Contacts of the helix formed by residues 36 - 64 (chain W) in PDB entry 2JD6
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 36 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PHE* 4.7 14.6 - - + -
31W PHE* 3.0 31.8 + - + +
32W GLU* 5.1 0.4 - - - -
34W LEU* 4.3 19.1 - - + +
35W GLY* 1.3 76.8 - - - +
37W GLU* 1.3 58.8 + - - +
39W PHE* 3.1 18.2 + - + +
40W ALA* 2.9 27.8 + - - +
83W PRO* 4.0 19.5 - - + -
151W LEU* 4.3 25.6 - - + +
152W PHE* 5.5 1.1 - - - +
155W ASP* 3.2 30.5 - - + +
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Residues in contact with GLU 37 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS* 3.0 46.4 + - - +
140B LYS* 6.1 1.3 - - - +
32W GLU* 3.8 23.1 - - - +
35W GLY* 3.2 14.4 + - - +
36W LEU* 1.3 73.6 - - - +
38W GLY* 1.3 57.7 + - - +
40W ALA* 3.9 1.4 - - - +
41W ASN* 3.0 38.0 + - - +
155W ASP* 3.4 4.7 + - - +
159W SER* 5.3 0.4 - - - -
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Residues in contact with GLY 38 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W GLU* 1.3 78.2 - - - +
39W PHE* 1.3 61.8 + - - -
41W ASN* 4.0 0.6 - - - -
42W TRP* 3.1 23.6 + - - +
155W ASP* 2.8 33.3 + - - -
158W LEU* 3.7 9.6 - - - +
159W SER* 3.6 20.9 - - - -
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Residues in contact with PHE 39 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31W PHE* 3.5 31.9 - + + -
36W LEU* 3.1 16.8 + - + +
38W GLY* 1.3 75.3 - - - +
40W ALA* 1.3 62.8 + - - +
42W TRP* 3.2 7.1 + - - +
43W MET* 3.0 25.3 + - - +
83W PRO* 5.1 0.4 - - + -
87W PHE* 3.7 28.7 - + - -
137W ILE* 4.5 1.1 - - + -
141W LEU* 4.1 19.5 - - + -
151W LEU* 4.0 30.5 - - + -
154W LEU* 4.3 10.8 - - + -
155W ASP* 3.1 45.7 + - + -
158W LEU* 3.5 26.0 - - + -
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Residues in contact with ALA 40 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28W ALA* 3.4 29.5 - - - +
31W PHE* 3.7 2.2 - - - +
32W GLU* 3.3 35.9 - - - +
36W LEU 2.9 16.5 + - - +
37W GLU 3.9 3.8 - - - +
38W GLY 3.3 0.2 - - - -
39W PHE* 1.3 77.2 - - - +
41W ASN* 1.3 57.0 + - - +
43W MET 3.3 1.0 + - - -
44W LYS* 2.9 33.7 + - - +
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Residues in contact with ASN 41 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W GLU* 3.0 26.0 + - - +
38W GLY* 4.2 4.2 - - - +
40W ALA* 1.3 71.8 - - - +
42W TRP* 1.3 66.8 + - - +
44W LYS* 2.9 32.0 + - - +
45W ALA* 2.9 21.0 + - - +
159W SER* 5.3 8.9 + - - +
161W ARG 3.6 11.9 - - - +
162W ALA* 4.7 5.5 - - - +
163W PRO* 3.4 22.8 - - + +
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Residues in contact with TRP 42 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24W TYR* 5.9 0.7 - + - -
38W GLY 3.1 15.6 + - - +
39W PHE* 3.4 9.9 - - - +
41W ASN* 1.3 75.2 - - - +
43W MET* 1.3 89.0 + - + +
45W ALA* 3.2 2.8 + - - +
46W GLN* 2.8 49.4 + - + -
87W PHE* 4.2 13.0 - + + -
133W SER* 4.4 15.3 - - - -
134W VAL* 4.1 22.4 - - + -
137W ILE* 3.5 26.1 - - + +
158W LEU* 3.7 30.8 - - + +
161W ARG* 3.4 51.7 + - + +
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Residues in contact with MET 43 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24W TYR* 3.6 43.9 - - - +
27W MET* 3.5 35.4 - - + -
28W ALA* 3.7 9.4 - - - +
31W PHE* 4.0 12.3 - - + -
39W PHE 3.0 15.1 + - - +
40W ALA 3.7 4.9 - - - +
41W ASN 3.3 0.2 - - - -
42W TRP* 1.3 89.6 - - + +
44W LYS* 1.3 60.3 + - - +
46W GLN* 3.0 3.1 + - - +
47W ALA* 2.7 28.6 + - - +
87W PHE* 3.6 40.4 - - + -
90W ALA* 4.5 7.2 - - + -
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Residues in contact with LYS 44 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E LEU* 4.8 14.3 - - + +
58E TYR* 3.5 24.4 - - - -
59E ASN* 4.9 4.8 + - - -
25W PHE* 4.8 10.5 - - + -
28W ALA* 3.7 10.1 - - + -
32W GLU* 2.9 32.9 + - - -
40W ALA* 2.9 19.3 + - - +
41W ASN* 2.9 32.3 + - - +
43W MET* 1.3 74.8 - - - +
45W ALA* 1.3 65.0 + - - +
47W ALA* 3.1 11.0 + - - +
48W GLU* 2.9 24.1 + - - +
163W PRO* 3.9 20.1 - - + +
166W PRO* 6.4 0.4 - - + -
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Residues in contact with ALA 45 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41W ASN 2.9 14.0 + - - +
42W TRP 3.4 8.1 - - - +
44W LYS* 1.3 74.5 - - - +
46W GLN* 1.3 58.6 + - - +
48W GLU* 3.2 6.7 + - - +
49W GLU* 2.9 27.5 + - - +
161W ARG* 3.6 28.5 + - + +
162W ALA 3.8 8.5 - - - +
163W PRO* 3.8 23.0 - - - +
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Residues in contact with GLN 46 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24W TYR* 3.4 30.3 - - + -
42W TRP* 2.8 34.9 + - + +
43W MET* 3.0 9.2 + - - +
45W ALA* 1.3 73.4 - - - +
47W ALA* 1.3 65.6 + - - +
49W GLU* 3.0 19.9 + - - +
50W GLU* 3.0 36.6 + - - +
94W GLU* 4.7 2.4 + - - +
130W GLU* 3.0 28.2 + - - +
133W SER* 5.3 2.6 + - - -
134W VAL* 5.4 5.1 - - + +
161W ARG* 2.9 26.0 + - - +
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Residues in contact with ALA 47 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W ALA* 3.4 40.6 - - + +
24W TYR* 3.8 3.1 - - - +
25W PHE* 4.1 16.4 - - + +
43W MET 2.7 15.7 + - - +
44W LYS* 3.2 13.5 - - - +
46W GLN* 1.3 70.6 - - - +
48W GLU* 1.3 63.3 + - - +
50W GLU 3.0 10.7 + - - -
51W ILE* 3.1 15.5 + - + +
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Residues in contact with GLU 48 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E LEU* 4.3 26.6 - - + +
44W LYS 2.9 12.7 + - - +
45W ALA* 3.4 9.6 - - - +
47W ALA* 1.3 72.0 - - - +
49W GLU* 1.3 63.3 + - - +
51W ILE* 3.3 13.6 + - + +
52W GLY* 3.1 17.8 + - - -
163W PRO* 3.0 29.2 - - - +
164W LYS* 2.8 33.6 + - - +
165W LEU* 3.1 29.1 + - + +
166W PRO* 3.9 1.6 - - - +
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Residues in contact with GLU 49 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45W ALA 2.9 14.4 + - - +
46W GLN* 3.0 25.5 + - - +
48W GLU* 1.3 75.9 - - - +
50W GLU* 1.3 63.3 + - - +
52W GLY* 3.1 11.5 + - - -
53W HIS* 3.1 26.6 + - + +
126W GLU* 3.1 10.9 - - - +
130W GLU* 2.9 25.1 - - - +
161W ARG* 2.8 28.5 + - - +
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Residues in contact with GLU 50 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17W GLU* 2.8 31.4 - - - +
20W SER* 4.0 10.5 - - - -
21W ALA 3.7 6.7 - - - +
24W TYR* 3.7 22.8 - - + -
46W GLN* 3.0 33.6 + - - +
47W ALA 3.0 6.2 + - - +
49W GLU* 1.3 74.4 - - - +
51W ILE* 1.3 65.3 + - - +
53W HIS* 3.0 18.7 + - - +
54W ALA* 3.0 10.0 + - - +
94W GLU* 3.3 13.9 - - - +
97W ILE* 5.5 0.6 - - - +
130W GLU* 3.3 10.4 - - - +
201W FE 2.3 29.0 - - - -
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Residues in contact with ILE 51 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 6.5 0.9 - - + -
51E ILE* 4.2 27.6 - - + -
165E LEU* 4.3 20.6 - - + -
18W LEU* 4.5 14.6 - - + -
21W ALA* 3.8 15.0 - - + -
47W ALA* 3.1 15.2 + - + +
48W GLU* 3.3 15.5 + - + +
50W GLU* 1.3 73.2 - - - +
52W GLY* 1.3 63.4 + - - +
54W ALA* 3.1 10.0 + - + +
55W LEU* 3.1 33.2 + - + +
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Residues in contact with GLY 52 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E LEU* 5.7 3.1 - - - +
48W GLU 3.1 9.3 + - - -
49W GLU* 3.1 10.5 + - - -
51W ILE* 1.3 76.9 - - - +
53W HIS* 1.3 62.1 + - - +
55W LEU* 3.3 12.5 + - - +
56W ARG* 3.2 25.9 + - - +
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Residues in contact with HIS 53 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17W GLU* 3.2 19.7 - - - +
49W GLU* 3.1 20.9 + - + +
50W GLU* 3.0 15.4 + - - +
52W GLY* 1.3 72.9 - - - +
54W ALA* 1.3 69.2 + - - +
56W ARG* 3.2 14.9 + - - +
57W PHE* 3.2 18.1 + - - -
122W TRP* 3.9 21.2 - + - -
123W PHE* 3.8 13.2 - + + -
126W GLU* 3.4 34.0 + - + +
127W GLN* 4.5 2.7 + - - -
130W GLU* 4.0 18.8 - - - -
201W FE 2.1 28.4 - - - -
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Residues in contact with ALA 54 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 5.3 4.0 - - + -
14W LEU* 3.7 15.9 - - + +
17W GLU* 3.8 14.9 - - + +
18W LEU* 3.4 36.1 - - + -
50W GLU 3.0 10.0 + - - +
51W ILE* 3.1 9.8 + - + +
53W HIS* 1.3 75.9 - - - +
55W LEU* 1.3 57.8 + - + +
57W PHE* 3.1 7.9 + - - +
58W TYR* 2.9 25.5 + - - +
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Residues in contact with LEU 55 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 3.7 34.3 - - + -
44E LYS* 5.1 12.3 - - + -
48E GLU* 5.8 0.9 - - - +
165E LEU* 4.9 6.3 - - + -
166E PRO* 4.1 32.3 - - + -
51W ILE* 3.1 31.3 + - + +
52W GLY* 3.7 11.9 - - - +
53W HIS 3.3 0.2 - - - -
54W ALA* 1.3 73.4 - - + +
56W ARG* 1.3 54.6 + - + +
58W TYR* 3.1 11.2 + - + +
59W ASN* 2.7 48.8 + - - +
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Residues in contact with ARG 56 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52W GLY 3.2 15.4 + - - +
53W HIS* 3.2 11.8 + - - +
55W LEU* 1.3 76.6 - - - +
57W PHE* 1.3 56.7 + - - +
59W ASN* 3.8 9.0 - - - +
60W TYR* 2.9 30.1 + - - +
119W PHE* 3.6 8.1 - - + -
122W TRP* 3.5 61.4 - - - +
123W PHE* 3.7 28.3 - - + -
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Residues in contact with PHE 57 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W LEU* 3.8 23.1 - - + -
13W GLN* 3.3 37.2 - - + -
14W LEU* 4.1 19.5 - - + -
17W GLU* 3.9 14.6 - - + -
53W HIS 3.2 21.2 + - - -
54W ALA 3.1 8.3 + - - +
56W ARG* 1.3 73.5 - - - +
58W TYR* 1.3 66.5 + - - +
60W TYR* 3.9 0.5 - - - +
61W ILE* 3.0 33.8 + - + +
101W ILE* 4.1 11.9 - - + -
104W LEU* 4.1 4.9 - - + -
119W PHE* 3.5 26.9 - + - -
120W LEU* 4.2 1.3 - - + -
123W PHE* 3.2 39.5 - + - -
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Residues in contact with TYR 58 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 3.7 31.6 - + + -
28E ALA* 3.5 14.2 - - - +
29E ALA* 3.9 17.5 - - + -
32E GLU* 2.7 40.9 + - - +
44E LYS* 3.5 20.1 - - - -
14W LEU* 3.9 12.0 - - + +
54W ALA 2.9 13.6 + - - +
55W LEU* 3.1 15.7 + - + +
57W PHE* 1.3 80.3 - - - +
59W ASN* 1.3 76.7 + - - +
61W ILE* 3.3 1.4 + - - +
62W TYR* 3.2 46.1 + + - -
68W VAL* 3.9 19.7 - - + -
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Residues in contact with ASN 59 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E GLU* 6.0 0.2 - - - -
44E LYS* 4.9 5.5 + - - -
166E PRO* 6.2 2.4 - - - +
55W LEU* 2.7 32.0 + - - +
56W ARG* 3.9 7.2 - - - +
58W TYR* 1.3 89.2 - - - +
60W TYR* 1.3 58.3 + - - +
62W TYR* 3.3 5.1 + - - +
63W ASP* 2.8 39.8 + - - +
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Residues in contact with TYR 60 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2W LEU* 4.3 0.4 - - + -
10W LEU* 3.9 24.7 - - + -
56W ARG 2.9 9.2 + - - +
57W PHE 3.9 2.0 - - - +
58W TYR 3.3 0.2 - - - -
59W ASN* 1.3 75.4 - - - +
61W ILE* 1.3 67.2 + - + +
63W ASP* 3.1 6.6 + - + +
64W ARG* 3.0 52.0 + - + +
115W SER* 3.0 12.6 - - - -
116W THR* 2.7 53.2 + - + -
119W PHE* 3.4 54.5 - + + -
128X VAL* 4.3 17.3 - - + -
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Residues in contact with ILE 61 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2W LEU* 4.4 6.0 - - - +
7W LEU* 3.6 16.4 - - + -
10W LEU* 3.9 46.9 - - + -
11W ASN* 4.1 8.3 - - - +
14W LEU* 4.2 7.2 - - + -
57W PHE* 3.0 29.0 + - + +
58W TYR 3.7 2.9 - - - +
60W TYR* 1.3 76.7 - - + +
62W TYR* 1.3 61.6 + - + +
64W ARG* 3.2 5.2 + - - +
65W ASN 3.1 4.3 + - - -
66W GLY* 2.8 23.5 + - - -
67W ARG 3.5 35.0 - - - +
68W VAL* 4.0 16.6 - - + -
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Residues in contact with TYR 62 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ALA* 2.6 30.8 + - - +
32E GLU* 3.6 26.9 - - + -
33E ASP* 3.8 24.0 - - + -
58W TYR* 3.2 45.4 + + + +
59W ASN* 3.9 6.3 - - - +
61W ILE* 1.3 72.5 - - + +
63W ASP* 1.3 67.9 + - - +
65W ASN* 2.9 14.4 + - - +
66W GLY 3.5 21.8 - - - -
67W ARG* 3.8 4.9 - - - -
68W VAL* 3.2 39.8 + - + -
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Residues in contact with ASP 63 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1W MET* 3.9 10.7 - - - +
59W ASN* 2.8 30.9 + - - +
60W TYR* 3.1 9.4 + - - +
62W TYR* 1.3 74.3 - - - +
64W ARG* 1.3 60.5 + - - +
65W ASN* 3.3 2.8 + - - +
128X VAL* 3.9 24.7 - - + +
129X GLU* 5.8 3.4 - - - +
132X ALA* 3.7 33.9 + - + +
135X LYS* 6.0 0.2 - - - +
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Residues in contact with ARG 64 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1W MET* 3.3 63.5 + - + +
2W LEU* 3.6 25.3 + - + +
60W TYR* 3.0 56.5 + - + +
61W ILE 3.7 2.0 - - - +
62W TYR 3.1 0.4 - - - -
63W ASP* 1.3 76.3 + - - +
65W ASN* 1.3 72.4 + - - +
66W GLY* 3.2 1.5 + - - -
113W ASP* 4.8 2.8 + - - -
115W SER* 3.5 22.9 + - - -
102X TYR* 3.5 11.1 + - - -
127X GLN 5.3 0.2 - - - -
128X VAL* 4.0 24.9 + - - +
131X GLU* 3.7 19.4 + - - +
----------------------------------------------------------
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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