Contacts of the helix formed by residues 27 - 53 (chain B) in PDB entry 1UPX
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 LYS 27 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B MET* 4.4 0.4 - - - -
21B VAL* 4.8 7.2 - - + -
25B GLY 3.2 12.1 + - - +
26B LYS* 1.3 77.3 - - - +
28B PRO* 1.3 77.1 - - + +
29B GLU* 3.3 4.5 - - + +
30B THR* 3.0 18.5 + - - +
31B ALA* 2.9 19.1 + - - +
79B PHE* 5.5 0.2 - - - -
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Residues in contact with PRO 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ALA* 3.8 30.9 - - + +
4B MET* 3.9 13.2 - - + +
20B GLN* 3.2 39.9 - - - +
21B VAL* 4.6 4.3 - - + -
27B LYS* 1.3 88.9 - - + +
29B GLU* 1.3 60.4 + - + +
31B ALA* 3.3 2.8 + - + +
32B ALA* 2.9 27.2 + - - +
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 3.3 4.0 - - + +
28B PRO* 1.3 78.2 - - + +
30B THR* 1.3 66.2 + - - +
32B ALA* 3.3 1.4 + - - -
33B LEU* 3.0 22.2 + - + +
81B ASP* 4.2 15.1 - - - +
119B LYS* 4.5 10.4 + - - -
123B LEU* 3.4 44.3 - - + +
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Residues in contact with THR 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LYS* 3.8 17.0 - - + -
27B LYS* 3.0 22.9 + - - +
29B GLU* 1.3 79.0 - - - +
31B ALA* 1.3 61.6 + - - +
33B LEU* 3.2 4.9 + - - +
34B GLN* 3.0 31.5 + - - +
79B PHE* 3.9 24.1 + - + +
81B ASP* 2.6 29.0 + - - +
84B LEU* 3.8 18.4 - - + -
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B MET* 3.7 39.0 - - + -
5B PHE 5.5 1.6 - - - +
6B CYS* 5.3 2.5 - - + -
26B LYS* 3.8 19.0 - - - +
27B LYS 2.9 9.8 + - - +
28B PRO 3.5 8.5 - - - +
29B GLU 3.3 0.2 - - - -
30B THR* 1.3 78.1 - - - +
32B ALA* 1.3 56.3 + - - +
34B GLN* 3.3 4.4 + - - +
35B ASP* 3.0 36.2 + - - +
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ALA 5.7 2.0 - - - +
4B MET* 5.6 0.2 - - - +
28B PRO 2.9 13.6 + - - +
29B GLU* 3.5 10.1 - - - +
30B THR 3.2 0.4 - - - -
31B ALA* 1.3 73.9 - - - +
33B LEU* 1.3 59.8 + - - +
35B ASP* 3.2 5.6 + - - -
36B ALA* 2.9 25.7 + - - +
122B MET 5.3 0.2 - - - -
123B LEU* 3.7 20.4 - - + +
126B ALA* 3.2 32.0 - - + +
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU 3.0 16.1 + - - +
30B THR 3.2 6.9 + - - +
32B ALA* 1.3 75.1 - - - +
34B GLN* 1.3 57.7 + - - +
36B ALA* 3.3 4.9 + - + +
37B LEU* 2.9 29.1 + - - +
81B ASP* 3.5 52.9 - - + +
84B LEU* 4.1 16.3 - - + +
85B ALA* 4.5 3.1 - - + -
88B VAL* 4.1 3.6 - - + +
119B LYS* 4.0 17.3 - - + -
122B MET* 3.8 40.4 - - + -
123B LEU* 3.8 14.8 - - + -
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LYS* 3.3 37.4 + - - +
30B THR* 3.0 17.5 + - - +
31B ALA* 3.7 7.2 - - - +
33B LEU* 1.3 75.3 - - - +
35B ASP* 1.3 59.0 + - - +
37B LEU* 3.2 4.5 + - - +
38B ILE* 2.9 34.4 + - - +
72B ALA 4.0 6.2 + - - -
73B THR* 3.5 42.2 - - + +
74B ILE 5.2 1.8 + - - +
78B ASN 2.9 28.7 + - - +
84B LEU* 3.9 17.6 - - + +
151B LYS* 5.3 0.2 + - - -
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Residues in contact with ASP 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B MET* 6.0 0.3 - - - -
5B PHE 4.3 18.4 + - - +
6B CYS* 6.1 0.3 - - - +
31B ALA* 3.0 21.4 + - - +
32B ALA* 3.2 10.6 + - - +
34B GLN* 1.3 78.1 - - - +
36B ALA* 1.3 61.4 + - - +
38B ILE* 3.4 7.4 + - - +
39B TYR* 3.0 23.0 + - - +
126B ALA* 4.3 13.1 - - + +
129B VAL* 4.2 6.9 - - + +
130B GLY* 3.9 28.6 - - - +
131B VAL* 4.8 3.5 + - - +
144B TRP* 5.4 7.5 - - - -
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA 2.9 14.2 + - - +
33B LEU* 3.6 10.5 - - - +
35B ASP* 1.3 75.7 - - - +
37B LEU* 1.3 63.4 + - - +
39B TYR* 3.2 7.8 + - - +
40B VAL* 3.0 27.5 + - - +
88B VAL* 4.3 11.0 - - + -
114B TRP* 4.7 13.0 - - + -
122B MET* 4.1 25.4 - - + +
125B LYS* 5.6 0.7 - - + -
126B ALA* 4.5 3.1 - - + +
129B VAL* 4.6 5.6 - - + -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU 2.9 16.8 + - - +
34B GLN* 3.2 6.3 + - - +
36B ALA* 1.3 74.1 - - - +
38B ILE* 1.3 56.4 + - + +
40B VAL* 3.4 4.5 - - + +
41B THR* 2.7 37.2 + - - -
69B ASN* 3.6 52.0 - - + +
72B ALA* 4.6 0.4 - - + -
73B THR* 4.0 10.5 - - + -
84B LEU* 4.2 18.8 - - + +
87B ARG* 3.7 21.5 - - + +
88B VAL* 3.7 35.6 - - + +
91B THR* 3.9 2.0 - - - +
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 2.9 21.2 + - + +
35B ASP* 3.8 6.7 - - - +
37B LEU* 1.3 77.7 - - - +
39B TYR* 1.3 63.2 + - - +
41B THR* 3.2 4.2 + - - -
42B LYS* 2.9 53.5 + - + +
69B ASN 4.6 2.2 - - - +
70B LEU* 3.7 29.6 - - + -
73B THR* 3.4 33.2 - - + +
144B TRP* 4.1 20.0 - - + -
147B THR* 4.3 3.8 - - + -
151B LYS* 4.1 11.7 - - - +
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Residues in contact with TYR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASP 3.0 14.3 + - - +
36B ALA* 3.2 8.9 + - - +
38B ILE* 1.3 77.9 - - - +
40B VAL* 1.3 58.5 + - + +
42B LYS* 3.3 8.9 + - - +
43B GLY 3.0 21.1 + - - -
110B ASP* 2.6 37.2 + - - +
111B ALA* 3.2 40.8 + - + +
114B TRP* 4.1 23.6 - + + -
125B LYS* 3.8 14.4 - - + -
129B VAL* 3.5 49.0 - - + +
182B LEU* 5.0 13.5 - - + -
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ALA 3.0 13.2 + - - +
37B LEU* 3.4 17.3 - - + +
39B TYR* 1.3 80.6 - - + +
41B THR* 1.3 60.0 + - - +
43B GLY* 3.7 1.0 - - - +
44B LEU* 2.9 28.6 + - - +
88B VAL* 4.3 11.4 - - + +
91B THR* 3.6 24.7 - - + +
92B CYS* 4.0 7.2 - - - -
95B LYS* 3.7 27.2 - - - +
111B ALA 4.3 3.6 - - - +
114B TRP* 3.4 39.0 - - + +
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU 2.7 21.6 + - - -
38B ILE* 3.5 8.5 - - - -
40B VAL* 1.3 74.1 - - - +
42B LYS* 1.3 60.0 + - - +
44B LEU* 3.3 3.8 + - - +
45B GLY* 2.9 24.9 + - - -
66B VAL* 4.0 32.5 - - + +
69B ASN* 2.9 38.3 + - + +
70B LEU* 4.5 9.9 - - + -
91B THR* 4.2 5.8 - - - -
178B LEU* 4.0 12.7 - - + +
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Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 2.9 31.5 + - + +
39B TYR* 3.6 7.4 - - - +
41B THR* 1.3 73.5 - - - +
43B GLY* 1.3 58.3 + - - +
45B GLY* 3.2 2.3 + - - -
46B GLN* 2.9 26.9 + - - +
143B ARG* 4.9 1.4 + - - +
144B TRP* 3.7 28.3 - - - -
147B THR* 3.1 29.4 + - - -
178B LEU* 3.8 33.0 - - + +
179B ALA* 4.3 5.9 - - - -
181B THR* 3.1 26.4 + - - +
182B LEU* 3.5 35.0 - - + +
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Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR 3.0 11.5 + - - -
40B VAL 3.3 1.5 + - - -
41B THR 3.3 0.2 - - - -
42B LYS* 1.3 77.0 - - - +
44B LEU* 1.3 59.9 + - - +
46B GLN* 3.2 8.0 + - - +
47B ILE* 3.1 25.8 + - - +
95B LYS* 4.2 2.0 - - - -
109B SER* 4.9 0.4 - - - -
111B ALA* 3.7 34.0 - - - +
112B ALA* 3.7 8.1 - - - +
182B LEU* 4.7 0.9 - - - -
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL 2.9 17.8 + - - +
41B THR* 3.5 5.8 - - - +
42B LYS 3.3 0.2 - - - -
43B GLY* 1.3 75.0 - - - +
45B GLY* 1.3 56.6 + - - +
47B ILE* 3.2 2.1 + - + +
48B ALA* 2.9 29.7 + - + +
62B ILE* 4.1 15.3 - - + -
65B LEU* 3.9 28.7 - - + -
66B VAL* 3.8 23.8 - - + -
69B ASN* 5.3 0.4 - - - +
91B THR* 4.0 12.1 - - + -
94B ALA* 4.4 2.7 - - + -
95B LYS* 3.7 32.4 - - + +
98B LEU* 3.6 27.6 - - + -
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Residues in contact with GLY 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR 2.9 13.9 + - - -
42B LYS* 3.2 5.8 + - - -
44B LEU* 1.3 77.9 - - - +
46B GLN* 1.3 53.8 + - - +
48B ALA* 4.0 1.0 - - - +
49B THR* 2.7 37.9 + - - -
66B VAL* 5.4 0.9 - - - +
175B GLN* 3.6 34.8 - - - -
178B LEU* 4.9 2.5 - - - -
179B ALA* 4.0 0.4 - - - -
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Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS 2.9 12.6 + - - +
43B GLY* 3.2 8.9 + - - +
45B GLY* 1.3 75.7 - - - +
47B ILE* 1.3 64.2 + - - +
49B THR* 3.7 1.8 - - - -
50B ARG* 3.0 55.3 + - + +
107B GLY 4.1 10.1 + - - -
108B LEU* 4.6 3.6 - - - -
109B SER* 3.1 35.7 + - - +
112B ALA* 3.6 7.4 - - - +
179B ALA* 3.6 21.7 - - + +
182B LEU* 5.9 3.1 - - + -
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY 3.1 16.1 + - - +
44B LEU* 3.2 5.8 + - - +
46B GLN* 1.3 77.5 - - - +
48B ALA* 1.3 56.9 + - - +
50B ARG* 3.2 8.5 + - - +
51B LEU* 2.9 28.9 + - + +
95B LYS* 3.6 33.4 - - + +
98B LEU* 3.6 31.2 - - + +
99B ALA* 3.6 22.7 - - + +
102B LEU* 4.2 6.9 - - + +
108B LEU* 4.2 12.8 - - + -
112B ALA* 3.7 30.7 - - + +
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU 2.9 17.7 + - - +
45B GLY 4.0 1.8 - - - +
47B ILE* 1.3 77.1 - - - +
49B THR* 1.3 56.3 + - - +
51B LEU* 3.2 4.6 + - - +
52B ARG* 3.0 37.9 + - - +
58B VAL* 3.7 12.2 - - + +
62B ILE* 4.6 3.1 - - + -
98B LEU* 4.1 20.4 - - + +
175B GLN* 3.2 27.4 - - - +
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Residues in contact with THR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY 2.7 22.6 + - - -
46B GLN* 3.7 6.5 - - - -
48B ALA* 1.3 76.3 - - - +
50B ARG* 1.3 58.3 + - + +
52B ARG* 3.3 12.1 + - - +
53B ALA* 3.0 29.8 + - + +
172B ALA 4.7 0.3 + - - -
175B GLN* 3.3 3.1 + - - +
176B GLU* 3.3 47.9 + - + +
179B ALA* 4.6 5.2 - - + -
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Residues in contact with ARG 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLN* 3.0 40.9 + - + +
47B ILE* 3.2 4.9 + - - +
49B THR* 1.3 77.0 - - + +
51B LEU* 1.3 62.3 + - - +
53B ALA* 3.3 9.4 + - + +
54B GLU* 3.2 21.7 + - - +
102B LEU* 3.7 14.8 - - + +
104B ASP* 2.9 34.1 + - - +
105B LYS* 3.8 2.2 - - - +
106B SER* 2.8 33.9 + - - +
107B GLY 3.6 12.3 + - - -
108B LEU* 3.5 25.8 - - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE 2.9 16.7 + - - +
48B ALA 3.2 6.3 + - - +
50B ARG* 1.3 73.1 - - - +
52B ARG* 1.3 65.7 + - - +
54B GLU* 3.1 34.6 + - - +
56B LYS* 3.0 34.7 + - + -
57B ALA 5.0 2.9 - - - +
58B VAL* 4.0 13.7 - - + -
98B LEU* 3.6 50.5 - - + +
101B SER* 3.7 29.6 - - - +
102B LEU* 3.8 9.6 - - + +
----------------------------------------------------------
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 3.0 27.9 + - - +
49B THR* 3.3 11.5 + - + +
51B LEU* 1.3 75.9 - - - +
53B ALA* 1.3 57.8 + - - +
54B GLU 3.2 0.2 - - - -
55B GLY* 3.0 19.9 + - - -
56B LYS 3.6 10.3 - - - +
58B VAL* 3.7 29.9 + - + +
63B ASP* 3.2 20.8 + - - -
168B ASN 5.3 0.6 + - - -
171B ASP* 4.9 0.4 - - - +
172B ALA* 3.7 37.1 + - - +
175B GLN* 2.8 41.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B THR* 3.0 20.1 + - + +
50B ARG* 3.6 10.3 - - + +
51B LEU 3.1 0.4 - - - -
52B ARG* 1.3 75.7 - - - +
54B GLU* 1.3 56.4 + - - +
55B GLY 3.4 1.3 - - - -
----------------------------------------------------------
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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