Contacts of the helix formed by residues 38 - 67 (chain A) in PDB entry 1N1Q
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 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASN 5.1 2.0 + - - -
36A GLY 3.1 1.2 + - - -
37A PRO* 1.3 85.6 + - - +
39A PHE* 1.3 64.6 + - - +
40A PHE 3.4 2.7 - - - -
41A THR* 3.3 18.2 + - - +
42A LEU* 2.9 44.5 + - + +
93A ALA* 5.7 2.7 - - + -
147A PHE* 3.7 27.9 - - + -
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Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS 4.6 2.5 - - - -
32A TRP 4.9 4.9 - - - -
34A VAL* 3.1 44.3 - - + +
35A ASN* 4.1 10.5 - - + -
36A GLY 3.0 18.4 + - - +
37A PRO 3.3 1.6 - - - -
38A ASN* 1.3 76.9 - - - +
40A PHE* 1.3 93.4 + + + +
43A HIS* 2.7 70.4 + + + +
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Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO 5.0 4.6 + - - -
38A ASN 3.4 0.4 - - - -
39A PHE* 1.3 109.7 - + + +
41A THR* 1.3 63.7 + - - +
43A HIS* 3.8 5.9 - + + +
44A GLU* 3.2 24.6 + - - +
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 3.3 26.1 + - - +
40A PHE* 1.3 80.2 - - - +
42A LEU* 1.3 67.3 + - + +
44A GLU* 3.4 10.4 + - - +
45A LYS* 2.9 28.4 + - + +
147A PHE* 5.1 6.5 - - + -
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.8 23.6 - - + -
38A ASN* 2.9 25.1 + - + +
41A THR* 1.3 75.3 - - + +
43A HIS* 1.3 66.6 + - - +
44A GLU 3.0 1.8 - - - -
45A LYS* 4.0 13.2 - - + -
46A PHE* 2.8 50.2 + - + -
93A ALA* 3.9 18.4 - - + +
97A VAL* 3.9 32.1 - - + -
144A LEU* 5.8 3.4 - - + -
147A PHE* 4.1 26.0 - - + -
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 2.7 87.3 + + - +
32A TRP* 5.2 1.1 - - - -
34A VAL* 4.1 6.6 - - - +
39A PHE* 2.7 54.2 + + + +
40A PHE* 3.8 7.2 - + - +
42A LEU* 1.3 73.1 - - - +
44A GLU* 1.3 63.8 + - + +
47A GLU* 3.4 4.3 + - - -
62B GLU* 3.5 13.0 + - + -
515B FEO 3.7 15.6 - - - -
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE 3.2 15.3 + - - +
41A THR* 3.5 9.0 - - - +
42A LEU 3.0 0.2 - - - -
43A HIS* 1.3 81.1 - - + +
45A LYS* 1.3 65.5 + - - +
47A GLU* 3.1 14.2 + - - +
48A GLU* 3.1 21.9 + - + +
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 2.9 22.2 + - + +
42A LEU* 3.1 16.8 + - + +
44A GLU* 1.3 74.6 - - - +
46A PHE* 1.3 63.9 + - + +
48A GLU* 2.8 48.7 + - - +
49A LEU* 3.0 44.3 + - + +
140A HIS* 4.6 15.2 + - - -
143A MET* 4.8 16.8 - - - +
144A LEU* 4.6 18.8 - - + -
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Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.7 28.5 - - + +
30A PHE* 3.5 39.7 - - + -
31A HIS* 3.8 9.2 - - - -
34A VAL* 4.3 1.8 - - + -
42A LEU* 2.8 46.2 + - + +
43A HIS 4.1 0.2 - - - +
45A LYS* 1.3 76.8 - - + +
47A GLU* 1.3 57.2 + - - +
49A LEU* 3.7 11.8 - - + +
50A TYR* 2.9 34.0 + - - +
96A MET* 3.8 30.7 - - + -
97A VAL* 4.4 17.7 - - + -
100A VAL* 4.0 22.2 - - + -
144A LEU* 5.8 3.4 - - + -
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 3.7 19.0 + - + -
43A HIS* 3.4 5.3 + - - +
44A GLU* 3.1 16.7 + - - +
46A PHE* 1.3 75.0 - - - +
48A GLU* 1.3 65.3 + - - +
50A TYR* 3.4 29.4 + - + +
51A THR* 2.7 41.8 + - - +
515B FEO 4.3 13.4 + - - -
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 3.1 13.5 + - + +
45A LYS* 2.8 47.9 + - - +
47A GLU* 1.3 79.7 - - - +
49A LEU* 1.3 58.0 + - + +
51A THR* 3.4 7.1 + - - -
52A GLU* 3.1 38.8 + - + +
140A HIS* 3.6 19.0 - - - -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TRP* 4.8 2.4 - - - -
27A LEU* 3.6 24.9 - - + +
45A LYS* 3.0 34.5 + - + +
46A PHE* 3.8 16.2 - - + +
47A GLU 3.1 0.2 - - - -
48A GLU* 1.3 73.7 - - - +
50A TYR* 1.3 60.6 + - - +
51A THR 3.1 1.6 - - - -
52A GLU* 3.2 9.5 + - - +
53A ALA* 2.9 25.5 + - - +
100A VAL* 4.2 25.1 - - + -
104A PHE* 4.2 10.8 - - + -
140A HIS* 3.5 44.6 - - + +
144A LEU* 4.8 7.4 - - + -
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Residues in contact with TYR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.5 27.5 - + + +
27A LEU* 3.6 17.9 - - + +
28A HIS* 3.4 48.6 - + + -
31A HIS* 3.7 22.4 + + - -
46A PHE 2.9 26.0 + - - -
47A GLU* 3.4 34.2 + - + +
49A LEU* 1.3 71.1 - - - +
51A THR* 1.3 71.8 + - - +
53A ALA* 3.1 8.6 + - - +
54A SER* 2.9 25.8 + - - -
54B SER* 5.4 3.6 - - - -
58B ASP* 3.7 21.7 + - - +
515B FEO 3.9 0.7 + - - -
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 2.7 33.5 + - - +
48A GLU* 3.5 8.2 - - - -
50A TYR* 1.3 88.5 - - - +
52A GLU* 1.3 63.0 + - + +
54A SER* 3.3 10.0 + - - -
55A GLY* 3.3 15.4 + - - -
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TRP* 5.8 1.1 - - + -
48A GLU* 3.1 26.6 + - + +
49A LEU* 3.5 13.0 - - + +
51A THR* 1.3 75.7 - - + +
53A ALA* 1.3 63.4 + - - +
55A GLY* 2.9 4.7 + - - +
56A HIS* 2.9 46.1 + - + +
137A LEU* 6.0 0.5 - - - +
140A HIS* 2.9 37.3 + - - -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TRP* 3.5 33.1 - - + +
24A TYR* 4.0 22.7 - - - +
27A LEU* 4.2 2.7 - - + -
49A LEU 2.9 13.2 + - - +
50A TYR* 3.1 15.2 + - - +
52A GLU* 1.3 75.7 - - - +
54A SER* 1.3 62.5 + - - +
56A HIS* 3.1 3.4 + - - +
57A ILE* 2.9 29.6 + - - +
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.9 11.8 - - - -
50A TYR 2.9 12.8 + - - -
51A THR* 3.4 12.6 - - - -
53A ALA* 1.3 76.4 - - - +
55A GLY* 1.3 60.9 + - - +
57A ILE* 3.6 6.8 + - - +
58A ASP* 3.4 20.4 + - - +
24B TYR* 2.6 30.0 + - - -
28B HIS* 4.9 4.0 + - - -
50B TYR* 5.4 4.2 - - - -
54B SER* 5.7 0.9 + - - -
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Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR 3.3 6.2 + - - -
52A GLU* 2.9 8.8 + - - -
54A SER* 1.3 78.2 - - - +
56A HIS* 1.3 65.7 + - - +
58A ASP* 3.5 4.9 + - - +
59A THR* 3.1 32.1 + - - +
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Residues in contact with HIS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TRP* 3.5 58.8 - + + +
52A GLU* 2.9 41.3 + - + +
53A ALA 3.1 4.5 + - - +
55A GLY* 1.3 74.5 - - - +
57A ILE* 1.3 67.4 + - - +
59A THR* 3.1 7.3 + - - +
60A LEU* 2.8 36.2 + - + +
133A ILE* 3.5 35.1 + - + +
137A LEU* 5.4 3.0 - - - +
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.5 7.5 - - + +
20A TRP* 3.1 17.3 - - + +
21A VAL* 2.9 53.6 - - + +
24A TYR* 5.1 4.0 - - + -
53A ALA 2.9 21.7 + - - +
54A SER* 3.6 10.5 - - - +
56A HIS* 1.3 75.1 - - - +
58A ASP* 1.3 58.8 + - - +
60A LEU* 4.0 3.6 - - - +
61A ALA* 3.0 29.5 + - - +
24B TYR* 5.3 7.9 - - + +
25B VAL* 6.5 0.9 - - + -
28B HIS* 4.5 12.1 - - + +
32B TRP* 3.7 26.0 - - + -
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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 SER 3.4 9.6 + - - +
55A GLY* 4.0 6.7 - - - +
56A HIS 3.3 0.6 - - - -
57A ILE* 1.3 79.1 - - - +
59A THR* 1.3 61.8 + - + +
61A ALA* 4.0 0.2 - - - +
62A GLU* 3.0 41.4 + - - +
516A FEO 2.2 37.3 + - - -
28B HIS* 4.0 7.5 + - + -
31B HIS* 3.6 5.2 - - - -
32B TRP* 2.9 25.5 + - - +
50B TYR* 3.7 12.3 + - - +
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Residues in contact with THR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 3.1 17.0 + - - +
56A HIS* 3.1 16.2 + - - +
58A ASP* 1.3 77.8 - - + +
60A LEU* 1.3 66.8 + - - +
62A GLU* 3.8 5.7 - - - +
63A ARG* 2.9 29.6 + - - +
129A MET* 3.2 23.5 - - - +
133A ILE* 5.1 2.8 - - - +
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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
----------------------------------------------------------
13A LEU* 4.3 10.9 - - + +
16A GLN* 3.7 25.1 - - + +
17A VAL* 3.6 16.4 - - + +
20A TRP* 3.6 32.3 - - + +
56A HIS* 2.8 25.1 + - + +
57A ILE 4.0 0.9 - - - +
59A THR* 1.3 80.8 + - - +
61A ALA* 1.3 62.3 + - - +
63A ARG* 3.1 5.0 + - - +
64A VAL* 3.0 24.6 + - - +
111A LEU* 6.2 0.2 - - + -
129A MET* 3.7 25.1 - - + -
130A LEU* 3.9 21.5 - - + -
133A ILE* 5.3 9.2 - - + -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.7 8.5 - - + +
57A ILE 3.0 19.3 + - - +
60A LEU* 1.3 76.2 - - - +
62A GLU* 1.3 58.3 + - - +
64A VAL* 3.2 7.2 + - - +
65A LEU* 3.1 29.6 + - - +
71A PRO* 3.6 23.5 - - + +
32B TRP* 3.3 34.8 - - + +
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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
----------------------------------------------------------
58A ASP* 3.0 27.8 + - - +
59A THR* 4.0 5.1 - - - +
61A ALA* 1.3 72.8 - - - +
63A ARG* 1.3 60.3 + - - +
65A LEU* 3.4 14.3 + - + +
66A SER* 2.8 32.8 + - - +
516A FEO 2.1 43.7 + - - -
31B HIS* 3.2 8.8 + - - -
32B TRP* 3.9 14.1 - - + -
43B HIS* 3.5 12.2 - - + -
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.8 9.6 - - + -
59A THR 2.9 17.5 + - - +
60A LEU 3.1 5.6 + - - +
62A GLU* 1.3 73.6 - - - +
64A VAL* 1.3 66.6 + - - +
66A SER* 3.1 30.7 + - - -
67A ILE* 3.1 33.0 + - - +
123A ASP* 3.0 25.1 + - - -
125A ALA* 3.1 26.6 - - - +
126A THR* 3.1 25.3 + - - +
129A MET* 3.7 24.2 - - + -
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 4.2 7.4 - - + +
13A LEU* 3.6 28.5 - - + -
14A ASN* 3.7 22.0 - - - +
17A VAL* 4.7 0.4 - - + -
60A LEU 3.0 20.0 + - - +
61A ALA* 3.2 11.7 - - - +
63A ARG* 1.3 76.7 - - - +
65A LEU* 1.3 60.0 + - - +
67A ILE* 3.1 17.5 - - - +
69A GLY* 2.9 49.1 + - - -
70A SER 3.5 20.2 - - - +
71A PRO* 3.6 1.3 - - + -
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA 3.1 14.7 + - - +
62A GLU* 3.6 18.6 - - + +
64A VAL* 1.3 81.0 - - - +
66A SER* 1.3 61.5 + - - +
68A GLY* 3.1 13.7 + - - -
69A GLY 3.7 11.2 - - - +
70A SER* 4.9 0.7 - - - +
71A PRO* 3.7 22.7 - - + -
32B TRP* 3.6 46.7 - - + +
33B ASN* 4.2 7.9 - - - +
43B HIS* 6.5 0.4 - - + -
----------------------------------------------------------
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 2.8 24.9 + - - +
63A ARG* 3.1 29.0 + - - -
65A LEU* 1.3 76.0 - - - +
67A ILE* 1.3 60.2 + - - +
68A GLY 3.4 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 3.1 25.2 + - - +
6A GLN 4.9 3.8 - - - +
9A VAL* 4.0 18.6 - - + -
10A ALA* 3.8 36.6 - - + +
13A LEU* 4.1 8.7 - - + -
63A ARG* 3.1 44.6 + - - +
64A VAL 3.1 13.9 - - - +
66A SER* 1.3 77.6 - - - +
68A GLY* 1.3 57.5 + - - +
69A GLY 4.4 2.2 - - - +
123A ASP* 3.8 10.8 - - - +
----------------------------------------------------------
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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