Contacts of the helix formed by residues 53 - 80 (chain A) in PDB entry 1ZSP
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 ASP 53 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA* 2.9 16.9 + - - +
51A LYS* 3.2 13.8 - - + +
52A GLY* 1.3 73.2 - - - +
54A VAL* 1.3 62.7 + - - +
55A THR* 3.3 11.3 + - - -
56A ALA* 3.0 33.5 + - + +
57A GLN* 3.1 26.9 + - - +
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLY 3.1 2.1 + - - +
53A ASP* 1.3 69.1 + - - +
55A THR* 1.3 66.1 + - - +
57A GLN* 3.3 7.8 + - - +
58A ILE* 3.0 30.3 + - + +
2B HIS* 3.4 37.0 - - + +
38B LEU* 4.0 12.1 - - + -
42B GLU* 3.8 7.2 - - - +
64B LEU* 4.6 7.0 - - + -
68B GLY* 3.6 25.4 - - - +
71B HIS* 5.4 1.8 - - + -
72B ILE* 3.5 25.6 - - + -
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP* 3.3 8.6 + - - +
54A VAL* 1.3 79.7 - - - +
56A ALA* 1.3 64.4 + - - +
58A ILE* 3.2 4.7 + - - +
59A ALA* 2.9 23.2 + - + +
72B ILE* 3.6 25.6 - - - +
145B PRO* 5.6 0.3 - - - +
147B GLN* 3.9 40.3 + - + +
148B GLY* 3.9 16.9 + - - +
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA* 3.9 13.9 - - + -
53A ASP* 3.0 32.6 + - - +
55A THR* 1.3 79.3 - - - +
57A GLN* 1.3 63.0 + - - +
59A ALA* 3.1 8.1 + - - +
60A LEU* 3.0 32.5 + - + +
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 2.7 62.1 + - + +
48A ALA* 3.8 15.1 - - + +
49A LEU* 3.7 25.2 - - - +
53A ASP 3.1 22.2 + - - +
54A VAL* 3.6 10.6 - - - +
55A THR 3.3 0.2 - - - -
56A ALA* 1.3 75.4 - - - +
58A ILE* 1.3 63.0 + - - +
60A LEU* 3.2 10.5 + - - +
61A GLN* 3.4 11.4 + - - +
42B GLU* 2.8 24.5 + - - +
45B TYR* 5.5 0.8 - - - -
64B LEU* 3.7 23.4 - - + +
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.0 33.1 + - + +
55A THR 3.7 3.8 - - - +
57A GLN* 1.3 75.7 - - - +
59A ALA* 1.3 62.5 + - - +
61A GLN* 3.1 27.5 + - - +
62A PRO* 3.8 3.8 - - - +
64B LEU* 3.6 17.5 - - + +
65B LYS* 4.0 24.2 - - + -
69B GLY 3.9 15.0 - - - +
72B ILE* 4.2 2.7 - - + -
145B PRO* 3.6 35.4 - - + -
148B GLY 4.0 13.7 - - - +
149B THR* 4.1 10.5 - - + -
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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
----------------------------------------------------------
55A THR* 2.9 19.0 + - + +
56A ALA* 3.1 9.2 + - - +
58A ILE* 1.3 76.5 - - - +
60A LEU* 1.3 63.0 + - + +
62A PRO* 3.4 12.0 - - - +
63A ALA* 5.1 1.6 + - - +
147B GLN 5.2 1.3 - - - +
148B GLY* 3.3 23.1 + - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 4.0 13.4 - - + +
44A LYS* 3.9 32.5 - - + +
45A TYR* 3.7 47.6 - - + +
48A ALA* 4.4 3.8 - - + -
56A ALA* 3.0 26.6 + - + +
57A GLN* 3.6 5.4 - - - +
58A ILE 3.1 0.6 - - - -
59A ALA* 1.3 81.9 - - + +
61A GLN* 1.3 63.5 + - - +
62A PRO* 3.4 0.9 - - - -
63A ALA* 3.2 11.8 + - + +
64A LEU* 3.0 22.3 + - - +
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 5.1 6.8 + - + -
57A GLN 3.4 11.4 + - - +
58A ILE* 3.4 21.0 - - - +
60A LEU* 1.3 76.9 - - - +
62A PRO* 1.3 67.8 - - + +
64A LEU* 3.2 1.3 + - - -
65A LYS* 2.9 24.0 + - - +
45B TYR* 6.2 0.6 - - - -
61B GLN* 3.1 67.3 + - + +
64B LEU* 3.9 19.0 - - - +
65B LYS* 3.7 28.8 + - - +
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Residues in contact with PRO 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE 3.8 4.9 - - - +
59A ALA* 3.4 17.0 - - - +
60A LEU 3.5 0.7 - - - -
61A GLN* 1.3 92.7 - - + +
63A ALA* 1.3 55.9 + - - +
65A LYS* 3.9 9.4 - - + +
66A PHE* 2.9 33.1 + - - +
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.8 22.0 + - + +
59A ALA 5.1 0.9 + - - +
60A LEU* 3.2 13.5 + - + +
62A PRO* 1.3 80.6 - - - +
64A LEU* 1.3 58.0 + - - +
66A PHE* 4.5 2.7 - - - -
67A ASN* 2.9 44.0 + - - +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.8 25.1 - - + -
41A THR* 3.8 20.4 - - + +
42A GLU* 4.1 7.9 - - + +
45A TYR* 5.3 5.8 - - + -
60A LEU* 3.0 16.4 + - + +
61A GLN* 3.2 5.4 + - - +
63A ALA* 1.3 77.6 - - - +
65A LYS* 1.3 56.4 + - - +
67A ASN* 5.3 0.2 - - - -
68A GLY* 2.8 27.0 + - - +
45B TYR* 3.5 22.7 - - - +
54B VAL* 4.5 5.6 - - + -
57B GLN* 3.8 23.1 - - + +
58B ILE* 3.1 26.6 - - + +
61B GLN* 3.8 7.6 - - - +
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN 2.9 17.0 + - - +
62A PRO* 4.0 7.4 - - - +
64A LEU* 1.3 76.1 - - - +
66A PHE* 1.3 58.6 + - - +
69A GLY* 2.9 27.0 + - - -
143A GLN* 4.0 3.3 - - - +
144A ASP* 3.2 41.8 + - - +
145A PRO* 4.3 5.8 - - + -
149A THR* 4.5 6.0 - - + +
58B ILE* 3.2 26.6 - - + +
61B GLN* 3.6 20.0 - - - +
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 5.3 0.2 - - - +
62A PRO 2.9 19.9 + - - +
63A ALA* 4.0 3.6 - - - +
65A LYS* 1.3 79.5 - - - +
67A ASN* 1.3 77.4 + - - +
70A GLY* 3.1 19.8 + - - -
142A ASN* 4.7 8.5 - - + -
143A GLN* 3.3 35.3 - - + +
144A ASP* 5.9 0.7 - - - -
161A TRP* 3.5 35.0 - + - -
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Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 3.6 36.3 - - - +
37A ASN* 3.1 40.7 + - + +
38A LEU* 3.9 10.7 - - - +
41A THR* 4.5 1.9 + - - -
63A ALA* 2.9 32.5 + - - +
66A PHE* 1.3 93.4 - - - +
68A GLY* 1.3 65.7 + - - +
70A GLY* 3.3 1.6 + - - +
71A HIS* 3.0 19.2 + - - +
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Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.8 16.4 - - - +
64A LEU 2.8 19.5 + - - -
67A ASN* 1.3 74.1 - - - +
69A GLY* 1.3 60.5 + - - +
71A HIS* 3.0 4.5 + - - +
72A ILE* 2.9 31.9 + - - +
54B VAL* 3.5 23.1 - - - +
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Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU 4.0 0.2 + - - -
65A LYS* 2.9 16.1 + - - +
68A GLY* 1.3 76.5 - - - +
70A GLY* 1.3 57.4 + - - +
72A ILE* 4.3 1.1 - - - -
73A ASN* 2.8 36.2 + - - -
143A GLN 3.3 22.7 - - - -
145A PRO* 3.9 19.0 - - - +
54B VAL* 4.6 0.8 - - - +
58B ILE* 5.2 1.0 - - - +
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 4.4 0.6 + - - -
34A ALA* 4.2 12.3 - - - -
66A PHE 3.1 17.6 + - - -
67A ASN 3.3 4.7 + - - -
68A GLY 3.1 0.6 - - - -
69A GLY* 1.3 77.2 - - - +
71A HIS* 1.3 61.2 + - - +
74A HIS* 2.7 36.9 + - - +
143A GLN* 3.7 18.8 - - - +
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Residues in contact with HIS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HIS* 3.9 24.7 + + + +
3A SER 3.4 25.6 + - - -
5A PRO* 4.3 3.1 - - + -
31A HIS* 3.1 26.1 - + + -
34A ALA* 4.0 2.8 - - + +
35A VAL* 3.7 13.4 - - + +
38A LEU* 3.8 24.2 - - + -
67A ASN 3.0 13.3 + - - +
68A GLY 3.4 7.4 - - - +
70A GLY* 1.3 76.8 - - - +
72A ILE* 1.3 62.1 + - + +
75A SER* 2.7 48.3 + - - -
54B VAL* 5.0 5.2 - - + -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY 2.9 16.1 + - - +
69A GLY* 3.7 3.6 - - - +
71A HIS* 1.3 80.1 - - + +
73A ASN* 1.3 72.1 + - - +
75A SER* 3.7 3.4 - - - -
76A ILE* 3.3 37.4 + - + +
145A PRO* 4.1 24.0 - - + -
146A LEU 5.8 0.4 - - - +
154A PRO* 6.0 0.9 - - + -
54B VAL* 3.7 33.7 - - + +
55B THR* 3.5 30.7 - - - +
58B ILE* 5.1 0.2 - - + -
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Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 2.8 19.2 + - - +
70A GLY 4.2 1.6 - - - +
72A ILE* 1.3 75.8 - - - +
74A HIS* 1.3 57.5 + - - +
76A ILE* 3.3 4.7 + - - +
77A PHE* 2.9 26.9 + - - +
123A TRP* 3.4 33.0 - - + +
125A TRP* 3.8 23.0 - - + -
143A GLN* 2.9 43.5 + - - +
144A ASP 3.9 5.4 + - - -
145A PRO* 3.4 21.2 - - - +
146A LEU 4.3 0.5 + - - -
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Residues in contact with HIS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 3.2 20.5 + + - -
30A HIS* 5.1 4.4 - - + +
31A HIS* 3.5 35.5 - + + -
70A GLY* 2.7 28.2 + - - +
73A ASN* 1.3 71.9 - - - +
75A SER* 1.3 65.9 + - - +
77A PHE* 3.4 6.1 - + - +
78A TRP* 3.0 41.2 + + + +
123A TRP* 3.7 10.5 - + - -
143A GLN* 3.5 29.2 - - - -
159A ASP* 3.5 1.2 + - - -
163A HIS* 4.8 0.7 - + - -
199A MN 2.2 36.2 + - - -
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 4.1 11.0 - - - +
31A HIS* 3.4 15.1 + - - -
71A HIS* 2.7 39.9 + - - -
72A ILE* 3.7 5.8 - - - -
73A ASN 3.3 0.2 - - - -
74A HIS* 1.3 79.1 - - - +
76A ILE* 1.3 63.9 + - - +
78A TRP* 3.7 10.9 + - - +
79A THR* 3.6 19.4 + - - +
192A ARG* 5.2 0.7 - - - -
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.3 29.3 + - + +
73A ASN 3.7 5.6 - - - +
74A HIS 3.2 0.4 - - - -
75A SER* 1.3 78.0 - - - +
77A PHE* 1.3 64.8 + - - +
79A THR* 2.7 20.3 + - - -
80A ASN* 3.0 24.2 + - - +
125A TRP* 3.9 20.0 - - + -
154A PRO* 3.5 33.0 - - + -
155A LEU 5.1 0.9 - - - +
192A ARG* 3.8 38.6 - - - +
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 5.0 4.3 - - + -
23A MET* 6.0 0.9 - - + -
26A HIS* 4.1 21.3 - + - -
73A ASN 2.9 17.0 + - - +
74A HIS* 3.2 6.0 + + - +
76A ILE* 1.3 77.2 - - - +
78A TRP* 1.3 88.8 + + - +
80A ASN* 3.0 22.2 + - + +
81A LEU* 3.4 33.4 - - + +
123A TRP* 3.7 22.0 - + + -
125A TRP* 5.3 0.2 - - - -
157A GLY* 3.2 28.3 - - - -
158A ILE* 4.0 2.0 - - - -
159A ASP* 3.7 15.0 - - + -
164A ALA* 5.5 0.2 - - + -
176A TYR* 3.7 20.6 - - - -
180A ILE* 4.0 17.0 - - + -
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Residues in contact with TRP 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 4.4 11.2 - - + -
6A ASP 5.5 0.9 - - - +
7A LEU* 3.3 34.1 - - + -
8A PRO* 3.9 11.8 - - + +
9A TYR* 2.8 24.1 + - - -
23A MET* 3.7 26.0 - - + -
26A HIS* 3.5 43.1 - + + -
27A HIS* 3.9 25.8 + - + -
31A HIS* 2.9 29.6 - + - -
74A HIS* 3.0 30.9 + + + +
75A SER* 4.0 9.2 - - - +
76A ILE 3.3 0.4 - - - -
77A PHE* 1.3 96.1 - + - +
79A THR* 1.3 63.0 + - + +
81A LEU* 3.3 10.2 + - + +
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 4.5 14.8 - - + -
75A SER 3.6 12.6 - - - +
76A ILE 2.7 17.9 + - - -
78A TRP* 1.3 73.8 - - + +
80A ASN* 1.3 55.6 + - - +
81A LEU 3.2 6.5 - - - -
185A ASN* 3.2 15.0 + - - +
188A ASN* 3.2 36.8 + - - +
192A ARG* 2.9 23.1 + - - +
----------------------------------------------------------
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 3.0 27.3 + - - +
77A PHE* 3.0 13.3 + - + +
79A THR* 1.3 76.8 - - - +
81A LEU* 1.3 59.4 + - + +
155A LEU 3.3 14.9 + - - -
156A LEU* 3.4 18.5 - - + -
157A GLY* 2.9 31.0 + - - +
184A ILE* 3.6 10.2 - - - +
185A ASN* 2.7 29.2 + - - +
188A ASN* 2.8 23.3 + - - -
189A VAL* 4.4 2.8 - - - +
192A ARG* 3.7 5.7 - - - +
----------------------------------------------------------
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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