Contacts of the helix formed by residues 45 - 72 (chain D) in PDB entry 1IES
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 GLU 45 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE 4.9 0.7 - - - -
38D ASP* 6.1 0.7 - - - +
43D ALA 3.8 3.5 + - - +
44D LEU* 1.3 72.2 - - - +
46D GLY* 1.3 59.3 + - - +
48D CYS* 3.1 9.4 + - - +
49D HIS* 2.8 38.2 + - + +
167D GLU* 3.5 8.2 + - - +
168D ARG* 4.2 9.5 + - - +
172D LYS* 3.5 26.8 + - + -
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Residues in contact with GLY 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLU* 1.3 71.7 - - - +
47D VAL* 1.3 56.7 + - - +
49D HIS* 3.3 8.3 - - - +
50D PHE* 3.0 27.7 + - - +
167D GLU* 2.7 25.9 + - - -
171D LEU* 3.9 28.7 - - - +
172D LYS* 4.9 4.9 - - - +
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 3.6 34.8 - - + -
44D LEU* 3.2 21.0 + - + +
45D GLU 3.1 0.6 - - - -
46D GLY* 1.3 72.1 - - - +
48D CYS* 1.3 67.3 + - - +
50D PHE* 3.2 5.6 + - + +
51D PHE* 3.1 40.6 + - + -
92D THR* 3.8 28.0 - - + +
96D MET* 5.5 0.7 - - + -
166D PHE* 5.4 0.2 - - + -
167D GLU* 4.0 10.1 - - + -
171D LEU* 3.7 23.1 - - + -
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Residues in contact with CYS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D GLY* 3.2 29.5 - - - +
35D PHE* 5.1 1.8 - - - -
37D PHE* 3.7 13.7 - - + +
38D ASP* 4.2 17.9 - - + +
44D LEU 3.0 13.3 + - - +
45D GLU* 3.3 12.1 - - - +
47D VAL* 1.3 75.7 - - - +
49D HIS* 1.3 66.5 + - - +
51D PHE* 3.4 0.7 + - - -
52D ARG* 2.9 45.9 + - - +
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Residues in contact with HIS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLU* 2.8 24.1 + - + +
46D GLY* 3.3 13.0 - - - +
48D CYS* 1.3 74.0 - - - +
50D PHE* 1.3 67.0 + - - +
52D ARG* 3.1 8.2 + - + +
53D GLU* 2.8 50.9 + - + +
171D LEU 6.0 0.4 - - - +
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D GLY 3.0 10.1 + - - +
47D VAL* 3.4 11.0 - - - +
49D HIS* 1.3 79.1 - - - +
51D PHE* 1.3 94.3 + + - +
53D GLU* 3.3 11.2 + - - +
54D LEU* 3.2 40.8 + - + +
96D MET* 3.6 25.1 - - + -
140D LEU* 5.0 1.3 - - + -
143D LYS* 4.1 21.1 - - + -
144D MET* 4.0 17.3 - - + -
147D HIS* 3.7 32.3 - + - -
171D LEU* 4.4 13.5 - - + -
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Residues in contact with PHE 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 3.5 37.7 - + + +
33D LEU* 4.0 16.2 - - + -
34D GLY* 3.7 21.5 - - - +
37D PHE* 4.3 5.2 - + - -
47D VAL* 3.1 41.3 + - + +
50D PHE* 1.3 103.1 - + - +
52D ARG* 1.3 66.1 + - - +
54D LEU* 3.3 3.7 + - + +
55D ALA* 2.9 19.6 + - - +
92D THR 5.7 0.2 - - - -
95D ALA* 3.8 36.1 - - + -
96D MET* 4.2 8.7 - - + -
99D ALA* 3.7 21.5 - - + -
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Residues in contact with ARG 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR 5.0 1.1 - - - -
31D LEU* 4.6 12.4 - - - +
34D GLY* 4.1 9.2 - - - -
35D PHE* 3.4 49.5 - - - -
48D CYS* 2.9 37.3 + - - +
49D HIS* 3.6 8.3 - - + +
51D PHE* 1.3 77.3 - - - +
53D GLU* 1.3 63.3 + - + +
55D ALA* 3.2 17.2 + - - +
56D GLU* 3.2 12.1 + - - +
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D HIS* 2.8 45.1 + - + +
50D PHE* 3.6 10.6 + - - +
52D ARG* 1.3 72.5 - - + +
54D LEU* 1.3 62.7 + - + +
56D GLU* 3.2 12.0 + - - +
57D GLU* 3.0 30.7 + - - +
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 3.9 26.9 - - + -
50D PHE* 3.2 33.9 + - + +
51D PHE* 3.3 8.7 + - + +
53D GLU* 1.3 73.0 - - + +
55D ALA* 1.3 66.3 + - - +
57D GLU* 3.2 19.1 + - - +
58D LYS* 2.9 33.2 + - - +
140D LEU* 3.6 37.0 - - + -
143D LYS* 6.0 0.9 - - - +
144D MET* 3.5 27.4 - - + -
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D SER* 2.9 42.2 + - - +
30D TYR* 3.6 12.9 - - + +
31D LEU* 3.8 17.3 - - + +
51D PHE 2.9 14.2 + - - +
52D ARG* 3.2 12.3 + - - +
54D LEU* 1.3 74.9 - - - +
56D GLU* 1.3 63.8 + - - +
58D LYS* 3.1 0.9 + - - +
59D ARG* 3.0 9.6 + - - +
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Residues in contact with GLU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D ARG 3.2 7.4 + - - +
53D GLU* 3.2 13.8 + - - +
55D ALA* 1.3 77.1 - - - +
57D GLU* 1.3 65.3 + - - +
59D ARG* 3.1 35.8 + - - +
60D GLU* 2.9 42.6 + - - +
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D TYR* 5.3 0.5 - - - -
53D GLU* 3.0 21.7 + - - +
54D LEU* 3.4 28.3 - - + +
56D GLU* 1.3 78.7 - - - +
58D LYS* 1.3 61.8 + - + +
60D GLU* 3.4 14.6 + - - +
61D GLY* 3.0 23.2 + - - -
136D GLU* 4.2 29.4 - - - +
140D LEU* 4.9 7.3 - - - +
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Residues in contact with LYS 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D TYR* 3.5 47.1 - - + +
26D ALA* 4.2 3.1 - - + -
27D SER* 3.8 6.7 - - - +
30D TYR* 3.9 17.7 - - + -
54D LEU* 2.9 26.0 + - - +
55D ALA 3.7 3.8 - - - +
57D GLU* 1.3 75.9 + - - +
59D ARG* 1.3 64.4 + - - +
61D GLY 3.2 0.5 + - - -
62D ALA* 3.0 21.8 + - - +
103D GLU* 2.8 42.5 + - - -
106D LEU* 3.9 12.5 - - + +
136D GLU* 4.7 9.8 + - - +
137D GLU* 3.3 15.2 + - - -
140D LEU* 4.0 12.1 - - - +
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Residues in contact with ARG 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 4.7 9.4 - - + +
27D SER* 3.6 18.2 + - - +
55D ALA 3.0 7.7 + - - +
56D GLU* 3.2 40.2 + - - +
58D LYS* 1.3 73.1 - - - +
60D GLU* 1.3 81.9 + - - +
62D ALA* 3.2 8.9 + - - +
63D GLU* 2.9 57.3 + - + +
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLU* 2.9 36.4 + - - +
57D GLU* 3.6 18.5 - - - +
59D ARG* 1.3 95.0 + - - +
61D GLY* 1.3 55.4 + - - +
63D GLU* 3.3 10.5 + - - +
64D ARG* 2.9 48.5 + - - +
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Residues in contact with GLY 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D TYR* 4.2 8.3 - - - -
57D GLU 3.0 15.9 + - - -
58D LYS 3.2 3.3 + - - -
60D GLU* 1.3 73.1 - - - +
62D ALA* 1.3 62.6 + - - +
64D ARG* 3.2 11.4 + - - +
65D LEU* 3.0 21.5 + - - +
133D PHE* 3.5 29.0 - - - -
136D GLU* 6.1 0.9 - - - -
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D VAL* 4.1 12.8 - - + +
23D TYR* 3.7 18.8 - - + +
24D LEU* 3.4 30.1 - - + -
58D LYS 3.0 11.1 + - - +
59D ARG 3.4 9.0 - - - +
61D GLY* 1.3 74.9 - - - +
63D GLU* 1.3 57.5 + - + +
65D LEU* 3.3 9.1 + - - +
66D LEU* 2.9 33.5 + - + +
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 6.3 0.4 - - + -
59D ARG* 2.9 50.5 + - + +
60D GLU* 3.3 11.0 + - - +
62D ALA* 1.3 72.5 - - + +
64D ARG* 1.3 58.4 + - - +
66D LEU* 3.2 15.0 + - + +
67D LYS* 2.9 31.1 + - - +
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Residues in contact with ARG 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D GLU* 2.9 40.3 + - - +
61D GLY* 3.2 16.0 + - - +
63D GLU* 1.3 70.2 - - - +
65D LEU* 1.3 63.9 + - - +
67D LYS* 3.3 8.7 + - - +
68D MET* 3.0 21.5 + - - +
128D PHE* 3.9 15.4 - - + -
132D HIS* 3.7 41.0 + - + +
133D PHE* 4.0 9.2 - - + -
136D GLU* 5.4 6.6 + - - -
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D VAL* 4.0 14.4 - - + +
19D LEU* 4.0 36.1 - - + -
20D VAL* 3.8 22.2 - - + +
23D TYR* 4.0 16.4 - - + -
61D GLY 3.0 19.7 + - - +
62D ALA* 3.3 7.8 + - - +
64D ARG* 1.3 74.2 - - - +
66D LEU* 1.3 57.0 + - - +
68D MET* 3.2 13.4 + - + +
69D GLN* 2.9 28.4 + - - +
113D LEU* 5.2 0.2 - - + -
128D PHE* 3.7 26.6 - - + -
129D LEU* 4.7 4.9 - - + -
133D PHE* 3.7 14.6 - - + -
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Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ASN* 5.0 2.9 - - - +
20D VAL* 3.7 35.4 - - + -
24D LEU* 5.3 2.7 - - + -
62D ALA* 2.9 25.5 + - + +
63D GLU* 3.2 15.7 + - + +
65D LEU* 1.3 73.9 - - - +
67D LYS* 1.3 62.6 + - - +
69D GLN* 3.3 7.8 - - + +
70D ASN* 3.3 25.7 + - - +
76D ALA* 3.9 28.1 - - + +
77D LEU 6.2 0.2 - - - +
78D PHE* 3.9 22.9 - - + -
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D GLU 2.9 16.5 + - - +
64D ARG* 3.7 8.1 - - - +
66D LEU* 1.3 76.4 - - - +
68D MET* 1.3 56.1 + - - +
70D ASN* 3.4 9.6 + - + +
71D GLN* 3.0 46.3 + - + +
139E LYS* 4.6 15.2 - - - +
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Residues in contact with MET 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D TYR* 4.0 9.6 - - - -
16D VAL* 3.9 24.5 - - + -
64D ARG 3.0 13.3 + - - +
65D LEU* 3.6 9.6 - - + +
67D LYS* 1.3 72.4 - - - +
69D GLN* 1.3 66.4 + - - +
71D GLN* 3.1 13.8 + - - +
72D ARG* 3.0 44.0 + - - +
124D HIS* 4.4 16.6 - - + -
125D LEU* 3.7 25.8 - - + -
128D PHE* 3.7 50.7 - - + -
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Residues in contact with GLN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D TYR* 2.7 44.6 + - - -
13D GLU* 3.1 26.5 + - - +
16D VAL* 3.8 7.0 - - + +
17D ASN* 3.1 32.3 + - - +
20D VAL* 6.0 0.2 - - - +
65D LEU 2.9 13.6 + - - +
66D LEU* 3.3 16.8 - - + +
68D MET* 1.3 76.9 - - - +
70D ASN* 1.3 60.3 + - - +
72D ARG* 3.3 1.9 + - - +
73D GLY 3.2 4.2 + - - -
74D GLY* 2.8 44.9 + - - +
75D ARG 4.0 2.0 - - - -
76D ALA* 4.0 17.9 - - + +
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Residues in contact with ASN 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 3.8 5.0 - - - +
66D LEU 3.3 11.4 + - - +
67D LYS* 3.6 10.8 - - + +
68D MET 3.2 0.2 - - - -
69D GLN* 1.3 82.8 - - - +
71D GLN* 1.3 60.2 + - - +
72D ARG 3.4 0.5 + - - -
73D GLY* 3.5 8.3 + - - -
74D GLY 3.9 13.4 - - - +
75D ARG* 4.3 12.4 + - - +
76D ALA* 5.2 7.5 + - - +
142E LYS* 3.3 27.1 - - - +
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Residues in contact with GLN 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 3.4 17.7 - - - +
67D LYS* 3.0 31.7 + - + +
68D MET* 3.1 16.7 + - + +
70D ASN* 1.3 75.5 - - + +
72D ARG* 1.3 58.2 + - + +
124D HIS* 5.0 4.4 - - - -
128D PHE* 6.2 1.0 - - - -
135E ASP* 4.5 4.6 + - - -
138E VAL* 3.8 35.9 - - + +
139E LYS* 3.4 43.1 + - - +
142E LYS* 3.6 20.2 + - + +
----------------------------------------------------------
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Residues in contact with ARG 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 4.4 2.5 - - - +
5D ARG* 3.3 29.0 - - - +
6D GLN* 2.7 28.3 + - - +
7D ASN* 3.0 23.6 + - - +
8D TYR* 3.7 39.1 - - + +
68D MET* 3.0 34.0 + - + +
69D GLN 3.9 2.2 - - - +
70D ASN 3.3 0.2 - - - -
71D GLN* 1.3 76.8 - - + +
73D GLY* 1.3 59.6 + - - +
122D ASP* 2.7 32.3 + - - -
124D HIS* 3.6 30.9 + - + +
125D LEU* 5.1 1.4 - - - +
138E VAL* 4.0 20.4 - - - +
----------------------------------------------------------
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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