Contacts of the helix formed by residues 15 - 48 (chain B) in PDB entry 2YPT
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 ALA 15 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO* 1.4 72.8 - - - +
16B GLU* 1.4 67.5 + - - +
17B LYS 3.3 1.1 - - - -
18B ARG* 3.4 12.5 + - - +
19B ILE* 3.5 17.9 + - - +
371B GLU* 6.0 4.9 - - + -
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA* 1.4 78.7 - - - +
17B LYS* 1.3 63.2 + - + +
19B ILE* 3.3 14.7 - - - +
20B PHE* 3.4 2.9 + - - +
371B GLU* 3.9 22.1 - - + +
374B ALA* 4.2 14.1 - - + +
375B ALA* 3.3 33.9 - - - +
379B TYR* 6.0 0.9 - - + -
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO* 3.8 29.4 - - + +
15B ALA 3.3 1.4 - - - +
16B GLU* 1.3 76.3 - - + +
18B ARG* 1.4 61.7 + - - +
20B PHE* 3.7 9.5 + - - +
21B GLY* 3.3 18.5 + - - -
375B ALA* 5.6 0.9 - - - +
379B TYR* 5.0 8.7 + - - -
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B MET* 5.9 1.8 - - + -
14B PRO* 3.3 28.6 + - + +
15B ALA* 3.4 6.6 + - - +
16B GLU 3.3 0.4 - - - -
17B LYS* 1.4 76.8 - - - +
19B ILE* 1.4 60.2 + - + +
21B GLY* 3.5 1.8 + - - -
22B ALA* 3.1 26.5 + - - +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA 3.5 10.8 - - - +
16B GLU* 3.3 18.8 - - - +
18B ARG* 1.4 76.5 - - + +
20B PHE* 1.3 63.2 + - - +
22B ALA* 3.6 9.0 + - + +
23B VAL* 3.3 27.8 + - - +
371B GLU* 3.4 40.8 - - + +
372B LEU* 3.8 12.8 - - + +
375B ALA* 3.9 4.7 - - + -
376B PHE* 5.9 0.2 - - - -
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU 3.4 13.4 + - - +
17B LYS* 3.9 9.0 - - - +
18B ARG 3.3 0.4 - - - -
19B ILE* 1.3 78.3 - - - +
21B GLY* 1.3 64.8 + - - +
23B VAL* 3.4 17.1 + - - +
24B LEU* 3.4 42.0 + - + +
93B LEU* 4.0 30.5 - - + -
94B LEU* 4.1 19.5 - - + -
375B ALA* 3.3 34.1 - - + +
376B PHE* 3.7 33.2 - + - -
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Residues in contact with GLY 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LYS 3.3 12.4 + - - -
18B ARG 3.9 2.9 - - - -
19B ILE 3.4 0.2 - - - -
20B PHE* 1.3 81.5 - - - +
22B ALA* 1.4 54.2 + - - +
24B LEU* 3.3 6.8 + - - +
25B LEU* 2.8 38.3 + - - +
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG 3.1 17.1 + - - +
19B ILE* 3.6 13.5 - - + +
20B PHE 3.3 0.2 - - - -
21B GLY* 1.4 76.4 - - - +
23B VAL* 1.4 55.3 + - + +
25B LEU* 3.9 6.8 - - - +
26B PHE* 3.1 30.5 + - - +
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE 3.3 14.5 + - - +
20B PHE 3.4 8.7 - - - +
22B ALA* 1.4 76.9 - - + +
24B LEU* 1.3 59.5 + - + +
26B PHE* 3.4 6.5 + - - +
27B SER* 2.8 38.7 + - - +
93B LEU* 5.4 1.1 - - + -
376B PHE* 3.8 26.7 - - + -
394B PHE* 3.7 55.0 - - + +
395B ILE* 4.8 4.0 - - - +
397B SER* 5.6 2.0 - - - +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 3.4 42.3 + - + +
21B GLY* 3.3 9.7 + - - +
23B VAL* 1.3 80.5 - - + +
25B LEU* 1.4 63.9 + - - +
27B SER* 3.7 6.4 - - - -
28B TRP* 3.1 36.6 + - + +
90B THR* 3.9 29.6 - - + +
93B LEU* 4.0 21.5 - - + -
94B LEU* 3.8 29.4 - - + -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 2.8 23.0 + - - +
22B ALA* 3.9 7.9 - - - +
24B LEU* 1.4 72.2 - - - +
26B PHE* 1.3 57.9 + - - +
28B TRP* 3.6 4.3 + - - +
29B THR* 3.1 43.7 + - + +
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA 3.1 18.6 + - - +
23B VAL* 3.7 4.9 - - - +
25B LEU* 1.3 75.2 - - - +
27B SER* 1.3 61.7 + - - +
28B TRP 3.2 0.2 - - - -
29B THR* 2.9 21.2 + - - -
30B VAL* 3.0 43.9 + - + +
397B SER* 3.7 23.6 - - - -
398B PRO* 3.5 45.3 - - + -
401B GLU* 4.3 10.3 - - + -
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 2.8 28.4 + - - +
24B LEU* 3.7 9.5 - - - -
26B PHE* 1.3 79.5 - - - +
28B TRP* 1.4 57.7 + - - +
30B VAL* 4.2 5.1 - - - +
31B TYR* 3.4 19.2 + - - +
86B GLU* 3.2 25.2 - - - +
90B THR* 6.0 0.2 - - - -
93B LEU* 6.2 0.2 - - - +
394B PHE* 5.3 3.8 - - - -
397B SER* 5.1 6.8 + - - -
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Residues in contact with TRP 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.1 32.3 + - + +
25B LEU* 4.1 4.9 - - - +
27B SER* 1.4 77.1 - - - +
29B THR* 1.4 55.4 + - + +
30B VAL 3.3 0.2 - - - -
31B TYR* 3.3 39.2 + + - +
32B LEU* 2.8 53.1 + - + +
83B LEU* 4.9 6.3 - - + -
86B GLU* 3.7 28.9 + - + -
87B THR* 4.5 13.0 - - + -
90B THR* 2.7 45.2 + - + +
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Residues in contact with THR 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.1 30.0 + - + +
26B PHE* 2.9 26.2 + - - -
28B TRP* 1.4 71.6 - - + +
30B VAL* 1.4 56.5 + - - +
32B LEU* 3.3 12.6 + - + +
33B TRP* 2.8 34.6 + - - +
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.0 55.2 + - + +
27B SER* 4.2 5.4 - - - +
29B THR* 1.4 72.9 + - - +
31B TYR* 1.4 58.3 + - - +
33B TRP* 3.3 9.0 + - + +
34B GLU* 3.0 43.1 + - + +
401B GLU* 3.8 32.8 - - + +
455B TRP* 5.4 5.4 - - + -
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Residues in contact with TYR 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER 3.4 18.0 + - - +
28B TRP* 3.3 37.8 + + - +
29B THR 3.3 0.2 - - - -
30B VAL* 1.4 80.0 - - - +
32B LEU* 1.4 58.6 + - + +
34B GLU* 3.2 14.5 + - + +
35B THR* 2.7 58.2 + - + -
79B PHE* 3.8 15.5 + + - -
82B GLY* 3.9 21.1 - - - -
83B LEU* 3.3 38.9 + - + +
86B GLU* 3.5 24.5 - - + +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TRP* 2.8 37.9 + - + +
29B THR* 3.8 11.9 - - + +
31B TYR* 1.4 82.3 - - + +
33B TRP* 1.3 59.8 + - - +
35B THR* 3.8 9.8 - - + -
36B PHE* 2.9 29.3 + - - +
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Residues in contact with TRP 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR 2.8 18.4 + - - +
30B VAL* 3.4 11.2 - - + +
31B TYR 3.3 0.2 - - - -
32B LEU* 1.3 76.0 - - - +
34B GLU* 1.3 57.8 + - + +
36B PHE* 3.4 25.1 + + - +
37B LEU* 3.1 55.5 + - + +
451B LEU* 3.8 22.4 - - + -
455B TRP* 3.3 61.9 - + + +
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 3.0 29.6 + - + +
31B TYR* 3.6 12.6 - - + +
33B TRP* 1.3 76.5 - - + +
35B THR* 1.4 58.3 + - - +
37B LEU* 3.5 8.7 - - - +
38B ALA* 2.9 27.8 + - - +
401B GLU* 4.0 16.1 - - - +
455B TRP* 3.3 30.1 + - - +
456B HIS* 4.0 21.8 + - - +
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Residues in contact with THR 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TYR* 2.7 50.6 + - + +
32B LEU* 3.8 13.7 - - + -
33B TRP 3.3 0.2 - - - -
34B GLU* 1.4 73.7 - - - +
36B PHE* 1.4 54.3 + - - +
38B ALA* 3.2 8.3 + - + +
39B GLN* 2.8 36.2 + - + +
79B PHE* 4.2 29.1 - - + -
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Residues in contact with PHE 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU 2.9 18.5 + - - +
33B TRP* 3.4 20.6 + + - +
35B THR* 1.4 74.3 - - - +
37B LEU* 1.3 68.4 + - + +
39B GLN* 3.3 9.1 + - + +
40B ARG* 2.9 66.5 + - + +
43B ARG* 6.0 2.5 - - - -
451B LEU* 3.7 24.2 - - + -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 3.1 53.6 + - + +
34B GLU* 3.5 10.1 - - - +
36B PHE* 1.3 82.9 - - + +
38B ALA* 1.4 59.0 + - - +
40B ARG* 3.3 8.8 + - - +
41B GLN 3.0 24.3 + - - -
449B ASP* 5.6 0.2 - - - +
451B LEU* 3.4 35.2 - - + +
452B PHE* 3.2 24.6 - - + +
455B TRP* 3.5 29.4 - - + -
456B HIS* 3.9 12.3 - - + -
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU 2.9 18.6 + - - +
35B THR* 3.4 11.9 - - + +
37B LEU* 1.4 75.7 - - - +
39B GLN* 1.4 56.1 + - - +
41B GLN* 3.5 2.1 + - - +
42B ARG* 2.9 30.0 + - - +
75B SER* 4.4 7.0 + - - +
78B SER* 6.1 1.3 - - - +
79B PHE* 6.2 5.6 - - + -
452B PHE* 3.8 16.3 - - + -
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Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR* 2.8 22.2 + - + +
36B PHE* 3.5 11.2 - - + +
38B ALA* 1.4 68.4 - - - +
40B ARG* 1.3 64.1 + - - +
42B ARG* 3.4 7.1 + - + +
43B ARG* 3.1 44.4 + - + +
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 2.9 51.1 + - + +
37B LEU* 3.3 12.5 + - - +
39B GLN* 1.3 77.9 - - - +
41B GLN* 1.4 56.5 + - - +
43B ARG* 3.6 32.0 - - - +
44B ILE* 3.3 19.9 - - + +
449B ASP* 3.4 34.3 + - - +
451B LEU* 4.2 16.2 - - - +
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Residues in contact with GLN 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU 3.0 5.8 + - - +
38B ALA 4.1 2.7 - - - +
40B ARG* 1.4 72.1 - - - +
42B ARG* 1.4 63.4 + - - +
43B ARG 3.2 2.2 - - - -
44B ILE* 3.3 18.6 + - + +
45B TYR* 2.8 64.5 + - + -
447B VAL 3.7 2.3 - - - +
448B SER* 3.5 24.2 - - - -
449B ASP* 3.6 20.2 - - + +
452B PHE* 3.4 54.0 - - + -
457B TYR* 3.6 7.9 + - - -
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA 2.9 18.9 + - - +
39B GLN* 3.4 8.7 + - - +
41B GLN* 1.4 74.9 - - - +
43B ARG* 1.4 62.6 + - + +
45B TYR* 3.4 15.8 + - - +
46B LYS* 3.2 21.9 + - - +
75B SER* 3.7 17.7 - - - +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 6.0 2.0 - - - -
39B GLN* 3.1 35.6 + - + +
40B ARG* 3.6 29.1 - - - +
41B GLN 3.2 0.2 - - - -
42B ARG* 1.4 73.2 - - - +
44B ILE* 1.4 56.1 + - + +
46B LYS* 3.3 6.5 + - - +
47B THR* 2.7 45.4 + - - +
53E PRO* 5.2 12.5 + - + +
57E GLN* 3.9 30.7 + - - +
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Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG 3.3 19.7 - - - +
41B GLN* 3.3 18.6 + - - +
43B ARG* 1.4 78.4 - - + +
45B TYR* 1.4 53.9 + - - +
47B THR* 4.8 3.1 - - - -
48B THR* 2.6 49.4 + - + +
445B PHE* 4.5 2.2 - - + -
447B VAL* 3.8 42.4 - - + +
448B SER* 4.4 1.8 - - - +
449B ASP* 3.9 26.9 - - + +
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Residues in contact with TYR 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLN* 2.8 57.5 + - + -
42B ARG* 3.4 13.9 + - - +
43B ARG 3.3 0.2 - - - -
44B ILE* 1.4 76.3 - - - +
46B LYS* 1.3 54.4 + - - +
48B THR 4.0 1.7 - - - +
68B ARG* 2.8 46.6 + - - +
71B GLN* 3.6 52.1 + - + +
72B LEU* 4.7 10.5 - - + -
75B SER* 4.5 12.1 - - - -
445B PHE* 3.6 41.0 - + + +
447B VAL 4.6 0.2 - - - -
457B TYR* 4.2 5.7 + - - -
----------------------------------------------------------
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG 3.2 13.6 + - - +
43B ARG* 3.3 7.2 + - - +
45B TYR* 1.3 77.5 - - - +
47B THR* 1.4 61.7 + - - +
49B THR* 4.8 0.7 - - - -
68B ARG* 3.2 15.1 + - - +
53E PRO* 5.2 12.1 - - + -
54E GLU* 3.1 41.1 - - + +
----------------------------------------------------------
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG* 2.7 32.6 + - - +
44B ILE* 4.3 3.6 - - - -
46B LYS* 1.4 74.7 - - - +
48B THR* 1.4 60.0 + - + +
49B THR* 2.8 24.1 + - - +
54E GLU* 5.4 10.4 + - - +
57E GLN* 5.2 13.2 + - - +
----------------------------------------------------------
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Residues in contact with THR 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 2.6 42.2 + - + +
45B TYR 4.0 0.5 - - - +
47B THR* 1.4 70.5 - - + +
49B THR* 1.3 58.8 + - - +
50B HIS 3.6 11.0 - - - +
52B PRO* 5.9 2.5 - - + -
64B PHE* 3.5 17.6 - - - -
68B ARG* 3.6 12.1 + - - -
445B PHE* 3.3 22.5 - - - -
447B VAL* 4.4 15.2 - - + +
----------------------------------------------------------
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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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