Contacts of the helix formed by residues 27 - 54 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A MET* 4.4 0.7 - - - -
21A VAL* 4.6 9.0 - - + -
25A GLY 3.2 11.8 + - - +
26A LYS* 1.3 76.0 - - - +
28A PRO* 1.3 76.9 - - + +
29A GLU* 3.3 4.0 - - + +
30A THR* 3.1 18.3 + - - +
31A ALA* 2.9 19.8 + - - +
79A PHE* 5.5 0.2 - - - -
328A PHE* 6.5 0.4 - - - -
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Residues in contact with PRO 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 3.7 39.0 - - + +
4A MET* 4.0 13.3 - - + +
20A GLN 3.5 21.8 - - - +
21A VAL* 4.3 9.2 - - + -
27A LYS* 1.3 88.9 - - + +
29A GLU* 1.3 61.7 + - + +
31A ALA* 3.3 2.6 + - + +
32A ALA* 2.9 27.6 + - - +
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 3.3 2.7 - - + +
28A PRO* 1.3 80.3 - - + +
30A THR* 1.3 60.3 + - - +
32A ALA* 3.3 2.9 + - - +
33A LEU* 2.9 34.2 + - + +
81A ASP* 4.1 14.8 - - - +
119A LYS* 4.6 13.3 + - - +
123A LEU* 3.6 37.6 - - + +
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Residues in contact with THR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 3.9 16.8 - - + -
27A LYS* 3.1 24.6 + - - +
29A GLU* 1.3 77.9 - - - +
31A ALA* 1.3 62.5 + - - +
33A LEU* 3.2 4.5 + - - +
34A GLN* 3.0 35.4 + - - +
79A PHE* 3.9 22.9 + - + +
81A ASP* 2.6 29.8 + - - +
84A LEU* 3.7 17.9 - - + +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A MET* 3.7 35.7 - - + -
5A PHE 5.5 1.6 - - - +
6A CYS* 5.3 3.1 - - + -
26A LYS* 3.8 19.2 - - - +
27A LYS 2.9 11.9 + - - +
28A PRO 3.5 8.3 - - - +
30A THR* 1.3 75.3 - - - +
32A ALA* 1.3 57.7 + - - +
34A GLN* 3.3 4.7 + - - +
35A ASP* 2.9 36.6 + - - +
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA 5.8 2.0 - - - +
28A PRO 2.9 17.5 + - - +
29A GLU* 3.5 5.2 - - - +
30A THR 3.2 0.4 - - - -
31A ALA* 1.3 77.8 - - - +
33A LEU* 1.3 58.4 + - - +
35A ASP* 3.1 5.6 + - - -
36A ALA* 2.9 24.4 + - - +
123A LEU* 3.6 21.1 - - + +
126A ALA* 3.1 31.5 - - + +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU* 2.9 21.7 + - + +
30A THR 3.2 4.2 + - - +
32A ALA* 1.3 74.8 - - - +
34A GLN* 1.3 58.0 + - - +
36A ALA* 3.3 4.8 + - - +
37A LEU* 2.8 30.0 + - - +
81A ASP* 3.5 46.7 - - + +
84A LEU* 4.0 15.2 - - + +
85A ALA* 4.3 5.6 - - + +
88A VAL* 4.0 4.3 - - + +
119A LYS* 4.1 18.4 - - + -
122A MET* 3.9 39.3 - - + -
123A LEU* 3.9 13.7 - - + -
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Residues in contact with GLN 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 3.2 39.6 + - - +
30A THR* 3.0 21.2 + - - +
31A ALA* 3.7 5.2 - - - +
32A ALA 3.2 0.2 - - - -
33A LEU* 1.3 74.6 - - - +
35A ASP* 1.3 58.3 - - - +
37A LEU* 3.2 4.6 + - - +
38A ILE* 2.9 34.8 + - - +
72A ALA 3.9 6.9 + - - -
73A THR* 3.5 42.2 - - + +
74A ILE 5.3 1.8 + - - +
78A ASN 2.9 28.5 + - - +
79A PHE* 6.2 0.2 - - - -
84A LEU* 3.9 14.9 - - + +
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Residues in contact with ASP 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE 4.3 18.9 + - - +
6A CYS* 6.1 0.5 - - - +
31A ALA* 2.9 23.5 + - - +
32A ALA* 3.1 11.1 + - - +
34A GLN* 1.3 76.8 - - - +
36A ALA* 1.3 60.5 + - - +
38A ILE* 3.4 6.8 + - - +
39A TYR* 3.0 23.2 + - - +
126A ALA* 4.3 12.8 - - + +
129A VAL* 4.2 6.9 - - + +
130A GLY* 3.9 27.5 - - - +
131A VAL* 5.3 3.9 + - - +
144A TRP* 5.5 7.4 - - - -
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ALA 2.9 15.4 + - - +
33A LEU* 3.7 7.6 - - - +
35A ASP* 1.3 76.4 - - - +
37A LEU* 1.3 62.0 + - - +
39A TYR* 3.2 8.2 + - - +
40A VAL* 3.0 28.6 + - - +
88A VAL* 4.3 13.9 - - + -
114A TRP* 5.2 8.2 - - + -
122A MET* 4.0 26.2 - - + +
125A LYS* 5.6 1.3 - - + -
126A ALA* 4.3 4.4 - - + +
129A VAL* 4.6 5.4 - - - -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 2.8 17.3 + - - +
34A GLN 3.2 5.6 + - - +
36A ALA* 1.3 73.4 - - - +
38A ILE* 1.3 60.4 + - + +
40A VAL* 3.5 3.9 - - + +
41A THR* 2.7 32.9 + - - -
69A ASN* 3.6 50.5 - - + +
72A ALA* 4.6 0.9 - - + -
73A THR* 4.0 10.3 - - + -
84A LEU* 4.3 18.6 - - + +
87A ARG* 3.7 44.9 - - + +
88A VAL* 3.7 12.0 - - + +
91A THR* 3.9 2.2 - - - +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN 2.9 20.3 + - - +
35A ASP* 3.8 6.1 - - - +
36A ALA 3.3 0.2 - - - -
37A LEU* 1.3 74.4 - - - +
39A TYR* 1.3 63.6 + - - +
41A THR* 3.2 6.2 + - - +
42A LYS* 2.9 53.2 + - + +
69A ASN 4.7 1.6 - - - +
70A LEU* 3.5 31.2 - - + +
73A THR* 3.4 33.9 - - + +
144A TRP* 4.3 16.4 - - + -
147A THR* 4.3 6.1 - - + -
151A LYS* 4.0 12.3 - - - +
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Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP 3.0 13.9 + - - +
36A ALA* 3.2 9.2 + - - +
38A ILE* 1.3 79.3 - - - +
40A VAL* 1.3 71.2 + - + +
42A LYS* 3.2 7.8 + - + +
43A GLY 3.1 16.5 + - - -
110A ASP* 2.6 39.3 + - - +
111A ALA* 3.3 38.0 + - + +
114A TRP* 4.6 6.1 - + + -
125A LYS* 3.7 16.8 + - + -
129A VAL* 3.5 42.8 - - + +
182A LEU* 4.3 21.5 - - + -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 3.0 17.7 + - - +
37A LEU* 3.5 14.6 - - + +
39A TYR* 1.3 79.9 - - + +
41A THR* 1.3 57.5 + - - +
43A GLY* 3.6 1.4 - - - +
44A LEU* 2.9 27.7 + - - +
88A VAL* 4.4 12.6 - - + +
91A THR* 3.7 23.2 - - + +
92A CYS* 4.0 6.3 - - - -
95A LYS* 3.7 27.7 - - - +
111A ALA 4.3 5.2 - - - +
114A TRP* 3.6 37.0 - - + +
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU 2.7 21.6 + - - -
38A ILE* 3.2 8.5 + - - -
40A VAL* 1.3 74.8 - - - +
42A LYS* 1.3 60.7 + - - +
44A LEU* 3.3 3.9 + - + +
45A GLY* 2.9 25.1 + - - -
66A VAL* 3.9 34.2 - - + +
69A ASN* 2.9 37.9 + - + +
70A LEU* 4.6 9.0 - - + -
91A THR* 4.2 5.4 - - - -
178A LEU* 4.1 12.2 - - + +
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Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 2.9 33.7 + - + +
39A TYR* 3.2 9.4 + - - +
41A THR* 1.3 76.8 - - - +
43A GLY* 1.3 61.1 + - - +
45A GLY* 3.2 2.3 + - - -
46A GLN* 3.0 20.8 + - - +
143A ARG* 5.0 1.2 + - - +
144A TRP* 3.8 27.5 - - - -
147A THR* 3.1 27.9 + - - -
178A LEU* 3.6 34.8 - - + +
179A ALA* 4.0 6.9 - - - -
181A THR* 3.1 25.4 + - - +
182A LEU* 3.6 32.4 - - + +
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Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR 3.1 10.9 + - - -
40A VAL 3.3 3.8 + - - -
41A THR 3.2 0.4 - - - -
42A LYS* 1.3 77.0 - - - +
44A LEU* 1.3 60.8 + - - +
46A GLN* 3.2 6.3 + - - +
47A ILE* 3.1 25.6 + - - +
95A LYS* 4.2 1.6 - - - -
109A SER* 4.5 3.1 - - - -
111A ALA* 3.6 9.3 - - - +
112A ALA* 3.6 31.4 - - - +
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL 2.9 13.2 + - - +
41A THR* 3.3 9.4 + - - +
43A GLY* 1.3 75.0 - - - +
45A GLY* 1.3 63.2 + - - +
47A ILE* 3.2 2.7 + - + +
48A ALA* 2.9 23.0 + - + +
62A ILE* 4.1 14.4 - - + -
65A LEU* 3.8 29.2 - - + -
66A VAL* 3.8 26.2 - - + -
69A ASN* 5.3 0.2 - - - +
91A THR* 4.0 11.7 - - + -
94A ALA* 4.8 0.9 - - + -
95A LYS* 3.7 32.5 - - + +
98A LEU* 3.7 28.0 - - + -
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Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR 2.9 14.8 + - - -
42A LYS* 3.2 5.5 + - - -
44A LEU* 1.3 76.8 - - - +
46A GLN* 1.3 58.9 + - - +
48A ALA* 3.9 1.5 - - - +
49A THR* 2.7 30.5 + - - -
66A VAL* 5.3 0.6 - - - +
175A GLN* 3.5 38.0 - - - +
178A LEU* 5.0 2.0 - - - -
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Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS 3.0 10.6 + - - +
43A GLY* 3.2 8.0 + - - +
45A GLY* 1.3 77.5 - - - +
47A ILE* 1.3 61.9 + - - +
49A THR* 3.3 4.2 + - - -
50A ARG* 2.9 34.0 + - + +
107A GLY 3.1 25.5 + - - -
108A LEU* 3.8 13.9 - - + +
109A SER* 2.9 38.4 + - - +
112A ALA* 3.5 6.1 - - - +
179A ALA* 3.5 21.4 - - + +
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY 3.1 12.2 + - - +
44A LEU* 3.2 5.4 + - - +
46A GLN* 1.3 77.3 - - - +
48A ALA* 1.3 57.1 + - - +
50A ARG* 3.2 7.6 + - - +
51A LEU* 2.9 29.5 + - + +
95A LYS* 3.5 32.1 - - + +
98A LEU* 3.5 33.0 - - + +
99A ALA* 3.6 21.3 - - + +
102A LEU* 4.1 7.7 - - + +
108A LEU* 4.1 11.9 - - + -
112A ALA* 3.6 35.0 - - + +
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU 2.9 16.6 + - - +
45A GLY 3.9 2.2 - - - +
47A ILE* 1.3 75.8 - - - +
49A THR* 1.3 63.1 + - - +
51A LEU* 3.3 3.5 + - - +
52A ARG* 3.0 32.2 + - - +
58A VAL* 3.7 21.2 - - + +
62A ILE* 4.6 3.1 - - + -
98A LEU* 4.2 12.1 - - + +
175A GLN* 3.3 27.1 - - - +
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Residues in contact with THR 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY 2.7 22.7 + - - -
46A GLN* 3.5 6.7 - - - -
47A ILE 3.3 0.2 - - - -
48A ALA* 1.3 76.8 - - - +
50A ARG* 1.3 64.6 + - + +
52A ARG* 3.3 13.4 + - - +
53A ALA* 3.0 23.5 + - + +
172A ALA 4.7 0.2 + - - -
175A GLN* 3.5 2.6 - - - +
176A GLU* 3.3 49.1 + - + +
179A ALA* 5.1 2.7 - - + -
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Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN* 2.9 33.7 + - + +
47A ILE* 3.2 5.6 + - - +
49A THR* 1.3 77.7 - - + +
51A LEU* 1.3 62.7 + - - +
53A ALA* 3.2 10.6 + - - +
54A GLU* 3.0 30.0 + - - +
102A LEU* 3.8 17.6 - - + +
104A ASP* 2.9 43.2 + - - +
105A LYS 4.2 0.8 - - - -
106A SER 2.9 28.7 + - - +
107A GLY* 4.1 9.1 + - - -
108A LEU* 4.1 15.7 - - + +
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 2.9 17.9 + - + +
48A ALA 3.3 6.5 + - - +
50A ARG* 1.3 73.2 - - - +
52A ARG* 1.3 65.7 + - - +
54A GLU* 3.1 8.4 + - - -
56A LYS* 2.9 55.3 + - + +
57A ALA 4.9 3.6 - - - +
58A VAL* 3.9 13.7 - - + -
98A LEU* 3.7 40.6 - - + +
101A SER* 3.1 31.2 - - - +
102A LEU* 3.6 20.9 - - + -
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Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA* 3.0 28.1 + - - +
49A THR* 3.3 12.5 + - - +
51A LEU* 1.3 74.4 - - - +
53A ALA* 1.3 58.4 + - - +
55A GLY* 3.0 19.4 + - - -
56A LYS 3.9 8.5 - - - +
58A VAL* 3.7 30.1 + - + +
63A ASP* 3.4 18.2 + - - -
168A ASN* 4.5 13.1 + - - -
171A ASP* 4.9 0.6 - - - +
172A ALA* 3.9 35.1 + - - +
175A GLN* 2.9 41.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 3.0 15.2 + - + +
50A ARG* 3.6 14.6 - - - +
51A LEU 3.2 0.2 - - - -
52A ARG* 1.3 77.6 - - - +
54A GLU* 1.3 57.4 + - + +
55A GLY 3.2 1.0 + - - -
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 3.0 17.9 + - + +
51A LEU 3.1 8.4 + - - +
53A ALA* 1.3 76.7 - - + +
55A GLY* 1.3 60.2 + - - +
56A LYS* 2.7 46.7 + - + +
102A LEU* 3.7 17.4 - - - +
103A THR* 3.0 20.2 + - - -
104A ASP* 3.1 32.2 + - - +
----------------------------------------------------------
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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