Contacts of the helix formed by residues 38 - 63 (chain B) in PDB entry 1NNQ
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 PHE 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 3.7 35.0 - - + -
70A PRO* 5.3 2.5 - - + -
128A ALA* 4.0 20.2 - - + -
131A GLY* 3.8 25.6 - - - -
132A GLU 3.9 5.8 - - - -
133A ASP* 3.5 31.6 - - - +
33B ALA* 2.8 18.4 + - + +
34B GLU* 4.1 0.8 + - - -
36B GLU* 3.9 30.1 - - + -
37B GLY* 1.3 78.7 - - - -
39B PRO* 1.3 60.3 - - - +
40B ASN 3.3 2.7 - - - -
41B ILE* 3.2 18.5 + - + -
42B ALA* 3.0 25.5 + - - +
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Residues in contact with PRO 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASP* 3.1 11.7 - - + +
34B GLU* 4.8 8.0 - - + +
37B GLY* 3.4 10.5 - - - +
38B PHE* 1.3 87.4 - - - +
40B ASN* 1.3 63.2 + - - +
42B ALA* 3.3 10.2 - - + +
43B LYS* 2.9 26.2 + - - +
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Residues in contact with ASN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASP* 2.9 17.5 + - - +
134A ILE* 2.7 38.2 + - + +
135A GLU* 3.7 14.5 + - - -
136A ILE* 3.8 31.7 + - + +
39B PRO* 1.3 81.4 - - - +
41B ILE* 1.3 59.1 + - - +
43B LYS* 3.2 10.7 + - - +
44B LEU* 2.9 26.7 + - - +
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Residues in contact with ILE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 3.9 12.3 - - + -
73A LEU* 4.3 11.9 - - + -
121A TYR* 6.5 0.2 - - + -
124A ALA* 4.0 14.1 - - + +
128A ALA* 3.8 30.7 - - + +
132A GLU 4.6 0.2 - - - +
133A ASP* 3.0 16.4 + - - +
134A ILE* 3.8 27.6 - - + +
33B ALA* 4.2 1.3 - - + -
38B PHE* 3.2 22.4 + - + +
40B ASN* 1.3 74.6 - - - +
42B ALA* 1.3 57.8 + - - +
44B LEU* 3.1 5.8 + - + +
45B PHE* 2.8 53.5 + - + -
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA* 3.3 29.5 - - + +
33B ALA* 3.8 6.8 - - - +
34B GLU* 4.0 13.5 - - + +
38B PHE 3.0 12.6 + - - +
39B PRO* 3.3 13.7 - - + +
41B ILE* 1.3 76.2 - - - +
43B LYS* 1.3 56.0 + - - +
45B PHE* 3.2 4.0 + - - +
46B ARG* 2.9 36.1 + - - +
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Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 4.9 5.4 - - + -
137A LYS 6.0 0.9 - - - +
138A LYS* 6.0 0.7 - - - -
139A VAL* 4.8 8.1 - - + -
170A PHE* 4.2 31.9 - - + +
171A GLU* 4.7 9.9 - - - +
39B PRO 2.9 14.6 + - - +
40B ASN* 3.2 15.0 + - - +
42B ALA* 1.3 75.2 - - - +
44B LEU* 1.3 56.9 + - - +
46B ARG* 3.4 8.9 + - - +
47B ALA* 3.0 29.3 + - - +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 5.5 1.3 - - + -
120A LEU* 4.1 29.8 - - + +
121A TYR* 4.2 15.5 - - + -
124A ALA* 4.1 18.8 - - + -
134A ILE* 3.9 20.9 - - + -
136A ILE* 4.5 5.4 - - + +
139A VAL* 4.6 13.7 - - + -
150A VAL* 4.4 14.4 - - + -
40B ASN 2.9 13.3 + - - +
41B ILE* 3.1 9.8 + - + +
43B LYS* 1.3 72.7 - - - +
45B PHE* 1.3 65.9 + - - +
47B ALA* 3.5 3.2 + - - +
48B ILE* 3.1 50.6 + - + +
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Residues in contact with PHE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR* 4.6 5.2 - - + -
72A ASN* 4.5 2.5 - - + -
73A LEU* 3.5 31.6 - - + -
76A GLY* 6.0 0.7 - - - -
121A TYR* 3.5 34.3 - + - -
26B TYR* 3.5 31.9 - + - +
29B PHE* 3.7 54.3 - + + -
30B ALA* 3.8 6.1 - - + -
33B ALA* 4.2 3.8 - - + -
41B ILE* 2.8 40.9 + - + -
42B ALA 3.4 6.7 - - - +
44B LEU* 1.3 77.1 - - - +
46B ARG* 1.3 57.5 + - - +
48B ILE* 3.5 1.0 + - - +
49B ALA* 2.9 29.6 + - - +
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PHE* 3.9 16.2 - - + -
27B LEU* 4.6 14.3 - - + +
30B ALA* 3.9 18.2 - - + -
42B ALA* 2.9 22.7 + - - +
43B LYS* 3.8 7.6 - - - +
45B PHE* 1.3 72.7 - - - +
47B ALA* 1.3 65.7 + - - +
49B ALA* 3.3 7.8 + - - +
50B TYR* 3.0 22.3 + - - +
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 3.7 36.6 - - + -
141A ILE* 3.4 11.7 - - + +
170A PHE* 3.7 25.7 - - + -
43B LYS 3.0 18.4 + - - +
44B LEU 3.9 3.6 - - - +
45B PHE 3.3 0.2 - - - -
46B ARG* 1.3 78.0 - - - +
48B ILE* 1.3 60.2 + - + +
50B TYR* 3.1 15.1 + - - +
51B ALA 3.1 9.4 + - - -
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A HIS* 3.6 46.9 - - + +
120A LEU* 4.2 10.1 - - + -
121A TYR* 3.3 46.0 - - + +
141A ILE* 4.8 0.4 - - - -
148A THR* 4.5 8.5 - - + -
26B TYR* 3.8 4.3 - - + -
44B LEU* 3.1 30.9 + - + +
45B PHE 4.0 0.4 - - - +
47B ALA* 1.3 72.6 - - + +
49B ALA* 1.3 66.1 + - - +
51B ALA* 3.0 9.1 + - - +
52B GLU* 2.9 30.3 + - - +
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B HIS* 2.8 47.2 + - + +
26B TYR* 3.8 9.1 - - + -
27B LEU* 3.9 17.5 - - + -
45B PHE 2.9 18.5 + - - +
46B ARG 3.4 6.7 - - - +
48B ILE* 1.3 74.5 - - - +
50B TYR* 1.3 58.5 + - - +
52B GLU* 3.2 10.3 + - - +
53B PHE 3.0 15.8 + - - -
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Residues in contact with TYR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 5.2 3.8 + - - -
141A ILE* 3.7 22.4 - - + -
143A PRO* 3.8 14.1 - - + +
168A VAL* 3.5 35.1 - - + +
170A PHE* 3.4 28.5 - + + -
23B HIS* 4.8 2.2 - - - -
46B ARG 3.0 7.9 + - - +
47B ALA 3.1 8.7 + - - +
49B ALA* 1.3 76.8 - - - +
51B ALA* 1.3 55.7 + - - +
53B PHE* 3.2 34.6 + + - +
54B VAL* 3.0 44.4 + - + +
57B LYS* 5.8 0.7 + - - -
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A HIS* 3.8 19.7 - - + +
141A ILE* 3.8 16.4 - - + +
146A GLY* 3.6 24.5 - - - +
148A THR* 4.0 2.2 - - - +
47B ALA 3.1 7.4 + - - +
48B ILE* 3.0 11.9 + - - +
50B TYR* 1.3 74.3 - - - +
52B GLU* 1.3 66.4 + - - +
54B VAL* 3.1 7.8 + - - +
55B HIS* 3.1 26.3 + - + -
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MET* 4.4 2.2 - - - -
80A GLU* 3.1 6.8 - - - +
83A GLU* 5.4 0.4 - - - -
117A HIS* 3.5 4.1 + - - -
201A ZN 2.0 31.0 - - - -
19B GLU* 3.6 26.7 - - - +
22B ALA* 4.3 5.9 - - + +
23B HIS* 4.0 7.9 - - + +
26B TYR* 3.3 24.7 - - + -
48B ILE* 2.9 20.5 + - - +
49B ALA* 3.2 7.6 + - - +
51B ALA* 1.3 72.1 - - - +
53B PHE* 1.3 60.7 + - - +
55B HIS* 3.2 6.6 + - - +
56B ALA* 2.9 30.5 + - - +
202B ZN 2.3 32.8 - - - -
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Residues in contact with PHE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A MET* 3.5 28.8 - - + +
27A LEU* 4.0 30.1 - - + -
28A ILE* 3.8 20.4 - - + -
31A GLU* 3.3 30.3 - - + -
23B HIS* 4.0 11.9 - - + +
49B ALA 3.0 12.4 + - - +
50B TYR* 3.2 45.5 + + + +
52B GLU* 1.3 77.0 - - - +
54B VAL* 1.3 61.9 + - + +
56B ALA* 3.9 0.7 - - - +
57B LYS* 3.0 50.0 + - + +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 4.7 0.2 - - + -
142A CYS 4.0 3.1 - - - +
143A PRO* 3.5 31.2 - - + +
144A ILE 3.6 18.6 - - - +
145A CYS 4.0 0.9 - - - -
146A GLY* 3.7 19.1 - - - +
50B TYR* 3.0 45.1 + - + +
51B ALA* 3.1 10.0 + - - +
53B PHE* 1.3 82.1 - - + +
55B HIS* 1.3 62.4 + - - +
57B LYS* 3.7 7.2 - - - +
58B ASN* 3.0 33.3 + - - +
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Residues in contact with HIS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A THR 5.5 1.3 - - - -
109A TYR* 5.1 0.4 - - + -
110A ALA* 3.7 24.0 - - + -
113A ALA* 3.5 27.5 - - + +
114A GLU* 3.2 7.9 + - - -
117A HIS* 4.3 4.3 - + - -
145A CYS 3.2 29.6 + - - -
146A GLY* 3.8 2.8 - - - -
19B GLU* 3.5 19.5 - - + +
51B ALA* 3.1 14.7 + - + -
52B GLU* 3.3 7.1 + - - +
54B VAL* 1.3 78.0 - - + +
56B ALA* 1.3 56.4 + - - +
58B ASN* 3.4 11.0 + - - +
59B HIS* 3.0 35.5 + - - +
202B ZN 2.3 32.7 - - - -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A MET* 3.8 27.1 - - + -
28A ILE* 4.5 0.2 - - - -
16B PHE* 3.3 23.1 - - + -
19B GLU* 3.6 20.3 - - + +
20B SER* 4.4 1.8 - - - +
52B GLU 2.9 15.9 + - - +
53B PHE 4.0 0.2 - - - +
55B HIS* 1.3 72.9 - - - +
57B LYS* 1.3 61.4 + - - +
59B HIS* 3.2 4.2 + - - +
60B PHE* 2.8 31.0 + - - +
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 3.8 32.2 - - + +
31A GLU* 2.9 41.8 + - - +
35A GLN* 5.7 0.8 - - - +
143A PRO 4.9 12.9 + - - -
50B TYR* 5.8 0.6 + - - -
53B PHE* 3.0 35.6 + - + +
54B VAL* 3.7 7.2 - - - +
56B ALA* 1.3 75.5 - - - +
58B ASN* 1.3 64.2 + - - +
60B PHE* 3.2 1.0 + - - +
61B ILE* 2.8 57.8 + - + +
66B LEU* 5.8 0.9 - - + -
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Residues in contact with ASN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A THR* 3.6 22.9 + - + +
109A TYR* 4.0 18.8 - - - +
144A ILE* 3.0 27.9 + - - +
145A CYS* 4.5 1.6 - - - +
54B VAL* 3.0 25.6 + - - +
55B HIS* 3.5 12.1 - - - +
57B LYS* 1.3 82.8 - - - +
59B HIS* 1.3 61.8 + - - +
61B ILE* 3.9 7.3 - - - +
62B ALA* 2.9 25.5 + - - +
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Residues in contact with HIS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 2.8 35.8 + + - -
106A THR* 3.2 40.6 + - - -
107A THR* 4.3 0.4 - - + -
110A ALA* 4.6 1.1 - - + -
12B LEU* 3.5 32.4 - - + +
15B ALA* 3.7 20.0 - - + +
16B PHE* 3.9 7.4 - - + -
19B GLU* 3.8 13.7 + - + +
55B HIS* 3.0 24.8 + - + +
56B ALA 3.7 4.3 - - - +
58B ASN* 1.3 74.9 - - - +
60B PHE* 1.3 52.7 + - - +
62B ALA* 3.3 6.6 + - - +
63B LEU* 2.9 39.2 + - - +
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Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 3.5 38.4 - - + -
28A ILE* 4.1 20.2 - - + -
29A PHE* 3.8 22.4 - + - -
16B PHE* 3.4 30.0 - + + -
56B ALA 2.8 18.1 + - - +
57B LYS* 3.4 7.9 - - - +
59B HIS* 1.3 75.8 - - - +
61B ILE* 1.3 63.4 + - + +
63B LEU* 3.1 17.1 + - - +
65B LYS* 3.2 74.2 + - + +
66B LEU* 3.8 7.6 - - + -
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 5.5 0.2 - - + -
2B VAL* 4.6 4.7 - - - +
57B LYS* 2.8 45.2 + - + +
58B ASN* 3.9 7.4 - - - +
60B PHE* 1.3 70.3 - - + +
62B ALA* 1.3 60.9 + - - +
64B GLY* 2.8 21.9 + - - +
65B LYS 4.8 2.9 - - - +
66B LEU* 3.9 36.1 - - + +
----------------------------------------------------------
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU* 3.7 29.6 - - + +
106A THR* 4.1 8.7 - - + +
2B VAL* 3.5 7.1 - - - +
3B VAL* 3.1 31.6 + - + +
12B LEU* 3.8 15.7 - - + -
58B ASN 2.9 19.5 + - - +
59B HIS 3.6 4.5 - - - +
61B ILE* 1.3 76.9 - - - +
63B LEU* 1.3 58.7 + - - +
64B GLY 3.2 0.7 + - - -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL* 4.0 9.2 - - - +
3B VAL* 4.9 8.1 - - + +
9B LYS* 3.7 46.2 - - + +
12B LEU* 4.0 17.0 - - + +
13B GLU* 3.8 38.8 - - + +
16B PHE* 4.8 6.7 - - + -
59B HIS 2.9 20.6 + - - +
60B PHE* 3.1 11.8 + - - +
62B ALA* 1.3 75.8 - - - +
64B GLY* 1.3 61.4 + - - +
65B LYS* 3.3 25.6 + - + +
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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