Contacts of the helix formed by residues 37 - 65 (chain D) in PDB entry 3E1N
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 37 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D PHE* 2.9 24.1 + - + +
35D TRP* 3.7 36.3 - - + +
36D GLY* 1.3 73.7 - - - +
38D LYS* 1.3 64.1 + - - +
39D ARG 3.0 4.4 + - - -
40D LEU* 3.1 16.9 + - + +
41D ASN* 3.3 8.8 + - - +
83D VAL* 3.8 28.5 - - + -
150D LEU* 4.2 30.7 - - + +
153D GLN* 3.2 21.8 - - + -
154D ILE* 5.3 1.6 - - + -
140H LEU* 3.8 18.2 - - + -
143H LYS* 5.8 5.4 - - + +
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Residues in contact with LYS 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LYS* 5.4 10.8 - - + +
36D GLY* 2.8 18.3 + - - +
37D LEU* 1.3 71.5 - - - +
39D ARG* 1.3 55.7 + - - +
41D ASN* 3.4 10.1 + - - +
42D ASP* 3.1 35.2 + - - +
153D GLN 2.9 3.6 + - - +
154D ILE 3.2 30.6 + - - +
155D ARG* 4.4 8.1 - - - +
156D GLU* 3.9 34.3 + - - +
39H ARG* 5.8 4.1 - - - +
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Residues in contact with ARG 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LYS* 1.3 78.3 - - - +
40D LEU* 1.3 61.0 + - - +
42D ASP* 3.4 5.4 + - - +
43D VAL* 3.2 33.0 + - - +
133D TRP* 4.1 13.3 - - - +
137D GLU* 3.0 40.2 + - - -
140D LEU* 5.0 7.7 - - - +
149D TYR* 5.8 0.2 - - - -
152D ALA* 4.6 7.8 + - - +
153D GLN* 2.9 46.1 + - - +
155D ARG 4.0 15.0 - - - +
156D GLU* 4.5 14.1 - - - +
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D PHE* 3.7 28.0 - - + -
37D LEU* 3.1 18.5 + - + +
39D ARG* 1.3 81.3 - - - +
41D ASN* 1.3 62.1 + - - +
43D VAL* 4.5 2.0 - - - +
44D GLU* 2.9 35.9 + - + +
83D VAL* 4.1 16.4 - - + -
87D LEU* 5.1 3.4 - - + -
133D TRP* 4.0 25.8 - - + -
149D TYR* 3.4 30.7 - - + +
150D LEU* 5.6 0.2 - - + -
153D GLN* 3.5 38.1 + - + +
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Residues in contact with ASN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ALA* 3.2 33.4 - - - +
30D ARG* 3.4 31.0 + - - +
32D PHE* 3.9 1.4 - - - +
33D LYS* 3.5 36.8 - - + +
37D LEU 3.3 5.4 + - - +
38D LYS* 3.7 10.6 + - - +
39D ARG 3.3 0.2 - - - -
40D LEU* 1.3 74.4 - - - +
42D ASP* 1.3 82.6 + - - +
45D TYR* 2.9 29.2 + - - +
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Residues in contact with ASP 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LYS* 3.1 12.7 + - - +
39D ARG* 3.8 6.7 - - - +
40D LEU 3.4 0.2 - - - -
41D ASN* 1.3 88.6 + - - +
43D VAL* 1.3 65.8 + - + +
45D TYR* 3.7 3.2 - - - +
46D HIS* 2.9 42.2 + - + +
156D GLU* 2.9 42.2 - - - +
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ARG* 3.2 26.4 + - - +
40D LEU 3.5 1.1 + - - +
42D ASP* 1.3 78.3 - - + +
44D GLU* 1.4 57.6 + - - +
46D HIS* 3.0 8.7 + - - +
47D GLU* 2.9 36.0 + - + +
133D TRP* 3.4 55.4 - - + +
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Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D TYR* 3.3 27.5 - - + +
28D HIS* 3.1 19.4 - - - +
29D ALA* 3.8 15.7 - - + -
32D PHE* 3.6 20.1 - - + -
40D LEU 2.9 23.6 + - - +
43D VAL* 1.4 68.9 - - - +
45D TYR* 1.3 67.5 + - - +
47D GLU* 3.0 7.9 + - - +
48D SER* 2.8 23.7 + - - -
87D LEU* 4.2 3.0 - - - +
90D ASP* 2.7 28.0 - - - +
133D TRP* 3.7 24.8 - - + -
134D LEU* 4.2 3.3 - - - +
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Residues in contact with TYR 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D PHE* 3.5 31.2 - + - -
29D ALA* 3.6 11.1 - - + +
30D ARG* 3.3 28.9 - - - +
41D ASN* 2.9 22.3 + - - +
42D ASP* 3.7 4.0 - - - +
44D GLU* 1.3 78.2 - - - +
46D HIS* 1.3 81.1 + + - +
48D SER* 3.1 26.0 + - - -
49D ILE* 3.1 28.8 + - + +
200D HEM 3.1 44.4 + - + +
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Residues in contact with HIS 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ASP* 2.9 40.0 + - + +
43D VAL* 3.0 7.6 + - + +
45D TYR* 1.3 94.4 - + - +
47D GLU* 1.3 61.1 + - + +
49D ILE* 3.7 10.9 + - + +
50D ASP* 3.1 29.3 + - - +
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Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D TYR* 3.5 40.0 + - + -
43D VAL* 2.9 29.8 + - + +
44D GLU* 3.0 7.8 + - - +
46D HIS* 1.3 77.7 - - + +
48D SER* 1.3 59.9 + - - +
50D ASP* 3.1 9.4 + - - +
51D GLU* 2.9 31.5 + - - +
129D GLY 5.3 0.2 - - - -
130D HIS* 3.1 38.8 - - + +
133D TRP* 4.1 21.5 - - - +
134D LEU* 4.6 0.9 - - - +
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Residues in contact with SER 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ILE* 3.0 23.8 + - - +
25D TYR* 4.0 14.8 - - - +
26D PHE* 3.6 18.8 - - - +
44D GLU 2.8 11.2 + - - -
45D TYR* 3.1 15.0 - - - -
47D GLU* 1.3 75.4 - - - +
49D ILE* 1.3 59.5 + - - -
51D GLU* 3.1 7.3 + - - +
52D MET* 3.0 41.3 + - - +
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Residues in contact with ILE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D TYR* 3.1 45.2 + - + +
46D HIS* 3.8 14.1 - - - +
48D SER* 1.3 73.8 - - - +
50D ASP* 1.3 65.0 + - - +
52D MET* 3.1 25.5 + - + +
53D LYS* 2.9 32.5 + - - +
200D HEM 3.7 55.9 - - + +
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Residues in contact with ASP 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D HIS 3.1 18.9 + - - +
47D GLU* 3.1 11.9 - - - +
49D ILE* 1.3 77.4 - - - +
51D GLU* 1.3 64.1 + - - +
53D LYS* 3.0 19.0 + - - +
54D HIS* 3.0 28.2 + - + -
126D ASP* 4.8 12.7 - - - +
130D HIS* 2.9 31.1 + - + +
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Residues in contact with GLU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU* 2.7 16.2 - - - +
21D ALA* 3.6 15.7 - - + -
22D ILE* 3.5 21.6 - - + +
25D TYR* 3.4 13.1 - - + -
47D GLU 2.9 17.4 + - - +
48D SER* 3.1 2.9 + - - +
50D ASP* 1.3 74.7 - - - +
52D MET* 1.3 58.4 + - - +
54D HIS* 2.8 10.5 + - - +
55D ALA* 2.9 28.1 + - - +
94D GLU* 3.1 5.5 - - - +
130D HIS* 3.1 13.0 + - - -
300D FE2 2.0 31.0 - - - -
301D FE2 2.0 27.5 - - - -
400D UNK 3.3 5.0 + - - -
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Residues in contact with MET 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ILE* 3.7 14.8 - - + -
26D PHE* 4.5 1.3 - - + -
48D SER* 3.0 35.9 + - - +
49D ILE* 3.3 20.9 - - + +
51D GLU* 1.3 75.5 - - - +
53D LYS* 1.3 65.2 + - - +
55D ALA* 3.2 2.6 + - - +
56D ASP* 3.0 24.1 + - - +
200D HEM 2.3 111.0 - - + +
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Residues in contact with LYS 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ILE* 2.9 30.3 + - - +
50D ASP* 3.4 17.3 - - - +
52D MET* 1.3 76.4 - - - +
54D HIS* 1.3 67.2 + - + +
56D ASP* 3.4 7.1 + - - +
57D ARG* 3.1 30.0 + - - +
200D HEM 4.0 41.1 + - + +
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Residues in contact with HIS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU* 3.3 20.4 - - + +
50D ASP* 3.0 14.5 + - + +
51D GLU* 2.8 10.7 + - - +
53D LYS* 1.3 78.8 - - + +
55D ALA* 1.3 66.5 + - - +
57D ARG* 3.0 21.9 + - - +
58D TYR* 3.0 23.3 + - + -
123D ILE* 3.7 26.7 - - + +
126D ASP* 3.0 42.5 + - + +
127D GLU* 3.1 12.6 + - - -
130D HIS* 4.2 5.4 - + - -
300D FE2 2.4 29.3 - - - -
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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
----------------------------------------------------------
15D LEU* 3.7 24.6 - - + +
18D GLU* 3.9 6.7 - - + +
19D LEU* 4.5 3.6 - - + -
22D ILE* 4.0 12.1 - - + -
51D GLU 2.9 16.8 + - - +
52D MET 3.2 4.7 + - - +
54D HIS* 1.3 74.3 - - - +
56D ASP* 1.3 64.2 + - - +
58D TYR* 3.1 8.5 + - - +
59D ILE* 2.8 28.7 + - + +
200D HEM 4.0 15.9 - - + -
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Residues in contact with ASP 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 3.4 21.0 - - + -
30C ARG* 2.6 49.8 + - - -
52D MET 3.0 14.1 + - - +
53D LYS* 3.5 12.5 - - - +
55D ALA* 1.3 74.2 - - - +
57D ARG* 1.3 65.9 + - + +
59D ILE* 3.1 3.3 + - - +
60D GLU* 2.9 29.8 + - - +
200D HEM 4.1 11.1 - - + +
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Residues in contact with ARG 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D LYS* 3.1 17.5 + - - +
54D HIS* 3.0 14.7 + - - +
56D ASP* 1.3 78.0 - - + +
58D TYR* 1.3 63.0 + - - +
60D GLU* 3.9 5.5 - - - +
61D ARG* 3.0 24.6 + - - +
119D MET* 3.4 55.5 - - + +
122D GLU* 3.3 34.6 + - - +
123D ILE* 4.0 21.1 - - + +
126D ASP* 5.4 3.0 + - - -
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Residues in contact with TYR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 4.1 30.3 - - + +
14D LEU* 3.5 40.2 - - + +
15D LEU* 4.0 22.2 - - + -
18D GLU* 3.6 36.0 + - + -
54D HIS 3.0 24.3 + - - -
55D ALA* 3.4 5.2 - - - +
57D ARG* 1.3 74.8 - - - +
59D ILE* 1.3 58.6 + - - +
61D ARG* 3.1 4.5 + - - +
62D ILE* 2.8 38.1 + - + +
101D LEU* 3.6 16.5 - - - +
119D MET* 4.6 6.5 - - - -
120D MET* 4.4 6.9 - - + +
123D ILE* 3.6 28.1 - - + +
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Residues in contact with ILE 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 3.9 24.5 - - + -
27C LEU* 4.3 9.4 - - + +
30C ARG* 4.1 15.7 - - + -
15D LEU* 3.8 24.2 - - + -
55D ALA* 2.8 29.3 + - + +
56D ASP* 3.1 4.9 + - - +
58D TYR* 1.3 71.9 - - - +
60D GLU* 1.3 59.0 + - - +
62D ILE* 3.5 2.2 + - - +
63D LEU* 3.0 46.8 + - + +
69D PRO* 3.9 15.5 - - + +
71D LEU* 3.9 26.0 - - + -
200D HEM 4.5 4.7 - - + -
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ARG* 3.0 41.1 + - + +
33C LYS* 3.1 30.1 + - - -
34C ASN* 5.1 1.0 + - - -
56D ASP* 2.9 27.6 + - - +
57D ARG* 4.0 5.8 - - - +
59D ILE* 1.3 75.9 - - - +
61D ARG* 1.3 58.8 + - - +
63D LEU* 3.6 7.7 + - - +
64D PHE* 2.9 29.0 + - - +
119D MET* 6.2 0.2 - - + -
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 5.0 4.4 - - - +
11D LEU* 3.7 21.3 - - + -
57D ARG 3.0 17.9 + - - +
58D TYR* 3.5 4.0 - - - +
60D GLU* 1.3 75.8 - - - +
62D ILE* 1.3 55.4 + - - +
64D PHE* 2.9 36.0 + - - +
65D LEU* 2.7 52.5 + - + +
113D ASP* 2.9 29.5 + - - -
115D VAL* 3.1 32.3 - - - +
116D SER* 2.9 20.3 + - - +
119D MET* 3.8 28.2 - - + +
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Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ILE* 4.0 12.8 - - + +
11D LEU* 3.6 25.4 - - + +
12D ASN* 3.4 43.3 - - - +
15D LEU* 4.4 6.5 - - + -
58D TYR 2.8 27.9 + - - +
59D ILE 3.9 3.1 - - - +
61D ARG* 1.3 71.9 - - - +
63D LEU* 1.3 64.2 + - - +
65D LEU* 3.1 7.3 + - - +
66D GLU 3.0 5.9 + - - -
67D GLY* 2.9 49.9 + - - +
68D LEU 3.8 2.0 - - - +
69D PRO* 3.6 19.3 - - + -
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.3 2.7 - - + -
30C ARG* 3.6 43.7 - - + +
31C MET* 3.9 19.7 - - + +
34C ASN* 3.8 24.2 + - + +
59D ILE* 3.0 29.6 + - + +
60D GLU* 3.7 5.6 - - - +
62D ILE* 1.3 76.2 - - - +
64D PHE* 1.3 65.9 + - - +
66D GLU* 2.9 15.9 + - - +
67D GLY 3.8 7.2 - - - +
68D LEU* 5.8 2.2 - - + -
69D PRO* 3.3 28.7 - - + -
----------------------------------------------------------
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Residues in contact with PHE 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASN* 3.9 13.9 + - - +
1D MET* 3.3 63.7 + - + +
60D GLU 2.9 18.2 + - - +
61D ARG* 2.9 36.8 + - - +
63D LEU* 1.3 76.8 - - - +
65D LEU* 1.3 64.8 + - + +
66D GLU* 3.0 7.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 3.2 24.2 - - + +
2D LYS* 3.9 0.5 - - - +
3D GLY* 3.0 36.7 + - - -
7D VAL* 4.5 5.2 - - + -
8D ILE* 3.6 18.2 - - + +
11D LEU* 4.0 18.4 - - + -
61D ARG* 2.7 42.1 + - - +
62D ILE 3.1 4.9 + - - +
64D PHE* 1.3 80.2 - - + +
66D GLU* 1.3 67.2 + - - +
67D GLY 3.5 0.7 + - - -
113D ASP* 3.8 10.5 - - - +
116D SER* 3.7 22.0 - - - +
----------------------------------------------------------
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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