
44A PHE* 3.0 14.1 + - + +
45A PHE* 2.9 39.5 + - + -
83A VAL* 3.6 30.3 - - + -
87A LEU* 4.2 28.5 - - + -
137A LEU* 4.3 19.3 - - + -
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 3.7 23.8 - - + +
31A ALA* 6.1 0.2 - - - +
33A VAL* 4.1 11.1 - - + +
38A ARG* 3.0 52.8 + - + +
41A LEU* 1.3 77.3 - - - +
43A PRO* 1.4 68.6 - - + +
45A PHE* 3.4 5.2 + - - +
46A GLU* 2.9 45.9 + - + +
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Residues in contact with PRO 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN 3.3 25.6 - - - +
40A VAL* 3.3 9.0 - - - +
42A LYS* 1.4 94.5 - - + +
44A PHE* 1.3 55.4 + - - +
46A GLU* 3.6 8.9 - - + +
47A SER* 2.9 29.6 + - - -
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Residues in contact with PHE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 5.3 0.7 - + - -
40A VAL* 3.7 10.2 + - + +
41A LEU* 3.0 17.7 + - + +
43A PRO* 1.3 77.4 - - - +
45A PHE* 1.3 83.0 + + - +
47A SER* 2.5 27.7 + - - -
48A GLU* 3.2 40.2 + - - +
87A LEU* 5.0 0.2 - - + -
130A HIS* 4.9 6.1 - + - -
133A GLU* 4.1 22.9 - - + -
134A LEU* 3.7 33.4 - - + -
137A LEU* 4.0 21.1 - - + -
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Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 3.5 46.8 - + + +
29A ASN* 3.6 31.4 - - + -
30A ALA* 3.9 5.8 - - + +
33A VAL* 4.1 4.7 - - + -
41A LEU* 2.9 45.6 + - + +
42A LYS 3.7 3.1 - - - +
44A PHE* 1.3 82.7 - + - +
46A GLU* 1.3 62.7 + - - +
48A GLU* 3.0 15.5 + - - +
49A ILE* 3.2 14.2 + - - +
86A MSE 3.8 33.4 - - + -
87A LEU* 3.9 29.2 - - + -
90A ALA* 5.0 5.4 - - + -
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN* 5.7 1.0 + - - -
30A ALA* 3.9 15.7 - - + +
42A LYS* 2.9 43.0 + - + +
43A PRO* 3.6 9.0 - - + +
45A PHE* 1.3 72.1 - - - +
47A SER* 1.3 62.4 + - - +
49A ILE* 3.2 39.2 + - - +
50A SER* 3.8 4.3 + - - -
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO 2.9 18.4 + - - -
44A PHE* 2.5 28.9 + - - -
46A GLU* 1.3 73.5 - - - +
48A GLU* 1.3 67.2 + - - +
49A ILE 3.4 0.3 + - - -
50A SER* 3.5 13.4 + - - -
51A ASP* 3.6 10.2 + - - +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 3.5 47.0 + - + -
44A PHE* 3.3 46.9 - - + +
45A PHE* 3.0 8.0 + - - +
47A SER* 1.3 82.6 + - - +
49A ILE* 1.3 62.2 + - - +
51A ASP* 3.2 7.9 + - - +
52A GLU* 3.0 29.5 + - - +
130A HIS* 3.2 44.7 + - - +
134A LEU* 5.1 1.0 - - - +
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 4.2 21.7 - - + +
26A TYR* 3.7 18.8 - - + +
27A ASN* 3.7 35.4 - - + +
30A ALA* 5.0 0.4 - - + -
45A PHE 3.2 9.3 + - - +
46A GLU* 3.2 39.6 + - + +
48A GLU* 1.3 75.1 - - - +
50A SER* 1.3 57.4 + - - +
52A GLU* 3.3 4.0 + - - +
53A GLN* 3.0 53.6 + - - +
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU 3.8 4.1 + - - -
47A SER* 3.5 8.8 + - - -
48A GLU 3.4 0.4 - - - -
49A ILE* 1.3 75.9 - - - +
51A ASP* 1.3 66.6 + - - +
53A GLN* 3.4 15.6 + - - +
54A GLY* 3.1 18.0 + - - -
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Residues in contact with ASP 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER 3.6 9.3 + - - +
48A GLU 3.2 10.3 + - - +
49A ILE 3.2 0.2 - - - -
50A SER* 1.3 78.6 - - - +
52A GLU* 1.3 69.9 + - - +
54A GLY* 3.1 12.6 + - - -
55A HIS* 3.3 19.4 + - - -
126A ASP* 2.5 25.3 - - - +
130A HIS* 2.5 35.9 - - + -
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 2.4 43.8 - - - +
22A ALA* 3.9 18.3 - - + +
23A ILE* 3.8 21.2 - - + +
26A TYR* 4.4 9.9 - - + -
48A GLU* 3.0 16.2 + - - +
49A ILE 3.9 0.7 - - - +
51A ASP* 1.3 93.1 - - - +
53A GLN* 1.3 55.9 + - - +
55A HIS* 3.2 13.6 + - - +
56A ALA* 2.8 34.5 + - - +
94A GLU* 4.3 5.3 - - - +
127A GLU* 3.2 28.1 - - - +
130A HIS* 3.8 8.0 + - - -
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Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.8 25.9 - - + +
49A ILE* 3.0 45.1 + - + +
50A SER* 3.5 13.5 - - - +
52A GLU* 1.3 76.6 - - - +
54A GLY* 1.3 56.5 + - - +
56A ALA* 3.3 2.6 + - - +
57A LEU* 3.0 28.9 + - - +
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Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A SER 3.1 6.9 + - - -
51A ASP 3.1 9.0 + - - -
53A GLN* 1.3 76.4 - - - +
55A HIS* 1.3 61.4 + - - +
57A LEU* 3.5 9.4 + - - +
58A TYR* 3.0 28.1 + - - +
119A LYS* 5.5 2.2 + - - -
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Residues in contact with HIS 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 3.2 21.7 + - + +
51A ASP* 3.3 19.0 + - - -
52A GLU* 3.2 25.3 + - - +
54A GLY* 1.3 74.6 - - - +
56A ALA* 1.3 67.0 + - - +
58A TYR* 3.2 3.5 + - - +
59A LEU* 2.9 30.7 + - - +
119A LYS* 4.9 8.3 - - - -
123A MSE 3.6 42.5 - - + +
126A ASP* 3.0 20.8 + - + +
127A GLU* 2.9 25.2 + - - +
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.4 27.2 - - + +
19A GLU* 4.2 10.7 - - + +
20A TYR* 4.0 20.6 - - + -
23A ILE* 4.1 12.3 - - + -
52A GLU 2.8 20.0 + - - +
53A GLN 3.3 5.4 + - - +
55A HIS* 1.3 74.5 - - - +
57A LEU* 1.3 62.3 + - - +
59A LEU* 3.3 0.4 + - - -
60A ALA* 3.0 23.5 + - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN 3.0 16.4 + - - +
54A GLY* 3.8 8.7 - - - +
55A HIS 3.3 0.2 - - - -
56A ALA* 1.3 77.3 - - - +
58A TYR* 1.3 62.9 + - - +
60A ALA* 4.0 4.4 - - + +
61A GLU* 3.0 55.3 + - + +
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLY 3.0 17.1 + - - +
55A HIS* 3.6 4.9 - - - +
57A LEU* 1.3 77.3 - - - +
59A LEU* 1.3 67.3 + - + +
61A GLU* 3.4 12.9 + - + +
62A LYS* 2.9 46.6 + - + +
115A GLU* 2.8 38.4 + - - -
116A LEU* 3.5 24.7 - - + +
119A LYS* 3.4 48.2 - - + +
123A MSE 4.1 14.6 - - + -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.8 32.5 - - + +
15A ASP* 4.0 10.8 - - + -
16A LEU* 3.9 27.1 - - + +
19A GLU* 3.7 17.5 - - + -
55A HIS* 2.9 23.5 + - + +
56A ALA* 3.8 3.6 - - - +
58A TYR* 1.3 87.0 - - + +
60A ALA* 1.3 61.8 + - - +
62A LYS* 3.2 3.4 + - + +
63A ILE* 2.8 36.1 + - + +
101A TYR* 3.3 30.5 - - + +
120A LEU* 5.5 0.4 - - + -
123A MSE 4.6 5.6 - - + -
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.9 12.3 - - + +
20A TYR* 4.6 7.6 - - - +
56A ALA 3.0 16.9 + - - +
57A LEU* 4.2 4.5 - - + +
59A LEU* 1.3 76.0 - - - +
61A GLU* 1.3 63.4 + - + +
63A ILE* 4.3 0.4 - - - -
64A LYS* 3.1 21.5 + - - +
70A PRO* 3.3 34.5 - - + +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 3.0 50.3 + - + +
58A TYR* 3.7 12.1 - - + +
60A ALA* 1.3 78.9 - - + +
62A LYS* 1.3 55.8 + - - +
64A LYS* 3.4 5.7 + - - +
65A THR* 2.9 33.5 + - - +
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.9 21.1 - - + -
58A TYR* 2.9 46.6 + - + +
59A LEU* 3.2 5.6 + - - +
61A GLU* 1.3 73.1 - - - +
63A ILE* 1.3 67.5 + - - +
65A THR* 3.2 16.3 + - - +
66A LEU* 2.9 43.3 + - + +
113A MSE 6.2 0.8 - - - -
115A GLU* 2.6 24.7 + - - -
116A LEU* 4.5 21.1 - - + +
----------------------------------------------------------
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.1 12.3 - - + +
12A LEU* 3.6 44.9 - - + +
13A ASN* 3.4 21.5 - - - +
16A LEU* 4.0 16.4 - - + -
59A LEU 2.8 22.8 + - - +
60A ALA* 3.7 3.8 - - - +
62A LYS* 1.3 76.2 - - - +
64A LYS* 1.3 62.4 + - - +
66A LEU* 3.1 12.7 + - - +
67A GLY 3.2 0.3 + - - -
68A GLY* 2.9 33.4 + - - -
69A THR 3.6 9.4 - - - +
70A PRO* 3.6 24.0 - - + -
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA 3.1 14.7 + - - +
61A GLU* 3.7 5.8 - - - +
63A ILE* 1.3 78.8 - - - +
65A THR* 1.3 61.2 + - - +
67A GLY* 3.0 15.1 + - - -
68A GLY 3.7 11.8 - - - +
70A PRO* 4.3 15.9 - - + -
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 2.9 24.7 + - - +
62A LYS* 3.2 24.6 + - + +
64A LYS* 1.3 72.2 - - - +
66A LEU* 1.3 64.4 + - + +
67A GLY 3.2 1.1 + - - -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MSE 4.7 3.5 - - - +
5A VAL* 4.1 15.2 - - + +
8A LEU* 3.8 26.7 - - + -
9A ILE* 3.5 24.9 - - + +
12A LEU* 3.8 20.4 - - + -
62A LYS* 2.9 37.5 + - + +
63A ILE 3.1 4.9 + - - +
65A THR* 1.3 81.9 - - + +
67A GLY* 1.3 57.8 + - - +
68A GLY 3.5 0.7 - - - -
113A MSE 3.8 26.0 - - + -
116A LEU* 4.9 0.4 - - + -
----------------------------------------------------------
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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