Contacts of the helix formed by residues 50 - 73 (chain A) in PDB entry 1O0W
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 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.1 24.0 - - - +
29A ALA* 2.9 22.6 + - - +
30A LEU 4.6 1.0 - - - -
31A CYS 2.9 21.9 + - - +
32A HIS* 4.5 12.3 - - - +
33A SER 4.8 0.9 + - - -
49A SER* 1.3 71.4 - - - +
51A GLU* 1.3 66.5 + - - +
52A LYS 3.4 2.2 - - - -
53A LEU* 3.3 3.7 + - - +
54A GLU* 2.8 31.5 + - - +
107A LEU* 5.8 0.2 - - - +
124A ILE* 5.4 0.8 + - - +
127A ASP* 4.6 6.5 - - - +
128A ALA* 3.8 23.4 - - - +
131A ALA* 3.6 11.4 - - + -
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A SER* 3.9 19.3 + - - +
49A SER* 2.7 27.3 + - - +
50A ASN* 1.3 83.6 - - - +
52A LYS* 1.3 63.1 + - + +
54A GLU* 3.4 15.4 + - - +
55A PHE* 3.1 20.6 + - - +
78B VAL* 3.7 25.1 - - + +
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 6.4 1.6 - - - -
48A GLU* 5.6 6.0 + - - +
49A SER* 4.6 6.4 + - - +
50A ASN 3.4 0.8 - - - -
51A GLU* 1.3 73.8 - - + +
53A LEU* 1.3 66.1 + - + +
55A PHE* 3.2 10.3 + - - +
56A LEU 3.1 17.2 + - - -
70B TYR* 3.5 26.7 - - + -
73B TYR 4.4 3.8 - - - -
74B PRO* 2.9 34.9 + - - -
75B GLU* 4.3 3.2 + - - +
76B ALA 3.2 25.8 + - - +
77B GLU* 5.2 1.2 - - - +
78B VAL* 3.9 15.0 - - + +
81B LEU* 3.9 16.8 - - + -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.7 14.1 - - + +
28A ARG* 3.3 35.4 - - + +
29A ALA* 3.5 24.2 - - + +
49A SER 5.4 0.4 + - - -
50A ASN 3.3 7.0 + - - +
52A LYS* 1.3 77.7 - - + +
54A GLU* 1.3 52.1 + - - +
56A LEU 3.1 0.5 + - - -
57A GLY* 2.6 33.6 + - - -
131A ALA* 3.8 16.3 - - + +
134A ALA* 3.0 19.0 - - + +
135A ALA* 4.1 7.9 - - + +
138A LEU* 3.6 17.3 - - + -
70B TYR* 3.1 32.8 - - + +
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN* 2.8 21.8 + - - +
51A GLU* 3.5 14.5 - - - +
52A LYS 3.2 0.2 - - - -
53A LEU* 1.3 76.8 - - - +
55A PHE* 1.3 62.1 + - - +
58A ASP* 3.0 25.1 + - - +
127A ASP* 3.3 57.5 - - - +
130A GLU* 3.6 19.2 - - + +
131A ALA* 3.7 11.1 - - + +
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Residues in contact with PHE 55 (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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51A GLU 3.1 13.1 + - - +
52A LYS* 3.2 12.3 + - - +
54A GLU* 1.3 79.3 - - - +
56A LEU* 1.3 66.1 + - + +
58A ASP* 3.7 8.6 + - - +
59A ALA 3.9 5.5 + - - -
66B CYS* 3.5 54.2 - - + -
69B LEU* 3.8 20.2 - - + -
70B TYR* 4.5 4.7 - - + -
78B VAL* 4.2 16.8 - - + -
81B LEU* 3.8 51.4 - - + -
82B ALA* 4.1 10.8 - - + -
85B LYS* 4.3 9.6 - - + -
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS 3.1 11.8 + - - +
53A LEU 3.7 5.6 - - - +
55A PHE* 1.3 78.3 - - - +
57A GLY* 1.3 68.3 + - - +
59A ALA* 3.0 7.3 + - - +
60A VAL* 3.0 23.0 + - + +
134A ALA* 3.9 10.1 - - + -
137A TYR* 4.4 7.2 - - + -
138A LEU* 3.8 33.7 - - + -
63B LEU* 3.7 25.4 - - + -
66B CYS* 4.0 6.7 - - + +
67B GLU* 3.8 27.4 - - + +
70B TYR* 3.8 30.3 - - + -
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Residues in contact with GLY 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU 2.6 16.4 + - - -
54A GLU 3.3 1.3 + - - -
56A LEU* 1.3 74.6 - - - +
58A ASP* 1.3 55.3 + - - +
60A VAL* 3.2 5.3 + - - +
61A LEU* 2.9 30.0 + - - +
130A GLU* 3.1 32.0 - - - +
133A LEU* 4.5 2.9 - - - +
134A ALA* 3.5 11.0 - - - +
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Residues in contact with ASP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 3.0 16.5 + - - +
55A PHE* 4.0 6.7 - - - +
56A LEU 3.2 0.4 - - - -
57A GLY* 1.3 75.3 - - - +
59A ALA* 1.3 58.3 + - - +
61A LEU* 3.6 5.0 + - - +
62A GLU* 3.0 32.6 + - - +
89A ALA* 5.4 2.9 - - - +
130A GLU* 2.5 35.7 - - - +
85B LYS* 5.6 3.6 + - - -
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Residues in contact with ALA 59 (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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55A PHE 3.9 1.4 + - - +
56A LEU 3.0 10.7 + - - +
58A ASP* 1.3 78.9 + - - +
60A VAL* 1.3 65.2 + - - +
62A GLU* 3.8 10.1 - - - +
63A LEU* 3.1 23.9 + - - +
59B ALA 4.8 1.2 - - - +
62B GLU* 3.9 4.5 - - + +
63B LEU* 3.8 32.6 - - + +
66B CYS* 3.8 26.9 - - + -
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.0 23.1 + - + +
57A GLY* 3.2 11.4 + - - +
59A ALA* 1.3 76.2 - - - +
61A LEU* 1.3 58.4 + - - +
63A LEU* 3.8 2.3 - - - +
64A PHE* 2.9 27.5 + - - +
133A LEU* 4.4 11.7 - - + +
134A ALA* 4.5 1.8 - - - -
137A TYR* 3.9 28.5 - - + -
142A TYR* 4.5 7.0 - - + -
145A ILE* 3.2 38.4 - - + -
63B LEU* 3.8 23.6 - - + -
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Residues in contact with LEU 61 (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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57A GLY 2.9 17.0 + - - +
58A ASP* 3.7 5.4 - - - +
60A VAL* 1.3 76.5 - - - +
62A GLU* 1.3 57.9 + - - +
64A PHE* 3.2 12.2 + - + +
65A VAL* 2.8 44.9 + - + +
89A ALA* 3.9 23.3 - - + +
94A LEU* 3.5 35.4 - - + -
130A GLU* 3.6 15.7 - - + +
133A LEU* 3.9 23.1 - - + -
153A PHE* 4.3 20.0 - - + -
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Residues in contact with GLU 62 (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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58A ASP* 3.0 21.4 + - - +
59A ALA* 3.8 7.3 - - - +
60A VAL 3.4 0.2 - - - -
61A LEU* 1.3 75.1 - - - +
63A LEU* 1.3 58.3 + - - +
65A VAL* 3.9 3.3 - - - +
66A CYS* 2.8 45.0 + - - -
85A LYS* 4.4 23.4 + - + +
89A ALA* 5.7 4.7 - - - -
58B ASP* 3.5 17.5 - - - +
59B ALA* 3.4 29.5 + - + +
62B GLU* 3.5 22.7 - - - +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA 3.1 16.9 + - - +
60A VAL 3.8 3.1 - - - +
62A GLU* 1.3 76.0 - - - +
64A PHE* 1.3 58.9 + - - +
67A GLU* 2.8 31.7 + - - +
142A TYR* 3.7 16.6 - - + +
56B LEU* 4.0 15.7 - - + -
59B ALA* 3.7 17.9 - - + +
60B VAL* 3.9 28.0 - - + +
63B LEU* 3.4 30.3 - - + -
137B TYR* 3.9 29.6 - - + +
142B TYR* 5.3 3.8 - - + -
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Residues in contact with PHE 64 (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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60A VAL 2.9 18.8 + - - +
61A LEU* 3.2 14.6 + - + +
63A LEU* 1.3 78.1 - - - +
65A VAL* 1.3 71.3 + - + +
67A GLU* 3.9 1.7 - - - +
68A ILE* 3.3 36.9 + - + +
133A LEU* 6.0 2.9 - - + -
142A TYR* 3.2 20.8 + + + +
145A ILE* 4.0 20.9 - - + -
146A LYS* 4.0 25.1 - - + -
149A PHE* 3.5 33.4 - - + -
150A GLU* 3.5 21.3 - - + -
153A PHE* 3.6 31.4 - + + -
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Residues in contact with VAL 65 (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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61A LEU* 2.8 41.2 + - + +
62A GLU* 4.0 3.8 - - - +
64A PHE* 1.3 79.1 - - + +
66A CYS* 1.3 66.7 + - - +
68A ILE* 3.1 5.5 + - - +
69A LEU* 3.0 39.7 + - + +
85A LYS* 4.0 15.3 - - + +
88A ALA* 4.0 24.2 - - + -
89A ALA* 4.9 6.1 - - + -
153A PHE* 4.4 10.5 - - + -
157A ILE* 3.9 17.5 - - + -
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Residues in contact with CYS 66 (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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62A GLU* 2.8 30.8 + - - +
63A LEU 4.0 0.9 - - - +
65A VAL* 1.3 75.0 - - - +
67A GLU* 1.3 57.5 + - - +
69A LEU* 4.3 0.7 - - - -
70A TYR* 2.8 31.9 + - - +
85A LYS* 3.4 32.1 - - - -
55B PHE* 3.6 36.5 - - + +
56B LEU* 4.1 8.1 - - + -
59B ALA* 3.9 22.2 - - + -
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Residues in contact with GLU 67 (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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63A LEU* 2.8 22.1 + - + +
64A PHE 3.9 2.0 - - - +
66A CYS* 1.3 72.6 - - - +
68A ILE* 1.3 65.1 + - + +
70A TYR* 3.8 2.4 - - - +
71A LYS* 2.7 63.6 + - + +
142A TYR* 2.7 26.9 + - - +
146A LYS* 4.2 13.6 + - + -
56B LEU* 3.8 16.1 - - + +
137B TYR* 2.5 41.9 + - + -
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Residues in contact with ILE 68 (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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64A PHE* 3.3 48.2 + - + +
65A VAL 3.1 6.8 + - - +
67A GLU* 1.3 79.7 - - + +
69A LEU* 1.3 57.3 + - - +
71A LYS* 4.9 2.2 - - - -
72A LYS* 2.9 47.6 + - + +
73A TYR* 5.1 0.4 - - + -
150A GLU* 4.0 29.4 - - + +
153A PHE* 4.2 7.2 - - + -
154A GLU* 4.0 15.0 - - + -
157A ILE* 3.8 33.0 - - + -
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Residues in contact with LEU 69 (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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65A VAL* 3.0 25.3 + - + +
66A CYS 3.6 5.8 - - - +
68A ILE* 1.3 76.1 - - - +
70A TYR* 1.3 64.8 + - - +
73A TYR* 3.0 33.8 + - + +
81A LEU* 3.5 32.3 - - + +
84A VAL* 3.8 13.5 - - + -
85A LYS* 3.7 18.4 - - - +
157A ILE* 3.7 27.8 - - + -
161A MET* 3.8 21.1 - - + -
55B PHE* 3.8 20.0 - - + -
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A CYS 2.8 20.5 + - - +
67A GLU 3.8 3.8 - - - +
69A LEU* 1.3 76.1 - - - +
71A LYS* 1.3 72.1 + - + +
73A TYR 4.3 0.4 - - - -
74A PRO* 4.1 18.0 - - - +
81A LEU* 5.1 4.9 - - + -
25B LEU* 4.4 8.0 - - + +
28B ARG* 5.4 6.6 + - - -
52B LYS* 3.5 46.0 - - + -
53B LEU* 3.3 32.6 - - + +
55B PHE* 4.4 7.4 - + + -
56B LEU* 3.9 22.2 - - + -
138B LEU* 3.5 22.4 - - + +
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 2.7 52.7 + - + +
68A ILE* 4.2 2.7 - - - +
70A TYR* 1.3 88.9 - - + +
72A LYS* 1.3 67.0 + - + +
74A PRO* 3.8 9.0 - - - +
146A LYS* 5.0 6.1 - - - +
150A GLU* 6.2 0.2 - - - +
138B LEU* 3.7 23.9 - - - +
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Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 2.9 40.1 + - + +
71A LYS* 1.3 77.2 - - + +
73A TYR* 1.3 84.4 + - + +
74A PRO* 3.3 11.4 - - - +
150A GLU* 5.6 0.7 - - - +
154A GLU* 3.9 26.8 + - + +
158A GLU* 5.7 8.5 - - - -
218A ARG* 6.1 0.9 - - - +
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Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 4.7 2.5 - - + -
69A LEU* 3.0 37.0 + - + +
70A TYR* 4.3 1.0 - - - +
72A LYS* 1.3 101.8 - - + +
74A PRO* 1.3 63.9 - - - +
75A GLU 3.1 2.9 - - - +
76A ALA* 3.0 30.4 + - + +
81A LEU* 4.3 5.1 - - + +
157A ILE* 3.5 23.9 - - + +
158A GLU* 3.1 44.2 + - - +
161A MET* 3.8 29.8 - - + -
52B LYS* 5.1 1.0 - - - -
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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