Contacts of the helix formed by residues 67 - 89 (chain D) in PDB entry 1B06
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 67 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 4.7 7.2 - - + -
55D LEU* 3.8 26.7 - - + -
65D TYR* 3.6 13.8 + - + -
66D ASP* 1.3 70.8 - - - +
68D GLN* 1.3 63.0 - - - +
70D ILE* 2.9 13.3 + - + +
71D LEU* 2.9 49.1 + - + +
122F VAL* 5.0 2.7 - - + +
125F GLU* 3.8 39.0 - - + +
126F SER* 3.8 26.5 - - - +
129F SER* 4.5 10.3 - - - +
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Residues in contact with GLN 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ASP 3.1 1.0 + - - -
67D LEU* 1.3 78.6 - - - +
69D GLY* 1.3 55.9 + - - +
71D LEU* 4.2 6.0 - - - +
72D ARG* 3.0 41.9 + - - +
69E GLY* 4.4 13.5 - - - +
72E ARG* 4.7 6.4 + - + -
129F SER* 2.9 47.6 + - - +
130F LEU 4.1 0.4 - - - +
131F PRO* 3.8 20.1 - - + +
151F THR* 3.2 29.1 + - - +
153F GLU* 4.4 7.8 - - - +
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Residues in contact with GLY 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU* 4.8 3.9 - - - +
66D ASP 2.7 17.8 + - - -
68D GLN* 1.3 74.4 - - - +
70D ILE* 1.3 55.6 + - - -
72D ARG* 4.7 1.2 - - - +
73D GLY* 3.2 22.5 + - - -
66E ASP* 4.1 11.4 - - - -
68E GLN* 4.4 11.2 - - - +
69E GLY* 3.6 24.8 - - - -
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Residues in contact with ILE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 4.1 30.6 - - + +
51D ARG* 4.2 17.7 - - + +
52D LEU* 4.3 18.2 - - + +
55D LEU* 4.1 20.2 - - + -
60D LEU* 5.3 0.7 - - + -
65D TYR* 4.1 19.1 - - + -
66D ASP 4.1 1.3 - - - +
67D LEU* 2.9 12.2 + - + +
69D GLY* 1.3 75.8 - - - +
71D LEU* 1.3 64.9 + - + +
73D GLY* 3.3 1.9 + - - -
74D LEU* 3.0 40.6 + - + +
66E ASP* 3.6 31.0 - - - +
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 5.1 9.6 - - + -
67D LEU* 2.9 46.1 + - + +
68D GLN* 4.2 9.6 - - - +
70D ILE* 1.3 72.9 - - - +
72D ARG* 1.3 60.9 + - - +
74D LEU* 3.1 22.7 + - + +
75D THR 3.3 1.2 + - - -
126F SER* 4.0 17.0 - - - +
129F SER* 4.4 0.9 - - - +
148F GLN* 4.7 1.8 - - - +
149F ILE* 3.9 26.9 - - + +
150F MET* 3.2 27.2 - - + +
151F THR* 4.0 37.5 - - + +
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Residues in contact with ARG 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C PRO* 4.3 10.9 - - - +
153C GLU* 2.8 43.4 + - - -
157C MET* 5.8 1.2 - - - -
68D GLN* 3.0 26.6 + - - +
69D GLY* 4.7 1.3 - - - +
71D LEU* 1.3 74.0 - - - +
73D GLY* 1.3 64.9 + - - +
75D THR* 3.3 19.0 + - - +
76D PHE* 3.3 14.6 + - - +
156D PHE* 3.5 36.1 - - + -
157D MET* 5.0 5.3 - - - -
68E GLN* 4.6 5.0 + - + -
72E ARG* 3.3 54.3 - - - +
150F MET* 5.2 0.9 - - - -
153F GLU* 4.1 7.5 + - - -
157F MET* 6.4 0.2 - - - -
158F ASN* 4.3 10.3 + - - +
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Residues in contact with GLY 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 3.4 16.6 - - - -
69D GLY 3.2 19.6 + - - -
70D ILE 3.7 0.2 - - - -
71D LEU 3.2 0.8 - - - -
72D ARG* 1.3 77.9 - - - +
74D LEU* 1.3 58.0 + - - +
76D PHE* 3.6 4.7 + - - +
77D ASN* 2.9 37.0 + - - -
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ALA* 3.8 14.6 - - - +
48D LEU* 3.6 25.4 - - + -
49D LEU* 4.4 11.0 - - + -
52D LEU* 4.0 20.2 - - + -
70D ILE* 3.0 27.4 + - + +
71D LEU* 3.1 13.4 + - + +
73D GLY* 1.3 76.0 - - - +
75D THR* 1.3 57.4 + - - +
77D ASN* 4.9 0.2 - - - -
78D ILE* 2.7 60.8 + - + +
148F GLN* 3.7 26.0 - - - +
150F MET* 4.2 7.0 - - + -
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Residues in contact with THR 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LEU 3.3 9.2 + - - -
72D ARG* 3.3 17.4 + - - +
74D LEU* 1.3 77.1 - - - +
76D PHE* 1.3 59.7 + - - +
79D ASN* 2.9 48.9 + - - +
156D PHE* 3.9 12.1 - - + +
150F MET* 3.7 14.8 - - - +
158F ASN* 2.6 48.9 + - + +
159F HIS 3.8 0.4 - - - +
160F ILE* 4.0 10.5 - - + -
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Residues in contact with PHE 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C PRO* 3.8 33.0 - - + -
132C GLY* 3.7 19.1 - - - -
41D TYR* 4.0 21.9 - + - -
72D ARG 3.3 15.0 + - - +
73D GLY* 3.7 5.4 - - - +
74D LEU 3.2 0.2 - - - -
75D THR* 1.3 80.7 - - - +
77D ASN* 1.3 80.0 + - - +
80D GLY* 3.0 24.1 + - - -
154D ASN* 3.3 25.8 - - - -
155D HIS* 3.6 19.8 - + - +
156D PHE* 3.9 22.4 - + + -
172D PHE* 5.2 1.3 - + - -
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Residues in contact with ASN 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D GLY 4.2 1.2 - - - +
41D TYR* 3.6 44.8 - - - +
44D GLY* 3.9 11.1 - - - -
45D ALA* 3.6 20.2 - - - +
48D LEU* 3.8 14.3 - - - +
73D GLY* 2.9 25.4 + - - +
74D LEU 4.3 0.7 - - - +
76D PHE* 1.3 93.5 - - - +
78D ILE* 1.3 65.1 + - - +
80D GLY 3.3 0.6 + - - +
81D HIS* 3.0 23.7 + - - +
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Residues in contact with ILE 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D TYR* 3.7 35.9 - - + +
45D ALA* 4.1 12.6 - - + -
49D LEU* 5.4 1.3 - - + -
74D LEU* 2.7 44.9 + - + +
75D THR 4.7 0.2 - - - +
77D ASN* 1.3 72.1 - - - +
79D ASN* 1.3 56.8 + - - +
81D HIS* 3.3 5.8 + - - +
82D LYS* 3.0 54.5 + - + +
148F GLN* 4.1 19.1 - - + +
160F ILE* 4.0 28.9 - - + -
163F LEU* 5.8 0.4 - - + -
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Residues in contact with ASN 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D THR* 2.9 37.5 + - - +
78D ILE* 1.3 74.8 - - - +
80D GLY* 1.3 66.3 + - - +
82D LYS* 4.6 4.3 - - - +
83D LEU* 2.9 32.8 + - - +
155D HIS* 3.4 25.1 - - + +
156D PHE* 3.6 6.3 - - - +
159D HIS* 3.7 3.3 + - - -
159F HIS 2.9 23.7 + - - -
160F ILE* 3.6 8.9 - - - +
161F ALA* 3.0 34.0 + - - +
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Residues in contact with GLY 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D TYR* 3.8 12.0 - - - -
76D PHE 3.0 19.3 + - - -
77D ASN 3.3 2.2 + - - -
78D ILE 3.2 0.4 - - - -
79D ASN* 1.3 77.5 - - - +
81D HIS* 1.3 60.1 + - - +
83D LEU* 5.1 0.2 - - - -
84D HIS* 2.5 34.0 + - - +
155D HIS* 3.8 26.0 - - - +
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Residues in contact with HIS 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D TYR* 3.7 26.4 - + + +
10D GLU 3.8 19.8 + - - -
12D PRO* 4.0 14.6 - - + -
38D HIS* 3.1 28.6 + - - +
41D TYR* 3.8 9.1 - - + +
42D VAL* 3.7 16.8 - - + +
45D ALA* 5.8 1.3 - - + -
77D ASN 3.0 16.2 + - - +
78D ILE* 3.6 4.7 - - - +
80D GLY* 1.3 74.3 - - - +
82D LYS* 1.3 79.0 + - + +
84D HIS 3.2 2.3 + - - -
85D ALA* 3.0 25.4 + - + +
143F GLU* 2.7 31.8 + - - -
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Residues in contact with LYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D TYR* 4.2 2.9 - - - -
78D ILE* 3.0 41.4 + - + +
79D ASN* 4.2 4.9 - - - +
81D HIS* 1.3 81.3 - - + +
83D LEU* 1.3 65.6 + - + +
85D ALA* 3.4 8.6 + - - +
86D ILE* 3.2 31.8 + - + +
141F ASP* 2.6 37.1 + - - -
142F ASN* 5.3 2.2 - - - +
143F GLU* 2.8 35.5 + - - +
160F ILE* 4.2 16.6 - - + -
161F ALA* 4.6 12.3 - - + +
162F GLU* 6.1 0.9 - - - +
163F LEU* 4.3 7.7 - - + +
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ASN* 2.9 23.5 + - - +
82D LYS* 1.3 76.1 - - + +
84D HIS* 1.3 61.0 + - - +
86D ILE* 3.4 14.7 + - + +
87D TYR* 3.0 27.0 + - - +
135D TRP* 3.6 48.5 - - + +
137D VAL* 5.7 0.2 - - + -
155D HIS* 3.6 25.4 - - - +
159D HIS* 3.9 14.8 - - + +
165D VAL* 4.8 4.7 - - + -
168D ILE* 4.1 18.5 - - + +
161F ALA* 3.8 24.9 - - + -
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Residues in contact with HIS 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D HIS* 3.2 20.3 + + - -
38D HIS* 3.7 26.7 - + + +
41D TYR* 3.4 26.7 - + - -
80D GLY 2.5 29.1 + - - +
81D HIS 3.2 3.2 + - - +
83D LEU* 1.3 76.3 - - - +
85D ALA* 1.3 63.7 + - - +
87D TYR* 3.3 7.9 + + - +
88D TRP* 2.8 44.4 + + - +
135D TRP* 3.5 22.2 - + - -
155D HIS* 3.8 7.2 - + - -
170D ASP* 3.3 1.4 + - - -
174D HIS* 3.9 0.4 + - - -
325D FE 2.2 31.7 - - - -
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Residues in contact with ALA 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PRO* 4.6 12.1 - - + -
38D HIS* 3.8 12.1 - - + -
81D HIS* 3.0 19.3 + - + +
82D LYS* 3.5 13.5 - - - +
83D LEU 3.2 0.2 - - - -
84D HIS* 1.3 79.7 - - - +
86D ILE* 1.3 59.9 + - + +
88D TRP* 3.9 5.2 + - - +
89D ASN* 3.0 31.9 + - - +
203D ARG* 5.5 0.4 - - - -
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Residues in contact with ILE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D LYS* 3.2 22.1 + - + +
83D LEU* 3.4 14.8 + - + +
84D HIS 3.2 0.2 - - - -
85D ALA* 1.3 75.2 - - + +
87D TYR* 1.3 55.6 + - - +
89D ASN* 3.2 3.6 + - - +
90D ASN* 2.8 41.2 + - + +
165D VAL* 4.0 23.8 - - + -
166D ILE 5.9 0.2 - - - +
168D ILE* 3.9 17.9 - - + -
203D ARG* 3.6 40.3 + - - +
161F ALA* 5.8 0.4 - - + -
162F GLU* 3.7 31.9 - - + +
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Residues in contact with TYR 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ILE* 4.2 8.8 - - - +
30D ILE* 6.1 0.2 - - + -
33D HIS* 3.7 22.2 + + - -
83D LEU 3.0 18.3 + - - +
84D HIS* 3.4 9.2 - + - +
86D ILE* 1.3 76.7 - - - +
88D TRP* 1.3 101.4 + + - +
90D ASN* 3.1 12.1 + - - +
91D MET* 3.5 40.4 + - + +
135D TRP* 3.9 10.3 - + + -
168D ILE* 3.9 27.3 - - + +
169D VAL* 4.4 1.3 - - - -
170D ASP* 3.6 30.7 - - + +
175D ALA* 4.5 2.1 + - - +
187D TYR* 2.8 24.1 + - - -
191D TRP* 4.5 3.8 - - - -
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Residues in contact with TRP 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PRO* 5.5 2.2 - - + -
13D GLN 5.8 1.6 - - - -
14D LEU* 3.8 20.2 - - + -
15D PRO* 3.9 21.8 - - + -
16D TYR* 2.8 29.6 + + - +
30D ILE* 4.1 22.7 - - + -
33D HIS* 3.5 37.2 - + + -
34D TYR* 4.0 29.7 - + + -
38D HIS* 2.9 31.1 + + - -
84D HIS* 2.8 34.0 + + + +
85D ALA* 4.1 6.3 - - - +
86D ILE 3.4 0.4 - - - -
87D TYR* 1.3 98.6 - + - +
89D ASN* 1.3 61.3 + - - +
91D MET* 3.4 18.4 + - + +
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Residues in contact with ASN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PRO* 3.4 24.2 - - - +
85D ALA* 3.0 21.6 + - - +
86D ILE* 3.2 7.1 + - - +
88D TRP* 1.3 73.0 - - - +
90D ASN* 1.3 57.1 + - - +
91D MET 3.1 6.8 + - - +
196D ASN* 3.1 26.3 + - - -
199D ASP* 3.2 22.1 - - - +
203D ARG* 4.1 8.9 - - - +
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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