Contacts of the helix formed by residues 15 - 48 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 1.4 72.4 - - - +
16A GLU* 1.3 66.7 + - + +
17A LYS 3.3 0.7 - - - -
18A ARG* 3.4 12.4 + - - +
19A ILE* 3.5 17.5 + - - +
371A GLU* 6.0 5.2 - - + -
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 5.1 0.2 - - - +
15A ALA* 1.3 79.2 - - + +
17A LYS* 1.3 61.3 + - - +
19A ILE* 3.3 15.2 - - - +
20A PHE* 3.4 3.5 + - - +
371A GLU* 3.9 20.8 - - + +
374A ALA* 4.2 13.0 - - + +
375A ALA* 3.3 35.4 - - - +
379A TYR* 6.0 0.9 - - + -
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 3.8 26.4 - - + +
15A ALA 3.3 1.0 - - - +
16A GLU* 1.3 76.7 - - - +
18A ARG* 1.4 62.8 + - - +
20A PHE* 3.7 8.3 + - - +
21A GLY* 3.3 18.7 + - - -
375A ALA* 5.6 0.4 - - - +
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A MET* 5.9 2.2 - - + -
14A PRO* 3.3 28.5 + - + +
15A ALA* 3.4 6.7 + - - +
16A GLU 3.3 0.2 - - - -
17A LYS* 1.4 78.1 - - - +
19A ILE* 1.4 58.9 + - + +
21A GLY* 3.6 1.8 + - - -
22A ALA* 3.1 26.2 + - - +
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 3.5 11.0 - - - +
16A GLU* 3.3 18.4 - - - +
18A ARG* 1.4 77.2 - - + +
20A PHE* 1.3 64.0 + - - +
22A ALA* 3.5 8.9 + - + +
23A VAL* 3.3 26.9 + - - +
371A GLU* 3.4 39.9 - - + +
372A LEU* 3.8 13.5 - - + +
375A ALA* 3.9 4.5 - - + -
376A PHE* 6.0 0.4 - - - -
395A ILE* 5.4 9.4 - - + +
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Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU 3.4 13.5 + - - +
17A LYS* 3.9 8.3 - - - +
18A ARG 3.4 0.6 - - - -
19A ILE* 1.3 76.7 - - - +
21A GLY* 1.3 64.7 + - - +
23A VAL* 3.3 17.1 + - - +
24A LEU* 3.4 39.8 + - + +
93A LEU* 3.8 31.4 - - + -
94A LEU* 4.1 18.8 - - + -
375A ALA* 3.3 32.8 - - + +
376A PHE* 3.6 37.5 - + - -
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS 3.3 12.2 + - - -
18A ARG 3.6 2.9 + - - -
20A PHE* 1.3 80.6 - - - +
22A ALA* 1.4 53.2 + - - +
24A LEU* 3.3 6.9 + - - +
25A LEU* 2.8 38.9 + - - +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG 3.1 18.0 + - - +
19A ILE* 3.5 12.8 - - + +
20A PHE 3.3 0.2 - - - -
21A GLY* 1.4 75.5 - - - +
23A VAL* 1.4 56.1 + - + +
25A LEU* 3.9 6.8 - - - +
26A PHE* 3.1 30.3 + - - +
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE 3.4 13.7 - - - +
20A PHE 3.4 9.2 - - - +
21A GLY 3.3 0.2 - - - -
22A ALA* 1.4 76.2 - - + +
24A LEU* 1.4 58.5 + - + +
26A PHE* 3.4 6.0 + - - +
27A SER* 2.8 39.1 + - - +
93A LEU* 5.3 1.1 - - + -
376A PHE* 3.8 24.2 - - + -
394A PHE* 3.7 53.8 - - + +
395A ILE* 4.3 14.6 - - + -
397A SER* 5.7 1.8 - - - +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.4 43.4 + - + +
21A GLY* 3.3 9.7 + - - +
23A VAL* 1.4 79.7 - - + +
25A LEU* 1.4 64.3 + - - +
27A SER* 3.4 6.5 + - - -
28A TRP* 3.1 35.8 + - + +
90A THR* 3.8 30.3 - - + +
93A LEU* 3.8 20.4 - - + -
94A LEU* 3.8 29.2 - - + -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY 2.8 23.4 + - - +
22A ALA* 3.9 7.2 - - - +
24A LEU* 1.4 72.0 - - - +
26A PHE* 1.3 57.5 + - - +
28A TRP* 3.6 4.0 + - - +
29A THR* 3.1 44.8 + - + +
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 3.1 17.7 + - - +
23A VAL* 3.7 5.8 - - - +
25A LEU* 1.3 74.4 - - - +
27A SER* 1.3 61.0 + - - +
28A TRP 3.2 0.2 - - - -
29A THR* 2.9 22.0 + - - -
30A VAL* 3.0 44.0 + - + +
397A SER* 3.8 22.9 - - - -
398A PRO* 3.5 45.3 - - + -
401A GLU* 4.3 10.8 - - + -
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 2.8 29.0 + - - +
24A LEU* 3.4 9.2 + - - -
26A PHE* 1.3 79.8 - - - +
28A TRP* 1.4 57.0 + - - +
30A VAL* 4.2 4.9 - - - +
31A TYR* 3.3 19.8 + - - +
86A GLU* 3.4 24.5 - - - +
93A LEU* 6.1 1.1 - - - +
394A PHE* 5.3 4.0 - - - -
397A SER* 5.1 6.8 + - - -
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Residues in contact with TRP 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.1 32.1 + - + +
25A LEU* 4.1 4.5 - - - +
27A SER* 1.4 76.6 - - - +
29A THR* 1.3 56.0 + - + +
30A VAL 3.3 0.2 - - - -
31A TYR* 3.3 40.1 + + - +
32A LEU* 2.8 53.9 + - + +
83A LEU* 4.9 6.5 - - + -
86A GLU* 3.7 28.0 - - + -
87A THR* 4.5 14.1 - - + -
90A THR* 2.7 44.7 + - + +
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.1 30.7 + - + +
26A PHE* 2.9 26.3 + - - -
28A TRP* 1.3 71.6 - - + +
30A VAL* 1.4 55.5 + - - +
32A LEU* 3.3 12.3 + - + +
33A TRP* 2.8 35.1 + - - +
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.0 54.4 + - + +
27A SER* 4.2 5.6 - - - +
29A THR* 1.4 73.5 + - - +
31A TYR* 1.4 58.3 + - - +
33A TRP* 3.3 9.1 + - + +
34A GLU* 3.0 42.9 + - + +
401A GLU* 3.8 33.0 - - + +
455A TRP* 5.3 5.4 - - + -
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Residues in contact with TYR 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER 3.3 18.2 + - - +
28A TRP* 3.3 37.4 + + - +
29A THR 3.3 0.2 - - - -
30A VAL* 1.4 79.2 - - - +
32A LEU* 1.4 58.6 + - + +
34A GLU* 3.2 14.0 + - + +
35A THR* 2.7 59.7 + - + -
79A PHE* 3.9 14.0 + + - -
82A GLY* 3.9 20.2 - - - -
83A LEU* 3.3 40.3 + - + +
86A GLU* 3.6 24.9 - - + +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TRP* 2.8 37.8 + - + +
29A THR* 3.8 12.1 - - + +
31A TYR* 1.4 81.7 - - + +
33A TRP* 1.3 60.5 + - - +
35A THR* 3.8 10.1 - - + -
36A PHE* 2.9 30.0 + - - +
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Residues in contact with TRP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR 2.8 18.1 + - - +
30A VAL* 3.4 10.8 - - + +
31A TYR 3.3 0.2 - - - -
32A LEU* 1.3 75.4 - - - +
34A GLU* 1.3 58.9 + - + +
36A PHE* 3.4 23.0 + + - +
37A LEU* 3.1 58.1 + - + +
451A LEU* 3.8 23.1 - - + -
455A TRP* 3.3 61.6 - + + +
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 3.0 30.3 + - + +
31A TYR* 3.6 11.8 - - + +
33A TRP* 1.3 77.9 - - + +
35A THR* 1.4 57.7 + - - +
37A LEU* 3.5 8.3 - - - +
38A ALA* 2.9 27.4 + - - +
401A GLU* 4.0 15.6 - - - +
455A TRP* 3.3 30.9 + - - +
456A HIS* 4.0 20.9 + - - +
----------------------------------------------------------
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Residues in contact with THR 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TYR* 2.7 51.2 + - + +
32A LEU* 3.8 13.2 - - + -
34A GLU* 1.4 73.9 - - - +
36A PHE* 1.4 53.9 + - - +
38A ALA* 3.2 8.1 + - + +
39A GLN* 2.8 35.2 + - + +
79A PHE* 4.2 28.8 - - + -
----------------------------------------------------------
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Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU 2.9 18.1 + - - +
33A TRP* 3.6 20.9 - + - +
35A THR* 1.4 76.1 - - - +
37A LEU* 1.3 67.6 + - + +
39A GLN* 3.4 9.0 + - + +
40A ARG* 2.9 65.2 + - + +
451A LEU* 3.7 25.4 - - + -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 3.1 53.7 + - + +
34A GLU* 3.5 10.1 - - - +
35A THR 3.3 0.2 - - - -
36A PHE* 1.3 84.5 - - + +
38A ALA* 1.4 57.8 + - - +
40A ARG* 3.3 7.7 + - - +
41A GLN 3.0 23.9 + - - -
451A LEU* 3.6 25.1 - - + +
452A PHE* 3.2 25.6 - - + +
455A TRP* 3.5 44.2 - - + -
456A HIS* 4.0 6.7 - - + -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU 2.9 17.9 + - - +
35A THR* 3.2 11.6 + - + +
37A LEU* 1.4 73.9 - - - +
39A GLN* 1.4 56.5 + - - +
41A GLN* 3.5 2.1 + - - +
42A ARG* 2.9 29.9 + - - +
75A SER* 4.3 7.5 + - - +
78A SER* 6.1 0.9 - - - +
79A PHE* 6.2 6.1 - - + -
452A PHE* 3.8 15.9 - - + -
456A HIS* 6.1 0.2 - - + -
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 2.8 18.2 + - + +
36A PHE* 3.5 10.1 - - + +
38A ALA* 1.4 72.6 - - - +
40A ARG* 1.3 64.4 + - - +
42A ARG* 3.3 7.2 + - - +
43A ARG* 3.1 23.4 + - - +
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 2.9 51.9 + - + +
37A LEU* 3.4 11.7 - - - +
39A GLN* 1.3 76.8 - - - +
41A GLN* 1.4 57.7 + - - +
43A ARG* 3.6 13.6 - - - +
44A ILE* 3.3 20.3 - - + +
449A ASP* 3.4 34.0 + - - +
451A LEU* 4.2 15.7 - - - +
----------------------------------------------------------
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU 3.0 5.8 + - - +
38A ALA 4.1 3.1 - - - +
40A ARG* 1.4 72.6 - - - +
42A ARG* 1.4 63.8 + - - +
43A ARG 3.2 1.8 - - - -
44A ILE* 3.3 17.4 + - + +
45A TYR* 2.7 64.1 + - + -
447A VAL 3.8 1.6 - - - +
448A SER* 3.3 29.9 + - - -
449A ASP* 3.6 19.5 - - + +
452A PHE* 3.3 54.1 - - + -
457A TYR* 3.9 4.0 + - - -
----------------------------------------------------------
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA 2.9 17.9 + - - +
39A GLN* 3.3 9.6 + - - +
41A GLN* 1.4 74.8 - - - +
43A ARG* 1.4 63.2 + - - +
45A TYR* 3.4 16.1 + - - +
46A LYS* 3.2 21.1 + - - +
75A SER* 3.7 17.0 - - - +
----------------------------------------------------------
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN 3.1 12.8 + - - +
40A ARG* 3.6 13.2 - - - +
41A GLN 3.2 0.2 - - - -
42A ARG* 1.4 74.3 - - - +
44A ILE* 1.4 55.2 + - + +
46A LYS* 3.2 6.6 + - - +
47A THR* 2.7 46.1 + - - +
----------------------------------------------------------
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Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 3.3 19.1 - - + +
41A GLN* 3.3 16.7 + - - +
43A ARG* 1.4 78.0 - - + +
45A TYR* 1.4 54.4 + - - +
47A THR* 4.8 3.1 - - - -
48A THR* 2.6 48.4 + - + +
445A PHE* 4.5 2.5 - - + -
447A VAL* 3.8 42.6 - - + +
448A SER* 4.4 2.5 - - - +
449A ASP* 3.9 26.9 - - + +
----------------------------------------------------------
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Residues in contact with TYR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN* 2.7 55.5 + - - -
42A ARG* 3.4 13.4 + - - +
43A ARG 3.4 0.4 - - - -
44A ILE* 1.4 76.7 - - + +
46A LYS* 1.4 54.0 + - - +
48A THR 4.0 1.6 - - - +
68A ARG* 2.8 47.1 + - - +
71A GLN* 3.6 52.4 + - + +
72A LEU* 4.7 10.3 - - + -
75A SER* 4.5 10.5 - - - -
445A PHE* 3.6 42.4 - + + +
447A VAL 4.6 0.2 - - - -
457A TYR* 4.2 6.6 + - - -
----------------------------------------------------------
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG 3.2 10.7 + - - +
43A ARG* 3.7 9.2 - - - +
45A TYR* 1.4 77.9 - - - +
47A THR* 1.4 63.7 + - - +
49A THR* 4.8 1.6 - - - +
68A ARG* 3.1 21.8 + - - +
----------------------------------------------------------
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Residues in contact with THR 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 2.7 33.2 + - - +
44A ILE* 4.3 3.6 - - - -
46A LYS* 1.4 75.7 - - - +
48A THR* 1.4 60.0 + - + +
49A THR* 2.8 24.4 + - - +
----------------------------------------------------------
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Residues in contact with THR 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 2.6 41.5 + - + +
45A TYR 4.0 0.5 - - - +
47A THR* 1.4 70.9 - - + +
49A THR* 1.3 59.2 - - - +
50A HIS 3.5 10.8 - - - +
52A PRO* 6.0 2.0 - - + -
64A PHE* 3.6 9.6 - - - -
68A ARG* 3.6 17.5 + - - -
445A PHE* 3.3 22.2 - - - -
447A VAL* 4.4 17.4 - - + +
----------------------------------------------------------
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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