Contacts of the helix formed by residues 22 - 50 (chain D) in PDB entry 2UX1
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 22 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D SER* 1.3 87.4 - - - +
23D ALA* 1.3 59.2 + - - +
25D SER* 3.5 5.0 + - - +
26D LYS* 2.9 48.2 + - + +
83D LEU* 3.8 33.0 - - + +
139D GLU* 3.3 34.5 - - + +
140D GLY 5.4 0.4 - - - -
141D ASP* 4.2 19.3 - - + +
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Residues in contact with ALA 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D SER 3.4 10.6 - - - +
22D LEU* 1.3 77.1 - - - +
24D ASP* 1.3 59.7 + - - +
26D LYS* 3.6 10.7 + - - +
27D ALA* 3.1 27.9 + - - +
139D GLU* 3.7 1.5 + - - +
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Residues in contact with ASP 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ALA* 1.3 76.0 - - - +
25D SER* 1.3 66.6 + - - +
27D ALA* 3.1 6.9 + - - +
28D VAL* 3.0 24.3 + - - +
135D VAL* 3.4 21.9 - - + +
139D GLU* 3.0 21.7 + - + +
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Residues in contact with SER 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 3.8 7.2 - - - -
24D ASP* 1.3 71.3 - - - +
26D LYS* 1.3 64.4 + - - +
28D VAL* 3.1 8.6 - - - +
29D LEU* 3.0 28.2 + - - +
83D LEU* 4.9 2.5 - - - -
135D VAL* 3.4 8.0 + - - +
136D SER* 3.4 29.7 - - - -
139D GLU* 2.7 29.5 + - - +
141D ASP* 3.8 21.3 + - - +
144D THR* 4.9 4.0 - - - -
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Residues in contact with LYS 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 2.9 36.1 + - - +
23D ALA* 3.7 8.1 - - - +
25D SER* 1.3 76.2 - - - +
27D ALA* 1.3 64.5 + - - +
29D LEU* 3.3 5.5 + - - +
30D ASN* 3.0 20.3 + - - +
80D LEU* 3.5 33.0 - - + +
83D LEU* 3.2 39.1 + - + +
84D GLY* 4.4 8.5 + - - -
85D GLY* 4.1 9.9 - - - -
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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 ALA 3.1 18.1 + - - +
24D ASP* 3.1 8.4 + - - +
26D LYS* 1.3 76.9 - - - +
28D VAL* 1.3 57.1 + - - +
30D ASN* 3.4 6.6 + - - +
31D GLN* 2.9 27.2 + - - +
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Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASP 3.0 14.4 + - - +
25D SER* 3.1 24.7 - - - +
27D ALA* 1.3 74.8 - - - +
29D LEU* 1.3 60.4 + - - +
31D GLN* 3.3 6.7 + - + +
32D ALA* 2.8 28.6 + - - +
128D LEU* 4.1 20.1 - - + +
131D LYS* 4.3 6.7 - - + -
132D GLY* 3.5 39.7 - - - +
135D VAL* 4.2 13.2 - - + -
144D THR* 5.6 0.2 - - + -
148D PHE* 4.1 11.8 - - + -
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D SER 3.0 22.0 + - - +
26D LYS* 3.6 5.6 - - - +
28D VAL* 1.3 78.0 - - - +
30D ASN* 1.3 58.3 + - - +
32D ALA* 3.2 7.9 + - - +
33D VAL* 3.0 29.0 + - - +
76D MET* 3.6 39.0 - - + +
79D ARG* 4.0 7.6 - - + -
80D LEU* 3.9 24.5 - - + +
83D LEU* 3.9 27.6 - - + -
144D THR* 3.9 22.0 - - + -
147D ILE* 5.3 2.5 - - + -
148D PHE* 3.8 19.7 - - + -
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Residues in contact with ASN 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LYS 3.0 15.9 + - - +
27D ALA* 3.8 6.3 - - - +
28D VAL 3.2 0.2 - - - -
29D LEU* 1.3 73.6 - - - +
31D GLN* 1.3 66.2 + - - +
33D VAL* 3.1 6.5 + - - +
34D ALA 3.0 18.2 + - - -
80D LEU* 3.5 14.0 - - + +
86D ALA 3.4 20.0 + - - -
87D PRO* 3.3 7.3 - - - +
88D PHE* 2.8 69.2 + - + +
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Residues in contact with GLN 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ALA 2.9 14.7 + - - +
28D VAL* 3.4 13.5 - - + +
30D ASN* 1.3 75.8 - - - +
32D ALA* 1.3 63.0 + - - +
34D ALA* 3.2 5.3 + - - +
35D ASP* 2.9 54.9 + - - +
88D PHE* 4.3 4.2 - - - -
97D ASN* 3.0 30.1 + - - +
98D SER* 3.8 2.0 - - - +
99D GLN* 3.8 14.6 + - - +
124D TYR* 3.9 4.2 + - - +
128D LEU* 3.6 16.8 - - + -
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Residues in contact with ALA 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D VAL 2.8 17.7 + - - +
29D LEU* 3.2 11.2 + - - +
31D GLN* 1.3 74.0 - - - +
33D VAL* 1.3 56.5 + - - +
36D LEU* 2.8 38.4 + - + +
76D MET* 3.6 29.6 - - + -
128D LEU* 3.7 21.2 - - + +
129D PHE* 4.6 0.9 - - + -
148D PHE* 4.3 9.2 - - + -
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Residues in contact with VAL 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TRP* 4.3 6.1 - - + -
29D LEU 3.0 20.0 + - - +
30D ASN* 3.1 17.6 + - - +
32D ALA* 1.3 74.2 - - - +
34D ALA* 1.3 63.5 + - - +
36D LEU* 4.8 1.1 - - - -
37D SER* 3.0 28.2 + - - -
73D LEU* 3.5 22.9 - - + +
76D MET* 4.5 1.8 - - + -
77D SER* 3.7 36.8 - - - +
80D LEU* 5.2 0.9 - - + -
87D PRO* 4.7 2.2 - - + -
88D PHE* 3.6 27.4 - - + +
94D PHE* 3.7 11.9 - - + -
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Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ASN 3.0 12.0 + - - +
31D GLN* 3.6 7.0 - - - +
33D VAL* 1.3 77.2 - - - +
35D ASP* 1.3 62.1 + - - +
37D SER* 3.2 4.2 + - - -
38D VAL* 3.1 27.2 + - - +
88D PHE* 3.9 15.0 - - + -
94D PHE* 3.6 32.9 - - - +
97D ASN* 4.0 6.7 - - + +
98D SER* 3.8 15.5 - - - +
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Residues in contact with ASP 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D GLN* 2.9 29.6 + - - +
32D ALA 4.0 0.2 - - - +
34D ALA* 1.3 72.4 - - - +
36D LEU* 1.3 57.5 + - - +
38D VAL* 3.3 0.7 + - - -
39D ALA* 2.8 31.0 + - - +
98D SER* 2.5 32.8 + - - -
99D GLN 3.0 13.9 + - - -
100D LEU* 3.6 6.0 - - + +
124D TYR* 2.5 40.5 + - + -
125D LEU* 4.3 5.4 - - + -
128D LEU* 3.2 23.3 - - + +
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ALA* 2.8 28.5 + - + +
33D VAL 4.1 1.1 - - - +
35D ASP* 1.3 69.2 - - - +
37D SER* 1.3 59.5 + - - +
39D ALA* 4.1 1.8 - - - -
40D HIS* 2.8 31.4 + - - +
69D ILE* 3.6 43.0 - - + +
72D TYR* 3.8 5.8 - - + -
73D LEU* 3.7 40.2 - - + +
76D MET* 3.8 25.8 - - + -
125D LEU* 4.0 19.7 - - + -
129D PHE* 4.0 13.7 - - + -
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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
----------------------------------------------------------
91B LEU* 4.6 6.6 - - - +
33D VAL 3.0 15.0 + - - -
34D ALA 3.4 9.4 - - - -
36D LEU* 1.3 76.3 - - - +
38D VAL* 1.3 62.7 + - - +
40D HIS* 3.4 7.8 + - - +
41D SER* 3.2 19.9 + - - -
73D LEU* 3.7 18.5 - - - +
94D PHE* 3.5 45.2 - - - -
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Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.8 19.3 - - + -
34D ALA 3.1 14.5 + - - +
35D ASP 3.9 1.8 - - - +
37D SER* 1.3 72.4 - - - +
39D ALA* 1.3 65.9 + - - +
41D SER* 3.0 8.1 + - - -
42D ILE* 3.0 24.5 + - + +
94D PHE 3.7 10.3 - - - +
95D SER* 4.3 4.7 - - - -
98D SER* 3.5 24.7 - - - +
100D LEU* 3.8 28.7 - - + +
102D GLU* 3.7 26.9 - - + +
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Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ASP 2.8 21.8 + - - +
36D LEU* 3.6 6.1 - - - +
38D VAL* 1.3 73.4 - - - +
40D HIS* 1.3 62.5 + - - +
42D ILE* 3.4 4.6 + - - +
43D LEU* 3.0 31.0 + - + +
69D ILE* 4.7 7.0 - - + -
100D LEU* 4.0 4.6 - - + +
121D VAL* 3.7 30.4 - - + +
125D LEU* 4.0 17.0 - - + -
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Residues in contact with HIS 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ASP* 5.6 4.6 + - - -
36D LEU 2.8 17.5 + - - +
37D SER* 3.4 12.8 - - - +
39D ALA* 1.3 73.7 - - - +
41D SER* 1.3 62.2 + - - +
43D LEU* 3.3 8.4 + - - +
44D HIS* 3.0 24.3 + - - +
66D MET* 3.8 25.8 + - + +
69D ILE* 4.1 8.2 - - + +
70D ASP* 2.7 40.7 + - - +
73D LEU* 6.2 1.8 - - + -
1173D ZN 2.3 37.1 - - - -
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Residues in contact with SER 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B SER* 3.7 10.7 + - - +
91B LEU* 3.6 29.6 + - - +
94B PHE* 3.9 9.3 - - - -
37D SER 3.2 4.4 + - - -
38D VAL 3.0 8.8 + - - -
40D HIS* 1.3 87.1 - - - +
42D ILE* 1.3 55.0 + - - +
44D HIS* 3.2 5.6 + - - +
45D GLN* 2.9 29.0 + - - +
102D GLU* 2.7 27.8 + - - -
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Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B SER 5.6 0.2 - - - -
38D VAL* 3.0 29.6 + - + +
39D ALA* 3.8 7.0 - - - +
41D SER* 1.3 70.8 - - - +
43D LEU* 1.3 68.5 + - + +
45D GLN* 3.2 15.7 + - - +
46D VAL* 2.9 33.0 + - + +
100D LEU* 4.5 9.0 - - + -
101D LYS 4.1 18.8 - - - +
102D GLU* 4.0 16.2 - - + -
117D ARG* 5.3 11.7 - - + +
118D VAL* 5.8 2.0 - - + -
121D VAL* 4.0 31.6 - - + -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ALA* 3.0 22.2 + - + +
40D HIS* 3.3 0.9 + - - +
42D ILE* 1.3 77.9 - - + +
44D HIS* 1.3 57.6 + - - +
46D VAL* 3.4 5.5 + - - +
47D HIS* 3.0 27.0 + - - +
62D MET* 3.7 30.5 - - - +
65D TYR* 3.8 22.2 - - + -
66D MET* 3.6 23.6 - - + +
69D ILE* 3.8 29.6 - - + -
118D VAL* 3.9 28.0 - - + -
121D VAL* 5.9 3.4 - - + -
122D PHE* 4.3 9.4 - - + -
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Residues in contact with HIS 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ASP* 5.5 2.2 - - + -
73B LEU* 4.6 10.8 - - + -
74B ASP* 2.7 30.4 + - + -
40D HIS* 3.0 13.5 + + - +
41D SER* 3.2 6.3 + - - +
43D LEU* 1.3 74.4 - - - +
45D GLN* 1.3 66.6 + - - +
47D HIS* 3.2 16.7 - + - +
48D TRP* 3.1 60.8 + + + -
63D ASP* 5.4 0.2 + - - -
66D MET* 3.6 14.8 - - + +
1173D ZN 2.1 40.0 - - - -
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Residues in contact with GLN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B SER* 2.9 47.4 + - - +
90B THR* 3.9 1.2 - - - +
41D SER 2.9 14.0 + - - +
42D ILE* 3.2 18.3 + - - +
44D HIS* 1.3 76.7 - - - +
46D VAL* 1.3 58.9 + - - +
48D TRP* 3.2 1.9 + - - -
49D TYR* 2.9 43.2 + - + +
103D VAL* 2.7 41.1 + - - +
104D LEU 4.4 0.2 - - - +
105D GLY* 3.4 13.5 - - - +
106D ASP 5.4 0.4 - - - +
114D GLN* 5.6 2.6 - - - +
117D ARG* 4.4 8.3 + - - -
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Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ILE* 2.9 28.3 + - + +
43D LEU 3.6 6.7 - - - +
45D GLN* 1.3 76.9 - - + +
47D HIS* 1.3 63.9 + - - +
50D MET* 3.0 53.7 + - + +
62D MET* 3.8 17.9 - - + -
114D GLN* 3.6 40.2 - - + +
115D LEU* 5.6 0.2 - - + -
117D ARG* 5.2 4.3 - - + -
118D VAL* 4.1 19.7 - - + -
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Residues in contact with HIS 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASP* 3.5 5.8 - - - -
78B GLU* 3.0 7.9 + - - -
1173B ZN 2.0 37.6 - - - -
43D LEU 3.0 13.7 + - - +
44D HIS* 3.2 19.7 - + - +
46D VAL* 1.3 76.5 - - - +
48D TRP* 1.3 76.0 + + - +
50D MET* 4.2 5.8 - - - +
55D PHE* 4.3 1.6 - - - -
59D HIS* 2.7 74.0 + + - +
62D MET* 3.8 15.3 - - + +
63D ASP* 3.4 23.7 + - - -
66D MET* 4.0 3.1 - - + -
160G TRP* 4.8 0.2 - - - -
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Residues in contact with TRP 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 4.3 2.9 - - + -
73B LEU* 3.8 24.0 - - + -
74B ASP* 2.8 20.8 + - - -
77B SER* 3.1 33.2 - - - -
78B GLU* 3.5 24.7 + - + +
81B ILE* 3.6 30.1 - - + +
87B PRO* 3.9 8.5 - - + -
88B PHE 3.5 20.4 - - - -
89B SER* 4.1 17.9 - - - -
94B PHE* 4.8 6.1 - + - -
44D HIS* 3.1 47.5 + + + +
45D GLN 3.8 2.5 - - - +
46D VAL 3.2 0.2 - - - -
47D HIS* 1.3 94.5 - + - +
49D TYR* 1.3 66.4 - - + +
50D MET 3.4 3.5 + - - +
55D PHE* 5.3 0.3 - - - -
59D HIS* 5.1 0.9 - + - -
107D TYR* 3.9 7.3 - - - -
160G TRP* 4.6 7.2 + - - -
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Residues in contact with TYR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA* 3.1 13.0 - - + +
87B PRO* 2.5 48.8 + - + -
89B SER* 3.4 20.4 - - - -
45D GLN* 2.9 35.5 + - + +
48D TRP* 1.3 77.2 - - + +
50D MET* 1.3 65.6 + - - +
51D ARG* 3.3 2.6 + - - +
105D GLY* 3.5 22.0 + - - -
106D ASP* 3.4 27.4 - - - +
107D TYR* 3.5 61.1 - + - +
109D VAL 5.2 0.3 - - - +
114D GLN* 4.1 13.1 + - - +
----------------------------------------------------------
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Residues in contact with MET 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D VAL* 3.0 46.2 + - + +
47D HIS 4.2 2.0 - - - +
48D TRP 3.4 3.4 - - - +
49D TYR* 1.3 77.7 - - - +
51D ARG* 1.3 64.5 + - - +
55D PHE* 3.4 40.2 - - + +
58D TRP* 3.7 28.0 - - + +
59D HIS* 3.5 30.7 - - - -
62D MET* 4.7 1.3 - - + -
111D ILE* 3.3 25.1 - - + -
114D GLN* 4.2 16.6 - - + +
115D LEU* 4.9 5.6 - - + -
160G TRP* 5.4 0.7 + - - -
164G ALA* 3.8 2.1 - - - +
----------------------------------------------------------
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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).
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