Contacts of the helix formed by residues 20 - 45 (chain D) in PDB entry 4J4L
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 THR 20 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR* 4.1 9.6 - - + +
124B TYR* 3.8 29.4 - - + -
125B LEU 5.3 1.6 - - - +
126B THR* 4.2 7.9 - - - +
148B GLU* 3.3 33.2 + - + +
150B GLN* 3.2 26.3 + - - +
172B TYR* 4.1 15.8 - - - -
19D LEU* 1.3 74.5 - - - +
21D SER* 1.3 61.2 + - - +
23D GLU* 3.1 4.1 + - - -
24D ARG 3.0 22.2 + - - -
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Residues in contact with SER 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLN* 5.4 0.2 - - - +
172B TYR* 6.5 0.2 - - - -
19D LEU 4.3 7.6 + - - +
20D THR* 1.3 77.9 + - - +
22D SER* 1.3 65.4 + - - +
24D ARG* 3.4 9.6 + - - +
25D ILE* 3.3 32.2 + - - +
129D LYS* 5.4 7.1 - - - +
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Residues in contact with SER 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 3.5 29.0 + - - +
20D THR 3.2 0.4 - - - -
21D SER* 1.3 78.3 + - - +
23D GLU* 1.3 63.5 + - - +
25D ILE* 3.4 9.0 + - - +
26D ASP* 2.9 31.2 + - - +
129D LYS* 4.8 10.7 + - - +
181D LEU 4.7 11.3 + - - -
184D MET 5.5 5.2 - - - -
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Residues in contact with GLU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE* 4.8 9.6 - - - +
84B ASN* 3.5 28.6 + - - +
102B TYR* 3.4 21.0 + - - -
104B ALA* 3.5 15.4 - - - +
126B THR* 3.5 36.8 - - + +
150B GLN* 3.8 2.9 - - - +
152B TRP* 3.5 4.0 - - + -
19D LEU* 3.4 9.4 + - - +
20D THR 3.1 11.2 + - - +
22D SER* 1.3 80.0 - - - +
24D ARG* 1.3 56.0 + - - +
26D ASP* 3.5 12.9 + - + +
27D LYS* 2.9 29.8 + - - +
30D ARG* 4.9 0.4 + - - +
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Residues in contact with ARG 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLN* 3.3 14.4 - - - +
152B TRP* 3.8 12.3 - - + -
172B TYR* 3.2 16.6 + - - -
174B ASN* 3.5 17.6 - - - +
177B PHE* 5.9 2.1 - - - -
196B GLU* 2.8 27.5 + - - -
198B ASP* 2.7 34.9 + - - +
222B ARG* 4.1 19.8 - - - +
20D THR 3.0 8.3 + - - +
21D SER* 3.9 11.1 - - - +
22D SER 3.2 0.8 - - - -
23D GLU* 1.3 77.5 - - - +
25D ILE* 1.3 57.8 + - - +
27D LYS* 3.4 4.2 + - - +
28D GLN* 2.9 28.6 + - - +
125D PHE* 3.6 40.2 - - + -
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Residues in contact with ILE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D SER* 3.3 18.9 + - - +
22D SER* 3.4 10.1 + - - +
24D ARG* 1.3 73.1 - - + +
26D ASP* 1.3 70.4 + - - +
28D GLN* 2.8 19.1 + - - +
29D ILE* 2.9 15.2 + - + +
122D LEU* 4.1 12.1 - - + -
125D PHE* 3.7 32.5 - - + +
126D LEU* 4.1 11.7 - - + -
129D LYS* 3.8 31.9 - - + +
181D LEU* 3.8 33.0 - - + -
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Residues in contact with ASP 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASN* 6.2 0.4 - - - -
85B ASN* 3.7 3.9 - - - +
22D SER 2.9 19.2 + - - +
23D GLU* 3.5 17.3 - - - +
25D ILE* 1.3 79.4 - - - +
27D LYS* 1.3 63.2 + - - +
29D ILE* 3.4 4.0 + - - +
30D ARG* 2.6 59.0 + - - +
178D LEU* 3.3 15.8 - - + +
181D LEU* 6.4 0.9 - - - -
182D ARG* 2.9 41.1 + - - +
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Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLU* 2.9 33.5 + - - +
152B TRP* 3.5 35.0 - - + +
154B ASN* 5.4 6.1 + - - +
177B PHE* 3.3 57.4 - - + +
23D GLU 2.9 15.3 + - - +
24D ARG 3.4 9.9 - - - +
26D ASP* 1.3 74.0 + - - +
28D GLN* 1.3 57.7 + - - +
30D ARG* 3.0 23.4 + - + +
31D TYR* 3.0 33.1 + - - +
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Residues in contact with GLN 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PHE* 3.5 26.0 - - - -
201B TYR* 3.2 27.3 + - - -
24D ARG* 2.9 15.2 + - - +
25D ILE* 2.8 10.9 + - - +
27D LYS* 1.3 76.0 - - - +
29D ILE* 1.3 60.7 + - - +
31D TYR* 3.2 6.7 + - - +
32D ILE* 3.1 27.4 + - + +
118D SER* 3.2 20.2 - - - +
121D VAL* 3.5 13.6 - - - +
122D LEU* 3.9 23.6 - - + +
125D PHE* 3.8 22.9 - - + -
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Residues in contact with ILE 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ILE* 2.9 14.1 + - + +
26D ASP 3.7 7.6 - - - +
28D GLN* 1.3 75.0 - - - +
30D ARG* 1.3 63.3 + - - +
32D ILE* 3.2 10.3 + - - +
33D LEU* 3.1 26.2 + - + +
122D LEU* 3.7 26.5 - - + -
126D LEU* 6.1 0.2 - - + -
174D LEU* 4.1 23.3 - - + +
177D SER* 4.3 9.2 - - - -
178D LEU* 4.0 43.1 - - + +
181D LEU* 3.7 30.5 - - + -
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Residues in contact with ARG 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASN* 4.3 9.1 - - - +
85B ASN* 3.1 34.6 + - - +
128B GLU* 2.8 40.2 + - - -
152B TRP* 4.6 1.6 - - - -
23D GLU* 4.9 0.6 + - - +
26D ASP* 2.6 34.0 + - - +
27D LYS* 3.0 35.2 + - + +
29D ILE* 1.3 78.5 - - - +
31D TYR* 1.3 59.3 + - - +
33D LEU* 3.8 12.2 - - + +
34D ASP* 3.3 29.4 + - - +
178D LEU* 4.8 9.0 - - + -
182D ARG* 4.7 5.6 - - - +
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Residues in contact with TYR 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PHE* 3.6 35.7 - + + -
201B TYR* 3.7 26.0 - + + +
225B GLN* 4.6 3.1 + - - +
27D LYS* 3.0 19.6 + - - +
28D GLN* 3.6 9.2 - - - +
29D ILE 3.2 0.2 - - - -
30D ARG* 1.3 76.4 - - - +
32D ILE* 1.3 67.5 + - - +
34D ASP* 3.4 10.8 + - + +
35D GLY* 3.0 18.0 + - - -
111D GLN* 5.6 5.7 + - - -
114D ALA* 4.6 16.9 - - + +
118D SER* 3.6 28.0 - - - -
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Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D GLN 3.1 17.6 + - - +
29D ILE* 3.2 6.9 + - - +
31D TYR* 1.3 76.8 - - - +
33D LEU* 1.3 56.4 + - - +
35D GLY* 2.9 19.4 + - - -
36D ILE* 2.9 14.8 + - + +
115D VAL* 4.1 15.7 - - + +
118D SER* 3.8 31.9 - - - +
119D THR* 3.8 26.5 - - + +
122D LEU* 3.7 30.3 - - + -
170D PHE* 3.9 11.9 - - + -
174D LEU* 3.7 20.6 - - + -
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Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ILE* 3.1 30.7 + - + +
30D ARG* 3.9 13.0 - - + +
31D TYR 3.2 0.2 - - - -
32D ILE* 1.3 76.3 - - - +
34D ASP* 1.3 59.2 + - - +
36D ILE* 3.4 7.6 + - + +
37D SER* 3.0 28.8 + - - -
171D LYS* 4.0 30.1 - - + +
174D LEU* 3.7 31.0 - - + -
175D GLN* 4.5 17.3 - - + +
178D LEU* 4.8 10.3 - - + -
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Residues in contact with ASP 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ARG* 3.3 16.3 + - - +
31D TYR* 3.8 12.2 - - + +
32D ILE 3.4 0.2 - - - -
33D LEU* 1.3 74.3 - - - +
35D GLY* 1.3 66.7 + - - +
37D SER* 3.5 8.4 + - - -
38D ALA* 3.1 23.2 + - - +
111D GLN* 5.1 0.2 - - - +
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Residues in contact with GLY 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D TYR* 3.0 10.5 + - - -
32D ILE 2.9 12.2 + - - -
34D ASP* 1.3 73.8 - - - +
36D ILE* 1.3 62.4 - - - +
38D ALA* 3.4 4.9 + - - +
39D LEU* 3.2 23.6 + - - +
111D GLN* 3.2 29.4 - - - +
115D VAL* 3.7 10.5 - - - -
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Residues in contact with ILE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ILE* 2.9 17.1 + - + +
33D LEU* 3.5 11.7 - - + +
35D GLY* 1.3 72.4 - - - +
37D SER* 1.3 61.0 + - - +
39D LEU* 2.7 32.0 + - - +
40D ARG* 2.8 14.9 + - + +
115D VAL* 3.9 13.4 - - + +
167D LEU* 4.2 32.4 - - + +
170D PHE* 3.3 36.8 - - + -
171D LYS* 4.0 26.2 - - + +
174D LEU* 4.1 12.8 - - + -
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Residues in contact with SER 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASN* 5.8 6.4 + - - -
33D LEU 3.0 15.3 + - - -
34D ASP* 3.6 9.2 + - - -
36D ILE* 1.3 80.3 - - - +
38D ALA* 1.3 62.1 + - - +
40D ARG* 3.3 9.1 + - - +
41D LYS* 3.1 47.2 + - - +
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Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ASP 3.1 10.3 + - - +
35D GLY 3.6 9.6 - - - +
37D SER* 1.3 78.8 + - - +
39D LEU* 1.3 61.1 + - - +
41D LYS* 3.7 12.8 + - - +
42D GLU* 3.4 27.9 + - - +
111D GLN* 4.1 19.3 - - + +
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLY 3.2 15.7 + - - +
36D ILE* 2.7 14.3 + - - +
38D ALA* 1.3 71.4 - - - +
40D ARG* 1.3 61.7 + - - +
42D GLU* 3.6 1.3 + - - -
43D THR* 2.8 30.5 + - - -
101D LEU* 4.4 12.3 - - + -
105D PHE* 3.4 35.9 - - + -
108D SER* 4.5 5.6 - - - +
111D GLN* 3.7 22.0 - - + -
112D ALA* 3.8 21.3 - - - +
115D VAL* 3.9 22.2 - - + -
167D LEU* 3.9 24.5 - - + -
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Residues in contact with ARG 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LYS* 3.5 30.6 - - - +
171A THR* 3.8 24.5 - - - +
195A THR* 6.0 2.4 - - - +
36D ILE* 2.8 13.9 + - + +
37D SER* 3.7 11.3 + - - +
39D LEU* 1.3 74.2 - - - +
41D LYS* 1.3 76.6 + - - +
43D THR* 3.1 4.8 + - - -
44D CYS* 2.9 46.7 + - - +
50D CYS* 4.1 5.3 - - - +
164D HIS* 3.3 43.1 + - + +
167D LEU* 3.9 22.6 - - + +
168D ARG* 5.5 10.8 - - - +
171D LYS* 5.6 6.3 - - - +
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Residues in contact with LYS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASN* 3.5 29.2 - - - +
217A GLN* 3.7 28.7 - - - +
37D SER* 3.1 37.2 + - - +
38D ALA* 3.8 13.5 - - - +
40D ARG* 1.3 84.4 - - - +
42D GLU* 1.3 69.3 + - - +
44D CYS* 3.2 9.4 + - - +
45D ASN* 3.1 32.3 + - - +
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Residues in contact with GLU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ALA 3.4 16.3 + - - +
39D LEU* 4.3 4.0 - - - +
40D ARG 3.3 0.4 - - - -
41D LYS* 1.3 90.6 - - - +
43D THR* 1.3 61.2 + - - +
45D ASN* 3.1 31.9 + - - +
46D LYS* 3.9 18.6 + - - +
105D PHE* 4.9 9.2 - - + -
107D SER* 5.1 8.1 - - - +
108D SER* 4.3 19.5 - - - +
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Residues in contact with THR 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LEU 2.8 19.9 + - - -
40D ARG* 3.8 5.2 - - - -
42D GLU* 1.3 76.5 - - - +
44D CYS* 1.3 63.7 + - - +
46D LYS* 3.3 30.6 + - + +
47D SER* 4.5 1.4 + - - -
49D MET* 5.2 9.3 - - - +
50D CYS* 5.1 0.4 - - - -
105D PHE* 2.9 23.4 - - - -
160D ASP* 3.9 26.9 - - + +
163D THR* 3.8 22.7 - - + +
164D HIS* 4.9 9.2 - - + +
167D LEU* 5.1 0.9 - - - -
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Residues in contact with CYS 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LYS* 4.5 12.8 + - - +
40D ARG* 2.9 41.5 + - - -
41D LYS* 3.2 10.5 + - - +
43D THR* 1.3 71.6 - - - +
45D ASN* 1.3 58.8 + - - +
46D LYS 2.8 11.3 + - - -
47D SER* 3.2 21.7 + - - +
49D MET* 4.9 3.3 + - - -
50D CYS* 2.0 53.7 + - + +
164D HIS* 4.0 3.4 - - - -
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Residues in contact with ASN 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 5.8 1.8 + - - -
219A LYS* 3.5 23.7 - - - +
41D LYS* 3.1 14.4 + - - +
42D GLU* 3.1 30.6 + - - +
43D THR 3.4 1.0 - - - -
44D CYS* 1.3 73.2 - - - +
46D LYS* 1.3 58.7 + - - +
47D SER* 3.3 3.1 + - - +
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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