Contacts of the helix formed by residues 15 - 48 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D PRO* 1.4 72.4 - - - +
16D GLU* 1.4 66.8 + - - +
17D LYS 3.3 1.1 - - - -
18D ARG* 3.3 12.9 + - - +
19D ILE* 3.5 17.2 + - - +
371D GLU* 6.1 3.8 - - + -
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Residues in contact with GLU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ALA* 1.4 78.7 - - + +
17D LYS* 1.3 62.8 + - + +
19D ILE* 3.3 16.7 - - - +
20D PHE* 3.4 3.1 + - - +
371D GLU* 3.9 20.5 - - + +
374D ALA* 4.2 14.4 - - + +
375D ALA* 3.3 34.3 - - - +
379D TYR* 6.0 1.1 - - + -
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Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D PRO* 3.8 29.6 - - + +
15D ALA 3.3 1.4 - - - +
16D GLU* 1.3 77.2 - - + +
18D ARG* 1.4 62.1 + - - +
20D PHE* 3.7 9.1 + - - +
21D GLY* 3.2 18.5 + - - -
375D ALA* 5.6 0.7 - - - +
379D TYR* 5.0 8.9 + - - -
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Residues in contact with ARG 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D MET* 5.8 2.7 - - + -
14D PRO* 3.3 29.1 + - + +
15D ALA* 3.3 7.5 + - - +
16D GLU 3.3 0.6 - - - -
17D LYS* 1.4 77.0 - - - +
19D ILE* 1.4 60.6 + - + +
21D GLY* 3.4 2.0 + - - -
22D ALA* 3.1 26.6 + - - +
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Residues in contact with ILE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ALA 3.6 10.5 - - - +
16D GLU* 3.3 17.7 - - - +
18D ARG* 1.4 75.7 - - + +
20D PHE* 1.4 62.3 + - - +
22D ALA* 3.6 9.2 - - + +
23D VAL* 3.3 27.6 + - - +
371D GLU* 3.4 40.6 - - + +
372D LEU* 3.8 13.0 - - + +
375D ALA* 3.9 4.7 - - + -
376D PHE* 6.0 0.2 - - - -
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Residues in contact with PHE 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLU 3.4 14.4 + - - +
17D LYS* 3.8 9.4 - - - +
18D ARG 3.3 0.4 - - - -
19D ILE* 1.4 76.0 - - - +
21D GLY* 1.3 65.8 + - - +
23D VAL* 3.4 7.5 + - - +
24D LEU* 3.4 48.3 + - + +
93D LEU* 3.9 32.1 - - + -
94D LEU* 4.0 20.6 - - + -
375D ALA* 3.3 32.7 - - + +
376D PHE* 3.6 37.0 - + - -
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Residues in contact with GLY 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LYS 3.2 12.4 + - - -
18D ARG* 3.4 4.2 + - - -
19D ILE 3.4 0.2 - - - -
20D PHE* 1.3 83.7 - - - +
22D ALA* 1.3 51.5 + - - +
24D LEU* 3.4 6.8 + - - +
25D LEU* 2.8 38.1 + - - +
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Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ARG 3.1 16.0 + - - +
19D ILE* 3.6 13.5 - - + +
21D GLY* 1.3 73.6 - - - +
23D VAL* 1.4 58.9 + - + +
25D LEU* 3.9 6.9 - - - +
26D PHE* 3.1 29.6 + - - +
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Residues in contact with VAL 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ILE 3.3 13.8 + - - +
20D PHE 3.5 9.0 - - - +
21D GLY 3.3 0.2 - - - -
22D ALA* 1.4 76.5 - - + +
24D LEU* 1.4 59.0 + - + +
26D PHE* 3.4 6.9 + - - +
27D SER* 2.8 38.9 + - - +
93D LEU* 5.4 0.9 - - + -
376D PHE* 3.8 27.1 - - + -
394D PHE* 3.7 53.8 - - + +
395D ILE* 4.8 4.3 - - - +
397D SER* 5.7 1.3 - - - +
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Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D PHE* 3.4 46.6 + - + +
21D GLY* 3.8 8.7 - - - +
23D VAL* 1.4 80.0 - - + +
25D LEU* 1.4 63.6 + - - +
27D SER* 3.7 6.4 - - - -
28D TRP* 3.1 35.8 + - + +
90D THR* 3.8 29.6 - - + +
93D LEU* 3.9 21.5 - - + -
94D LEU* 3.8 29.6 - - + -
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Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D GLY 2.8 23.7 + - - +
22D ALA* 3.9 8.1 - - - +
23D VAL 3.4 0.2 - - - -
24D LEU* 1.4 71.7 - - - +
26D PHE* 1.3 57.5 + - - +
28D TRP* 3.6 5.0 + - - +
29D THR* 3.1 43.9 + - + +
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Residues in contact with PHE 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ALA 3.1 18.1 + - - +
23D VAL* 3.7 5.2 - - - +
25D LEU* 1.3 75.4 - - - +
27D SER* 1.3 61.4 + - - +
28D TRP 3.2 0.2 - - - -
29D THR* 2.9 21.3 + - - -
30D VAL* 3.0 44.7 + - + +
397D SER* 3.7 23.3 - - - -
398D PRO* 3.5 46.0 - - + -
401D GLU* 4.3 10.1 - - + -
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Residues in contact with SER 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D VAL* 2.8 28.8 + - - +
24D LEU* 3.4 9.5 + - - -
26D PHE* 1.3 79.8 - - - +
28D TRP* 1.4 58.1 + - - +
30D VAL* 4.2 5.1 - - - +
31D TYR* 3.4 23.6 + - - +
86D GLU* 3.4 20.9 - - - +
90D THR* 6.0 0.2 - - - -
93D LEU* 6.2 0.2 - - - +
394D PHE* 5.3 4.5 - - - -
397D SER* 5.1 6.8 + - - -
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Residues in contact with TRP 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 3.1 31.7 + - + +
25D LEU* 4.1 4.9 - - - +
27D SER* 1.4 78.4 - - - +
29D THR* 1.4 54.9 + - + +
30D VAL 3.3 0.2 - - - -
31D TYR* 3.3 39.4 + + - +
32D LEU* 2.8 53.1 + - + +
83D LEU* 4.9 6.5 - - + -
86D GLU* 3.7 27.4 - - + -
87D THR* 4.5 14.4 - - + -
90D THR* 2.7 43.9 + - + +
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Residues in contact with THR 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D LEU* 3.1 30.7 + - + +
26D PHE* 2.9 26.3 + - - -
28D TRP* 1.4 71.8 - - + +
30D VAL* 1.4 55.9 + - - +
32D LEU* 3.3 12.0 + - + +
33D TRP* 2.8 34.0 + - - +
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Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D PHE* 3.0 55.0 + - + +
27D SER* 4.2 6.1 - - - +
29D THR* 1.4 73.9 + - - +
31D TYR* 1.4 58.3 + - - +
33D TRP* 3.3 8.2 + - + +
34D GLU* 3.0 42.9 + - + +
401D GLU* 3.8 33.0 - - + +
455D TRP* 5.4 5.8 - - + -
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Residues in contact with TYR 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D SER 3.4 10.4 + - - +
28D TRP* 3.3 36.5 + + - +
29D THR 3.3 0.2 - - - -
30D VAL* 1.4 80.4 - - - +
32D LEU* 1.4 57.8 + - + +
34D GLU* 3.2 14.5 + - + +
35D THR* 2.8 59.8 + - + -
79D PHE* 3.9 13.7 + + - -
82D GLY* 3.9 20.9 - - - -
83D LEU* 3.3 39.0 + - + +
86D GLU* 3.3 32.8 - - + +
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D TRP* 2.8 37.9 + - + +
29D THR* 3.8 11.7 - - + +
31D TYR* 1.4 82.3 - - + +
33D TRP* 1.4 59.5 + - - +
35D THR* 3.8 10.1 - - + -
36D PHE* 2.9 29.8 + - - +
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Residues in contact with TRP 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D THR 2.8 18.7 + - - +
30D VAL* 3.4 11.7 - - + +
31D TYR 3.2 0.2 - - - -
32D LEU* 1.4 75.3 - - - +
34D GLU* 1.3 59.1 + - + +
36D PHE* 3.4 25.4 + + - +
37D LEU* 3.0 57.4 + - + +
451D LEU* 5.2 8.1 - - + -
455D TRP* 3.3 60.7 - + + -
----------------------------------------------------------
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Residues in contact with GLU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D VAL* 3.0 29.9 + - + +
31D TYR* 3.6 12.2 - - + +
33D TRP* 1.3 76.8 - - + +
35D THR* 1.4 53.5 + - - +
37D LEU* 3.4 9.2 - - - +
38D ALA* 2.9 31.9 + - - +
401D GLU* 3.9 15.9 - - - +
455D TRP* 3.3 30.3 + - + +
456D HIS* 4.0 20.4 + - - +
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Residues in contact with THR 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D TYR* 2.8 49.2 + - + +
32D LEU* 3.8 13.5 - - + -
33D TRP 3.3 0.2 - - - -
34D GLU* 1.4 74.5 - - - +
36D PHE* 1.4 53.5 + - - +
37D LEU 3.2 0.4 - - - -
38D ALA* 3.2 7.8 + - + +
39D GLN* 2.8 35.4 + - + +
79D PHE* 4.2 28.6 - - + -
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Residues in contact with PHE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU 2.9 17.9 + - - +
33D TRP* 3.6 29.8 - + - +
35D THR* 1.4 74.5 - - - +
37D LEU* 1.3 74.6 + - + +
39D GLN* 3.4 19.0 + - - +
40D ARG* 2.9 68.7 + - + +
451D LEU* 5.9 1.6 - - + -
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D TRP* 3.0 50.6 + - + +
34D GLU* 3.4 10.5 - - - +
36D PHE* 1.3 86.9 - - + +
38D ALA* 1.4 58.2 + - - +
40D ARG* 3.2 8.8 + - - +
41D GLN 3.0 24.1 + - - -
451D LEU* 3.8 21.8 - - + +
452D PHE* 3.2 23.9 - - + +
455D TRP* 3.6 44.4 - - + -
456D HIS* 3.9 7.2 - - + +
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Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D GLU 2.9 19.0 + - - +
35D THR* 3.2 11.9 + - + +
37D LEU* 1.4 74.2 - - - +
39D GLN* 1.4 55.8 + - - +
41D GLN* 3.5 2.3 + - - +
42D ARG* 2.9 30.6 + - - +
75D SER* 4.3 8.0 + - - +
78D SER* 6.0 2.2 - - - +
79D PHE* 6.2 6.5 - - + -
452D PHE* 3.8 16.1 - - + -
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Residues in contact with GLN 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D THR* 2.8 18.6 + - + +
36D PHE* 3.5 24.2 - - - +
38D ALA* 1.4 72.1 - - - +
40D ARG* 1.4 65.2 + - - +
42D ARG* 3.4 10.5 + - + +
43D ARG* 3.1 23.6 + - - +
----------------------------------------------------------
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Residues in contact with ARG 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D PHE* 2.9 55.6 + - + +
37D LEU* 3.2 12.5 + - - +
39D GLN* 1.4 77.9 + - - +
41D GLN* 1.4 58.6 + - - +
43D ARG* 3.6 13.5 - - - +
44D ILE* 3.3 19.6 - - + +
449D ASP* 3.4 33.8 + - - +
451D LEU* 4.5 10.8 - - - +
----------------------------------------------------------
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Residues in contact with GLN 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU 3.0 6.2 + - - +
38D ALA 4.1 1.6 - - - +
40D ARG* 1.4 72.2 - - - +
42D ARG* 1.3 63.5 + - - +
43D ARG 3.2 2.0 - - - -
44D ILE* 3.2 18.5 + - + +
45D TYR* 2.7 63.4 + - + -
447D VAL 3.8 1.2 - - - +
448D SER* 3.2 30.5 + - - -
449D ASP* 3.6 18.8 - - + +
452D PHE* 3.3 56.6 - - + -
457D TYR* 3.8 3.7 + - - -
----------------------------------------------------------
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ALA 2.9 19.7 + - - +
39D GLN* 3.4 10.7 + - - +
41D GLN* 1.3 75.8 - - - +
43D ARG* 1.4 61.4 + - - +
45D TYR* 3.4 12.5 + - - +
46D LYS* 3.2 27.3 + - + +
72D LEU* 3.2 32.2 + - + +
75D SER* 3.6 17.5 - - - +
76D THR* 2.6 50.2 + - - +
79D PHE* 6.4 1.3 - - - -
----------------------------------------------------------
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Residues in contact with ARG 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLN 3.1 12.4 + - - +
40D ARG* 3.6 13.2 - - - +
42D ARG* 1.4 74.9 - - - +
44D ILE* 1.4 56.7 + - + +
46D LYS* 3.2 6.9 + - - +
47D THR* 2.7 46.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ARG 3.3 20.0 - - - +
41D GLN* 3.2 17.0 + - - +
43D ARG* 1.4 78.2 - - + +
45D TYR* 1.3 54.2 + - + +
47D THR* 4.8 4.0 - - - -
48D THR* 2.6 49.6 + - + +
445D PHE* 4.5 2.2 - - + -
447D VAL* 3.9 42.0 - - + +
448D SER* 4.4 2.9 - - - +
449D ASP* 3.9 28.3 - - + +
----------------------------------------------------------
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Residues in contact with TYR 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLN* 2.7 56.9 + - + -
42D ARG* 3.6 13.7 - - - +
43D ARG 3.3 0.2 - - - -
44D ILE* 1.3 77.4 - - + +
46D LYS* 1.3 54.2 + - - +
48D THR 4.1 1.0 - - - +
68D ARG* 2.8 44.7 + - - +
71D GLN* 3.6 53.2 + - + +
72D LEU* 3.8 16.8 - - + +
75D SER* 4.6 11.0 - - - -
445D PHE* 3.6 42.4 - + + +
457D TYR* 4.1 7.1 + - - -
----------------------------------------------------------
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Residues in contact with LYS 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 4.3 7.8 - - - +
42D ARG* 3.2 21.0 + - + +
43D ARG* 3.2 9.8 + - - +
45D TYR* 1.3 75.7 - - - +
47D THR* 1.3 63.0 + - - +
49D THR* 4.8 0.7 - - - -
68D ARG* 3.1 21.2 + - - +
72D LEU* 3.8 21.8 - - + -
----------------------------------------------------------
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Residues in contact with THR 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ARG* 2.7 33.9 + - - +
44D ILE* 4.3 3.8 - - - -
46D LYS* 1.3 74.2 - - - +
48D THR* 1.4 59.1 + - + +
49D THR* 2.8 24.6 + - - +
----------------------------------------------------------
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Residues in contact with THR 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ILE* 2.6 42.6 + - + +
45D TYR 4.1 0.5 - - - +
47D THR* 1.4 71.2 - - + +
49D THR* 1.3 58.5 + - - +
50D HIS 3.6 10.5 - - - +
52D PRO* 6.1 1.8 - - + -
64D PHE* 3.5 16.7 - - - -
68D ARG* 3.6 13.5 + - - -
445D PHE* 3.3 21.8 - - - -
447D VAL* 4.3 15.4 - - + +
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il