Contacts of the helix formed by residues 23 - 55 (chain D) in PDB entry 6XXD
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 ASN 23 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D PRO* 1.3 73.0 - - - +
24D LEU* 1.3 61.3 + - - +
25D LEU* 3.4 4.7 + - - +
26D ALA* 2.9 36.1 + - - +
27D ALA* 3.5 19.4 + - - +
42G ASP* 5.2 2.4 + - - -
46G PHE* 3.7 21.0 - - + -
68G GLY* 2.8 34.8 + - - -
70G LYS* 4.8 8.4 - - - +
106H ASP* 3.1 38.3 + - - +
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Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ILE* 5.4 5.4 - - + -
22D PRO* 3.8 27.4 - - + +
23D ASN* 1.3 71.8 - - - +
25D LEU* 1.3 66.8 + - - +
27D ALA* 3.2 8.0 + - + +
28D ARG* 3.1 29.4 + - + +
44H VAL* 3.5 20.9 - - + -
48H GLU* 3.8 31.6 - - + +
57H TYR* 6.0 0.2 - - - -
88H TYR* 3.5 24.7 - - - +
104H THR 5.3 0.4 - - - +
105H PRO* 3.1 20.2 + - + +
108H GLY* 6.2 1.1 - - - -
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Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ASN* 3.4 1.2 + - - -
24D LEU* 1.3 78.4 - - - +
26D ALA* 1.3 61.3 + - - +
28D ARG* 3.5 8.8 + - + +
29D LYS* 3.3 46.3 + - + +
96D GLY* 5.9 2.2 - - - +
57H TYR* 6.2 0.4 - - - -
86H ASN* 3.1 30.7 - - + +
87H SER* 4.9 6.5 - - - +
105H PRO* 3.7 16.9 + - + +
106H ASP* 3.8 39.7 - - + +
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ASN* 2.9 27.4 + - + +
25D LEU* 1.3 73.4 - - - +
27D ALA* 1.3 65.8 + - - +
29D LYS* 3.4 26.9 + - - +
30D ARG* 3.8 5.5 + - - +
46G PHE* 3.7 25.1 - - + -
49G MET* 3.8 22.3 - - + +
67G LEU 4.4 7.6 - - - +
68G GLY* 4.9 0.4 - - - -
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ASN 3.5 13.2 + - - +
24D LEU* 3.2 12.6 + - + +
26D ALA* 1.3 80.9 - - - +
28D ARG* 1.3 60.3 + - + +
30D ARG* 3.8 6.6 + - - +
31D ALA* 3.6 17.2 + - - +
49G MET* 5.2 3.3 - - - -
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Residues in contact with ARG 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 3.1 17.2 + - - +
25D LEU* 3.9 9.9 - - + +
26D ALA 3.3 0.2 - - - -
27D ALA* 1.3 76.5 - - + +
29D LYS* 1.3 55.4 + - - +
31D ALA* 3.2 9.9 + - - +
32D ASN* 2.7 53.2 + - - +
48H GLU* 3.0 25.5 + - - +
51H GLN* 3.5 37.9 + - - +
52H ILE* 5.3 6.1 - - - +
57H TYR* 3.6 22.9 - - - -
86H ASN* 6.1 1.8 - - - +
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Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU* 3.3 46.1 + - + +
26D ALA* 3.4 16.0 + - - +
28D ARG* 1.3 76.9 - - - +
30D ARG* 1.3 59.5 + - + +
32D ASN* 3.4 3.0 + - - +
33D ASP* 3.1 34.5 + - - +
96D GLY* 3.6 23.5 + - - +
97D GLY* 3.6 19.8 - - - +
98D THR* 4.1 17.9 - - + -
49G MET* 5.8 1.3 - - + -
67G LEU 5.5 4.2 + - - +
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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
----------------------------------------------------------
26D ALA 4.0 11.2 + - - +
27D ALA* 3.8 6.7 + - - +
28D ARG 3.2 0.6 - - - -
29D LYS* 1.3 76.4 - - - +
31D ALA* 1.3 61.9 + - - +
33D ASP* 3.4 16.1 + - - +
34D THR* 2.9 26.4 + - - -
98D THR* 3.7 25.3 + - - +
111D LYS* 5.2 3.6 - - - +
49G MET* 3.5 47.1 + - + +
52G ILE* 4.3 26.9 - - + +
53G ASP* 2.7 41.5 + - - -
67G LEU* 4.2 10.7 + - - +
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ALA 3.6 11.9 + - - +
28D ARG* 3.2 12.7 + - - +
30D ARG* 1.3 78.4 - - - +
32D ASN* 1.3 62.5 + - - +
34D THR* 3.3 10.8 + - - -
35D VAL* 3.2 25.7 + - - +
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Residues in contact with ASN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ARG* 2.7 39.7 + - - +
29D LYS 3.5 5.6 - - - +
30D ARG 3.3 0.2 - - - -
31D ALA* 1.3 71.8 - - - +
33D ASP* 1.3 63.7 + - - +
35D VAL* 3.4 8.9 + - - +
36D VAL* 3.2 26.5 + - - +
94D HIS* 3.2 43.2 + - + -
96D GLY 2.9 24.5 + - - +
97D GLY* 4.3 1.1 - - - -
86H ASN* 3.5 13.6 + - - +
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Residues in contact with ASP 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LYS 3.1 16.9 + - - +
30D ARG* 3.6 20.2 + - - +
31D ALA 3.3 0.2 - - - -
32D ASN* 1.3 73.1 - - - +
34D THR* 1.3 57.7 + - - +
36D VAL* 3.3 3.8 + - - +
37D THR* 2.7 38.6 + - - +
94D HIS* 5.5 0.5 - - - +
97D GLY* 3.8 3.8 - - - -
98D THR* 2.7 50.2 + - - +
99D VAL 4.7 0.2 - - - +
101D PHE* 3.8 27.5 - - + -
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Residues in contact with THR 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ARG 2.9 16.4 + - - -
31D ALA* 3.3 12.7 + - - -
33D ASP* 1.3 76.8 - - - +
35D VAL* 1.3 57.4 + - - +
37D THR* 4.0 5.9 - - - -
38D ALA* 2.8 35.6 + - + +
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Residues in contact with VAL 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ALA 3.2 15.6 + - - +
32D ASN* 3.6 13.5 - - - +
33D ASP 3.3 0.6 - - - -
34D THR* 1.3 78.0 - - - +
36D VAL* 1.3 57.3 + - - +
38D ALA* 3.9 4.6 - - - +
39D TYR* 3.0 28.2 + - - +
73D PRO* 3.9 30.1 - - + -
76D VAL* 4.3 10.1 - - + -
94D HIS* 4.6 6.5 - - + +
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Residues in contact with VAL 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ASN 3.2 14.6 + - - +
33D ASP* 3.7 8.1 - - - +
35D VAL* 1.3 75.2 - - - +
37D THR* 1.3 60.1 + - - +
39D TYR* 3.5 4.5 + - - +
40D LEU* 3.0 32.2 + - + +
76D VAL* 4.5 11.2 - - + -
92D ALA* 3.5 32.9 - - + +
93D GLY* 3.7 4.5 - - - +
94D HIS* 3.4 35.7 - - + +
101D PHE* 3.6 26.0 - - + -
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Residues in contact with THR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ASP* 2.7 29.1 + - - +
34D THR* 4.0 6.5 - - - -
36D VAL* 1.3 75.1 - - - +
38D ALA* 1.3 57.0 + - - +
40D LEU* 3.6 2.0 + - - +
41D ASN* 2.9 32.3 + - + +
101D PHE* 3.3 22.8 - - + -
109D VAL* 4.3 23.7 - - + +
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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 THR* 2.8 23.5 + - + +
35D VAL* 3.9 6.1 - - - +
37D THR* 1.3 76.3 - - - +
39D TYR* 1.3 56.7 + - - +
41D ASN* 3.3 8.4 + - - +
42D ASP* 2.8 39.6 + - - +
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Residues in contact with TYR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D VAL 3.0 19.0 + - - +
36D VAL* 4.0 4.7 - - - +
38D ALA* 1.3 72.7 - - - +
40D LEU* 1.3 56.9 + - + +
42D ASP* 3.4 8.9 + - - +
43D ALA* 2.8 32.9 + - - +
61D GLN* 3.1 21.0 + - - -
69D LEU* 3.8 24.0 - - + +
70D LYS* 2.9 30.0 + - + -
71D SER 3.4 18.8 - - - -
72D THR* 3.5 7.0 + - - -
73D PRO* 3.7 26.0 - - + -
76D VAL* 5.4 3.6 - - + -
78D PHE* 3.6 44.6 - + + -
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D VAL* 3.0 25.9 + - + +
37D THR 3.9 0.2 - - - +
39D TYR* 1.3 73.5 - - - +
41D ASN* 1.3 59.6 + - - +
43D ALA* 3.5 2.8 - - - +
44D VAL* 2.9 34.8 + - - +
78D PHE* 3.9 18.8 - - + -
90D MET* 3.8 20.1 - - + +
92D ALA* 3.6 22.0 - - + -
101D PHE* 3.3 44.0 - - + +
102D ALA 3.9 1.8 - - - +
103D ALA* 3.8 9.0 - - + -
109D VAL* 3.8 25.8 - - + -
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Residues in contact with ASN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D THR* 2.9 22.5 + - + +
38D ALA* 3.5 8.3 + - - +
40D LEU* 1.3 75.4 - - - +
42D ASP* 1.3 62.0 + - - +
44D VAL* 3.7 7.1 + - - +
45D LYS* 3.5 49.7 + - - +
109D VAL* 4.0 12.8 - - + +
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Residues in contact with ASP 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ALA* 2.8 27.8 + - - +
39D TYR* 3.6 10.4 - - + +
41D ASN* 1.3 76.8 + - - +
43D ALA* 1.3 64.4 + - - +
45D LYS* 3.1 34.1 + - - +
46D PHE* 3.2 24.5 + - + -
69D LEU* 3.7 18.2 - - + -
70D LYS* 5.4 6.4 + - - -
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D TYR* 2.8 21.3 + - + +
40D LEU* 3.3 9.4 + - - +
42D ASP* 1.3 74.0 - - - +
44D VAL* 1.3 55.0 + - - +
46D PHE* 3.6 2.1 + - - +
47D GLN* 3.1 33.6 + - - +
64D LEU* 4.5 2.3 - - + +
69D LEU* 4.0 18.8 - - + +
78D PHE* 3.9 20.6 - - + -
90D MET* 3.6 20.0 - - + -
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Residues in contact with VAL 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU 2.9 21.0 + - - +
41D ASN* 3.8 9.4 - - - +
43D ALA* 1.3 74.2 - - - +
45D LYS* 1.3 64.5 + - + +
47D GLN* 3.5 5.9 + - - +
48D GLU* 3.2 28.8 + - + +
88D TYR* 3.4 25.3 + - + +
90D MET* 4.0 13.7 - - + -
103D ALA* 4.3 7.2 - - + -
104D THR 5.3 2.7 - - - +
108D GLY* 5.6 2.2 - - - -
109D VAL* 3.9 19.5 - - + +
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Residues in contact with LYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ASN* 3.5 41.2 + - - +
42D ASP* 3.1 24.7 + - - +
44D VAL* 1.3 79.2 - - + +
46D PHE* 1.3 64.6 + - + +
48D GLU* 3.1 11.0 + - - +
49D MET* 3.0 33.0 + - - +
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Residues in contact with PHE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ASP* 3.2 28.6 + - + +
43D ALA 4.3 2.2 - - - +
45D LYS* 1.3 81.5 - - + +
47D GLN* 1.3 59.8 + - - +
49D MET* 3.5 31.5 - - + +
50D TYR* 3.2 21.7 + - - +
64D LEU* 3.4 26.6 - - + +
67D LEU* 3.9 22.2 - - + +
68D GLY* 3.4 25.1 - - - -
69D LEU* 3.3 44.0 - - + -
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Residues in contact with GLN 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ALA 3.1 25.4 + - - +
44D VAL* 3.6 8.5 - - - +
45D LYS 3.2 0.2 - - - -
46D PHE* 1.3 77.3 - - - +
48D GLU* 1.3 56.9 + - - +
50D TYR* 3.5 3.5 + - - +
51D GLN* 3.1 25.5 + - - +
57D TYR* 3.5 30.5 - - + -
58D THR* 3.0 51.9 + - - +
64D LEU* 3.8 7.2 - - + +
80D ILE* 4.3 3.4 - - - +
88D TYR* 4.0 22.4 - - + +
90D MET* 3.4 32.5 - - + +
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Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D VAL* 3.2 19.4 + - + +
45D LYS* 3.1 10.4 + - - +
47D GLN* 1.3 76.0 - - + +
49D MET* 1.3 63.1 + - + +
51D GLN* 3.4 11.9 + - - +
52D ILE* 3.2 28.7 + - + +
57D TYR* 3.0 28.1 + - - -
88D TYR* 4.5 8.3 + - - -
105D PRO* 5.2 2.8 - - - +
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Residues in contact with MET 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LYS* 3.0 20.1 + - + +
46D PHE* 3.5 41.3 - - + +
47D GLN 3.3 0.2 - - - -
48D GLU* 1.3 75.3 - - + +
50D TYR* 1.3 61.2 + - - +
52D ILE* 3.4 16.5 + - + +
53D ASP* 3.2 28.1 + - - +
67D LEU* 3.6 24.4 - - + +
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Residues in contact with TYR 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D PHE 3.2 17.8 + - - +
47D GLN* 3.7 6.1 - - - +
48D GLU 3.4 0.2 - - - -
49D MET* 1.3 73.7 - - - +
51D GLN* 1.3 59.6 + - - +
53D ASP* 4.5 2.2 - - - +
54D ASN* 2.8 68.3 + - + +
56D SER* 3.5 19.7 - - - +
57D TYR 4.8 1.8 - - - -
58D THR* 3.3 38.4 - - + -
63D ALA* 3.8 17.5 - - + +
64D LEU* 4.7 0.7 - - + -
67D LEU* 3.4 27.9 - - + +
----------------------------------------------------------
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Residues in contact with GLN 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLN 3.1 14.3 + - - +
48D GLU* 3.4 18.6 - - - +
49D MET 3.3 0.4 - - - -
50D TYR* 1.3 74.1 - - - +
52D ILE* 1.3 62.4 + - + +
55D ASN* 3.2 53.9 + - - +
56D SER 3.0 27.0 + - - +
57D TYR* 3.2 32.6 - - + +
85D ALA 3.4 8.4 + - - +
86D ASN* 5.6 4.2 - - - +
----------------------------------------------------------
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Residues in contact with ILE 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D GLU* 3.2 19.1 + - + +
49D MET* 3.5 20.4 - - + +
50D TYR 3.3 0.4 - - - -
51D GLN* 1.3 79.7 - - + +
53D ASP* 1.3 69.3 + - - +
55D ASN* 4.0 8.2 + - - +
----------------------------------------------------------
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Residues in contact with ASP 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D MET 3.2 16.0 + - - +
50D TYR* 3.3 5.5 + - - +
52D ILE* 1.3 89.2 - - - +
54D ASN* 1.3 76.0 + - - +
55D ASN* 3.9 5.4 + - - +
67D LEU* 4.6 15.2 - - - +
----------------------------------------------------------
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Residues in contact with ASN 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D TYR* 2.8 64.9 + - + +
53D ASP* 1.3 89.0 - - - +
55D ASN* 1.3 72.8 + - - +
56D SER* 4.3 7.0 - - - +
67D LEU* 5.7 0.4 - - - +
----------------------------------------------------------
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Residues in contact with ASN 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D TYR 3.9 0.4 + - - -
51D GLN* 3.2 37.3 + - - +
52D ILE 4.0 10.5 + - - -
53D ASP 4.5 4.4 + - - +
54D ASN* 1.3 81.2 - - - +
56D SER* 1.3 60.1 + - - +
85D ALA* 4.2 8.8 - - - +
----------------------------------------------------------
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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).
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