Contacts of the helix formed by residues 37 - 68 (chain B) in PDB entry 1YWT
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 SER 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU 4.2 0.4 + - - -
36B LEU* 1.3 75.4 - - - +
38B CYS* 1.3 66.2 + - - +
39B GLU* 3.7 11.2 + - - +
40B GLU* 2.8 37.2 + - - +
41B ARG* 2.8 23.0 + - - +
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Residues in contact with CYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 1.3 75.0 - - - +
39B GLU* 1.3 63.2 + - - +
41B ARG* 3.2 36.8 + - - +
42B ASN* 2.9 39.1 + - - -
115B GLU* 5.7 5.2 - - - -
168B ILE* 5.7 3.1 - - - -
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 6.1 0.9 - - - -
11B LYS* 2.6 36.0 + - - +
37B SER* 3.2 9.3 + - - +
38B CYS* 1.3 79.1 - - - +
40B GLU* 1.3 67.1 + - - +
42B ASN* 3.3 9.6 + - - +
43B LEU* 3.2 27.7 + - + +
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ARG* 2.6 48.2 + - - -
7B ILE* 3.7 30.3 - - + +
26B MET* 3.7 7.5 - - + +
35B GLU 3.8 0.2 - - - +
36B LEU* 3.0 12.1 - - + -
37B SER* 2.8 37.3 + - - +
39B GLU* 1.3 79.8 - - + +
41B ARG* 1.3 64.0 + - - +
43B LEU* 3.1 21.7 + - + +
44B LEU* 3.1 10.6 + - - +
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Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 4.1 15.7 + - + +
37B SER* 2.8 15.5 + - - +
38B CYS* 3.2 48.4 + - - +
40B GLU* 1.3 72.7 - - - +
42B ASN* 1.3 61.1 + - - +
44B LEU* 3.2 6.7 + - - +
45B SER 3.1 17.5 + - - -
113B ASP* 5.2 4.2 + - - +
115B GLU* 4.0 11.5 + - - +
116B SER* 3.8 33.4 - - - +
119B PHE* 3.6 44.2 - - + +
120B TYR* 3.1 39.9 - - + +
168B ILE* 4.2 12.3 - - - +
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Residues in contact with ASN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B CYS* 2.9 36.6 + - - -
39B GLU* 3.7 8.5 - - - +
40B GLU 3.2 0.2 - - - -
41B ARG* 1.3 77.3 - - - +
43B LEU* 1.3 67.3 + - + +
45B SER* 3.4 7.7 + - - -
46B VAL* 2.9 36.6 + - + +
119B PHE* 4.2 16.0 - - - -
7D TYR* 6.2 0.3 - - - -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 4.6 11.0 - - + +
10B ALA* 4.9 0.9 - - + -
11B LYS* 4.2 39.3 - - + +
14B GLU* 3.7 15.5 - - - +
22B MET* 3.3 31.0 - - + +
26B MET* 3.8 23.1 - - - -
39B GLU* 3.2 21.7 + - + +
40B GLU* 3.1 16.1 + - + +
42B ASN* 1.3 78.4 - - - +
44B LEU* 1.3 58.8 + - - +
46B VAL* 4.6 0.9 - - - -
47B ALA* 3.0 28.1 + - - +
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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
----------------------------------------------------------
26B MET* 3.8 31.8 - - + +
30B VAL* 4.4 8.5 - - + -
36B LEU* 4.0 14.6 - - + -
40B GLU 3.1 9.7 + - - +
41B ARG 3.3 10.3 - - - +
42B ASN 3.1 0.2 - - - -
43B LEU* 1.3 78.1 - - - +
45B SER* 1.3 60.9 + - - +
47B ALA* 3.5 1.0 + - - +
48B TYR* 3.2 45.2 + - + +
102B LEU* 4.3 12.3 - - + -
107B LEU* 3.7 30.5 - - + -
119B PHE* 5.8 0.2 - - + -
120B TYR* 4.7 4.7 - - + -
123B MET* 4.1 22.4 - - + +
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ARG 3.1 3.2 + - - -
42B ASN* 3.4 12.5 + - - -
44B LEU* 1.3 77.0 - - - +
46B VAL* 1.3 64.8 + - - +
48B TYR 4.7 0.2 - - - +
49B LYS* 2.7 35.5 + - - +
119B PHE* 3.7 27.3 - - - -
123B MET* 4.2 20.2 - - - +
127B TYR* 4.5 2.3 + - - -
8D PRO* 4.4 19.2 - - - +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 3.6 24.2 - - - +
19B TYR* 4.5 5.8 - - + -
22B MET* 4.3 8.5 - - + -
42B ASN* 2.9 32.3 + - + +
43B LEU* 3.8 2.7 - - - +
45B SER* 1.3 80.2 + - - +
47B ALA* 1.3 62.9 + - - +
49B LYS* 4.2 3.6 - - - -
50B ASN* 2.5 47.6 + - - +
8D PRO* 5.5 10.1 - - + -
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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
----------------------------------------------------------
19B TYR* 4.1 5.4 - - - +
22B MET* 3.5 21.7 - - + +
23B ALA* 3.4 34.1 - - - +
26B MET* 4.9 1.1 - - + -
43B LEU 3.0 19.4 + - - +
44B LEU* 3.9 4.7 - - - +
46B VAL* 1.3 78.6 - - - +
48B TYR* 1.3 63.6 + - + +
50B ASN* 3.4 2.4 + - - +
51B VAL* 3.1 28.0 + - - +
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Residues in contact with TYR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA* 3.6 41.2 + - + +
24B ALA* 5.1 0.9 - - - -
27B LYS* 3.8 14.4 - - - +
44B LEU* 3.2 42.5 + - + +
45B SER 4.4 0.7 - - - +
47B ALA* 1.3 77.2 - - - +
49B LYS* 1.3 60.1 + - - +
51B VAL* 3.8 4.8 - - + +
52B VAL* 2.9 33.8 + - - +
95B VAL* 3.8 21.1 - - + -
98B THR* 3.9 21.1 - - + +
99B VAL* 3.3 31.2 - - + -
102B LEU* 4.2 11.3 - - + +
123B MET* 4.8 4.3 - - + -
127B TYR* 3.3 17.3 - - + +
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER* 2.7 26.6 + - - +
46B VAL* 3.7 5.4 - - - +
48B TYR* 1.3 72.0 - - - +
50B ASN* 1.3 61.1 + - - +
52B VAL* 3.4 4.8 - - + +
53B GLY* 2.8 32.2 + - - -
56B ARG* 4.2 4.2 - - - +
127B TYR* 3.4 8.6 + - - +
130B TYR* 3.5 21.3 - - + +
6D SEP 2.6 31.4 + - - -
7D TYR 5.1 0.2 - - - -
8D PRO* 2.8 48.7 + - + +
9D ALA* 3.3 23.2 + - - +
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Residues in contact with ASN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 3.3 49.1 + - + -
46B VAL* 2.5 46.6 + - - +
47B ALA 3.7 0.2 - - - +
49B LYS* 1.3 80.2 - - - +
51B VAL* 1.3 66.0 + - - +
53B GLY* 3.8 1.0 - - - -
54B GLY* 3.2 19.1 + - - -
9D ALA 6.1 1.8 - - - -
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 3.6 28.5 - - + +
20B GLU* 3.9 20.2 - - + +
23B ALA* 4.1 11.2 - - + -
47B ALA 3.1 19.0 + - - +
48B TYR* 3.8 8.5 - - + +
49B LYS 3.4 0.2 - - - -
50B ASN* 1.3 77.2 - - - +
52B VAL* 1.3 63.3 + - - +
54B GLY* 3.4 7.1 + - - -
55B GLN* 3.5 18.3 + - - +
95B VAL* 4.2 26.9 - - + -
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR 2.9 20.9 + - - +
49B LYS* 3.4 12.1 - - + +
51B VAL* 1.3 75.5 - - - +
53B GLY* 1.3 65.2 + - - +
55B GLN* 3.2 17.3 + - - +
56B ARG* 2.8 39.3 + - + +
92B LEU* 4.3 9.4 - - + -
95B VAL* 4.6 7.6 - - + -
96B CYS* 4.2 25.6 - - - -
127B TYR* 4.2 8.3 - - + -
130B TYR* 3.9 31.2 - - + -
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Residues in contact with GLY 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 2.8 28.1 + - - -
50B ASN* 3.3 2.4 + - - -
51B VAL 3.3 0.4 - - - -
52B VAL* 1.3 75.4 - - - +
54B GLY* 1.3 62.9 + - - +
56B ARG* 3.4 12.3 + - - +
57B ALA* 3.0 25.1 + - - +
60B ARG* 4.8 1.9 + - - -
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA 5.1 1.4 - - - +
18A ARG* 5.2 4.3 - - - +
50B ASN 3.2 12.3 + - - -
51B VAL 3.4 3.1 + - - -
52B VAL 3.2 0.6 - - - -
53B GLY* 1.3 76.9 - - - +
55B GLN* 1.3 57.3 + - - +
57B ALA* 3.4 5.7 + - - +
58B ALA* 2.9 28.3 + - - +
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Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.9 17.7 - - - +
51B VAL* 3.5 15.1 + - + +
52B VAL* 3.2 23.9 + - - +
54B GLY* 1.3 73.9 - - - +
56B ARG* 1.3 60.2 + - - +
58B ALA* 3.2 8.2 + - - +
59B TRP* 2.8 30.3 + - - +
88B VAL* 3.7 7.0 - - + +
91B GLU* 2.8 46.6 + - + +
92B LEU* 3.6 29.9 - - + -
95B VAL* 3.7 18.9 - - - +
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 4.2 4.4 - - - +
52B VAL* 2.8 33.5 + - + +
53B GLY* 3.8 8.3 - - - +
55B GLN* 1.3 72.8 - - - +
57B ALA* 1.3 57.8 + - - +
59B TRP* 3.4 4.9 + - - +
60B ARG* 3.0 59.8 + - + +
92B LEU* 3.6 21.5 - - + -
129B ARG* 4.2 0.4 - - - +
130B TYR* 3.2 37.5 - - + -
133B GLU* 3.0 37.1 + - - +
182B GLU* 5.6 2.6 + - - -
6D SEP 2.7 42.4 + - - -
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA 5.2 1.8 - - - +
53B GLY 3.0 18.6 + - - +
54B GLY* 3.6 5.8 - - - +
56B ARG* 1.3 75.1 - - - +
58B ALA* 1.3 66.9 + - - +
60B ARG* 3.3 23.8 + - - +
61B VAL* 3.0 32.1 + - + +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA* 3.9 24.1 + - + +
18A ARG* 3.5 33.2 - - + -
54B GLY 2.9 13.8 + - - +
55B GLN* 3.2 8.3 + - - +
57B ALA* 1.3 78.2 - - - +
59B TRP* 1.3 63.2 + - - +
61B VAL* 3.2 2.3 + - - +
62B LEU* 2.9 30.0 + - - +
88B VAL* 4.0 8.3 - - + -
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Residues in contact with TRP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLN 2.8 20.9 + - - +
56B ARG* 3.4 8.3 - - - +
58B ALA* 1.3 74.2 - - - +
60B ARG* 1.3 69.1 + - + +
62B LEU* 3.2 6.5 + - - +
63B SER* 2.8 56.6 + - - -
67B GLN* 6.3 0.2 - - - -
85B ARG* 3.9 21.4 - - + +
88B VAL* 4.0 7.7 - - + +
89B GLU* 2.8 52.5 + - + +
92B LEU* 5.1 4.0 - - + -
133B GLU* 3.5 25.1 - - + -
134B VAL* 3.6 30.5 - - + -
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Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLY 4.8 2.0 + - - -
56B ARG* 3.0 51.1 + - + +
57B ALA* 3.5 33.5 - - - +
59B TRP* 1.3 85.6 - - + +
61B VAL* 1.3 66.9 + - + +
63B SER* 3.3 8.6 + - - -
64B SER* 3.1 26.0 + - - -
133B GLU* 5.2 4.1 + - - +
3D ARG* 3.7 51.5 + - - +
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 3.6 36.3 - - + +
16A ALA* 4.0 9.4 - - + +
57B ALA* 3.0 23.2 + - + +
58B ALA 3.4 6.5 - - - +
60B ARG* 1.3 76.8 - - + +
62B LEU* 1.3 63.5 + - + +
64B SER* 2.6 22.4 + - - -
65B ILE* 3.1 26.3 + - + +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.0 33.4 - - + +
16A ALA* 4.2 7.4 - - + -
58B ALA 2.9 21.9 + - - +
59B TRP* 3.6 3.6 - - - +
61B VAL* 1.3 76.6 - - + +
63B SER* 1.3 66.8 + - - +
65B ILE* 2.8 10.2 + - + +
66B GLU* 2.8 22.6 + - - +
81B VAL* 3.8 9.8 - - + +
84B TYR* 3.6 39.5 - - + -
85B ARG* 4.1 21.8 - - + -
88B VAL* 3.7 23.8 - - + -
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Residues in contact with SER 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TRP* 2.8 44.8 + - - -
60B ARG* 3.3 11.1 + - - -
62B LEU* 1.3 72.4 - - - +
64B SER* 1.3 62.9 + - - +
66B GLU* 3.3 9.9 + - - +
67B GLN* 3.1 40.3 + - - +
85B ARG* 4.1 19.8 - - - +
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG 3.1 14.7 + - - -
61B VAL* 2.6 25.1 + - - +
63B SER* 1.3 75.3 + - - +
65B ILE* 1.3 63.0 + - - +
67B GLN* 3.3 7.4 + - - +
68B LYS* 2.9 48.7 + - - +
3D ARG* 5.3 7.0 - - - -
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.9 27.4 - - + -
15A GLN* 3.3 40.6 - - + +
61B VAL* 3.3 27.1 - - + +
62B LEU* 2.8 12.8 + - + +
64B SER* 1.3 83.9 + - - +
66B GLU* 1.3 62.2 + - - +
68B LYS* 3.6 12.7 + - - +
69B SER 3.3 15.4 - - - +
81B VAL* 4.0 12.0 - - + +
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU 2.8 12.0 + - - +
63B SER* 3.4 10.2 - - - +
64B SER 3.1 0.2 - - - -
65B ILE* 1.3 80.2 - - - +
67B GLN* 1.3 63.9 + - + +
69B SER* 3.5 10.4 + - - +
81B VAL* 3.7 18.1 - - + +
82B ARG* 3.2 36.3 + - - +
85B ARG* 2.5 39.5 + - - +
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Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TRP* 6.3 0.2 - - - -
63B SER* 3.1 32.8 + - - +
64B SER* 3.9 6.8 - - - +
66B GLU* 1.3 81.0 - - + +
68B LYS* 1.3 62.0 + - + +
69B SER* 2.9 8.3 + - - -
----------------------------------------------------------
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 2.9 33.7 + - - +
65B ILE* 3.6 9.5 - - - +
66B GLU 3.4 0.6 - - - -
67B GLN* 1.3 76.2 - - + +
69B SER* 1.3 77.4 + - - +
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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).
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