Contacts of the helix formed by residues 15 - 38 (chain P) in PDB entry 2DYS
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 PRO 15 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N PHE* 3.6 35.9 - - + -
14P SER* 1.3 91.8 - - - +
16P TRP* 1.3 76.4 + - + +
17P PRO 3.3 1.6 - - - -
18P LEU* 3.1 7.6 + - - +
19P THR* 3.0 22.7 + - - +
21W HIS* 3.4 41.7 - - + +
32W TYR* 3.7 19.1 - - + -
36W MET* 3.8 4.5 - - + -
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Residues in contact with TRP 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96N ARG* 5.0 2.5 - - - -
14P SER* 3.2 13.9 + - - -
15P PRO* 1.3 85.6 - - + +
17P PRO* 1.3 67.3 - - + +
19P THR* 3.1 16.7 + - + -
20P GLY* 2.8 26.7 + - - -
53P THR* 3.3 12.3 - - + +
56P GLN* 3.1 52.9 - - + +
57P TRP* 3.6 42.9 - + + -
59P ARG* 4.0 3.6 - - - -
60P ASP* 2.7 29.7 + - + -
21W HIS* 3.6 23.5 - + + +
32W TYR* 3.7 28.5 - + + -
35W THR* 4.1 13.5 - - + -
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Residues in contact with PRO 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96N ARG* 3.2 37.9 - - + +
99N ASN* 3.6 24.7 - - + +
100N MET* 3.6 29.3 - - + +
103N TRP* 4.9 1.3 - - - -
14P SER* 3.5 18.4 - - - +
15P PRO 3.6 0.2 - - - -
16P TRP* 1.3 93.1 - - + +
18P LEU* 1.3 56.1 + - - +
21P ALA* 2.9 29.3 + - - +
57P TRP* 3.9 13.2 - - + -
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Residues in contact with LEU 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N LEU* 3.8 50.9 - - + +
8N PHE* 4.2 10.5 - - + -
99N ASN* 5.0 0.6 - - - +
103N TRP* 4.0 35.4 - - + -
15P PRO 3.1 9.6 + - - +
17P PRO* 1.3 77.7 - - - +
19P THR* 1.3 67.0 + - + +
21P ALA* 3.1 6.9 + - + +
22P LEU* 2.9 50.1 + - + +
36W MET* 5.0 8.1 - - + -
40W LEU* 5.9 2.2 - - + -
101W CHD 4.3 7.2 - - - +
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Residues in contact with THR 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P PRO 3.0 11.8 + - - +
16P TRP* 3.1 24.9 + - + -
18P LEU* 1.3 75.1 - - - +
20P GLY* 1.3 59.4 + - - +
22P LEU* 3.3 2.7 + - - -
23P SER* 2.8 29.8 + - - -
53P THR* 3.0 21.3 + - - +
35W THR* 3.9 17.3 - - + -
36W MET* 3.6 31.4 - - + -
39W CYS* 3.7 21.9 - - - -
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Residues in contact with GLY 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100N MET* 4.5 9.9 - - - -
609N PGV 4.1 13.1 - - - +
16P TRP 2.8 13.6 + - - -
17P PRO 3.8 0.9 - - - -
19P THR* 1.3 79.0 + - - +
21P ALA* 1.3 60.5 + - - +
23P SER* 2.6 24.3 + - - -
24P ALA* 3.0 9.9 + - - +
53P THR* 3.5 19.7 - - - -
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Residues in contact with ALA 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100N MET* 4.4 3.0 - - + -
103N TRP* 3.4 41.1 - - + +
104N LEU* 3.9 18.5 - - + +
107N PRO* 4.2 5.8 - - + +
17P PRO 2.9 18.1 + - - +
18P LEU* 3.4 7.2 - - + +
20P GLY* 1.3 75.3 - - - +
22P LEU* 1.3 62.7 + - + +
24P ALA* 3.1 18.4 - - - +
25P LEU* 3.2 8.1 + - - +
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Residues in contact with LEU 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107N PRO* 4.9 9.9 - - + -
18P LEU* 2.9 42.2 + - + +
19P THR* 3.7 3.8 - - - +
21P ALA* 1.3 75.4 - - + +
23P SER* 1.3 59.2 + - - +
25P LEU* 3.0 15.2 + - + +
26P LEU* 2.9 34.1 + - - +
36W MET* 5.6 1.1 - - - -
39W CYS* 4.0 27.8 - - + +
40W LEU* 4.1 20.9 - - + -
43W THR* 3.5 31.4 - - + +
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Residues in contact with SER 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609N PGV 4.3 0.2 - - - +
19P THR 2.8 18.3 + - - -
20P GLY* 2.6 21.6 + - - -
22P LEU* 1.3 71.6 - - - +
24P ALA* 1.3 55.4 + - - +
26P LEU* 3.2 4.8 + - - +
27P MET* 2.9 36.2 + - - +
46P GLY 3.7 1.3 - - - -
49P THR* 3.1 29.6 - - - -
50P ASN* 3.3 35.3 + - - -
39W CYS* 4.8 0.2 - - - -
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Residues in contact with ALA 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104N LEU* 3.7 21.3 - - + -
152N LEU* 3.9 14.8 - - + -
609N PGV 4.1 13.9 - - + -
20P GLY 3.0 7.5 + - - +
21P ALA 3.1 12.1 - - - +
23P SER* 1.3 82.8 + - - +
25P LEU* 1.3 59.1 + - - +
27P MET* 3.5 13.1 + - - +
28P THR* 3.0 34.1 + - - +
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Residues in contact with LEU 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107N PRO* 3.9 39.3 - - + +
110N LEU* 4.0 25.6 - - + -
111N LEU* 4.3 17.9 - - + -
152N LEU* 4.4 4.2 - - - +
21P ALA 3.2 3.8 + - - +
22P LEU* 3.0 17.3 + - + +
24P ALA* 1.3 77.1 - - - +
26P LEU* 1.3 60.4 + - + +
28P THR* 3.1 4.2 + - - -
29P SER* 2.8 38.6 + - - +
43W THR* 4.2 23.3 - - + +
46W SER* 4.1 20.4 - - - +
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Residues in contact with LEU 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P LEU 2.9 19.2 + - - +
23P SER* 3.2 2.7 + - - +
25P LEU* 1.3 80.4 - - + +
27P MET* 1.3 51.4 + - - +
29P SER* 3.8 3.0 - - - -
30P GLY* 2.7 31.4 + - - -
42P LEU* 3.6 20.3 - - + +
45P ILE* 3.9 27.4 - - + -
46P GLY* 3.4 17.7 - - - +
49P THR* 4.0 15.7 - - - +
38W LEU 4.1 6.5 - - - +
39W CYS* 4.2 9.6 - - - +
42W GLY* 3.2 37.5 - - - +
43W THR* 3.6 10.3 - - - +
46W SER* 4.0 5.2 - - - +
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Residues in contact with MET 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609N PGV 4.4 13.7 - - + -
23P SER 2.9 22.3 + - - +
24P ALA* 3.8 15.3 - - - +
25P LEU 3.3 0.2 - - - -
26P LEU* 1.3 74.8 - - - +
28P THR* 1.3 61.2 + - + +
30P GLY* 3.5 0.3 - - - -
31P LEU* 2.8 35.6 + - + +
43P LEU* 3.6 11.1 - - + +
46P GLY* 3.5 22.9 - - - +
47P LEU* 3.7 29.2 - - + +
50P ASN* 3.5 27.4 - - - +
302P DMU 5.4 5.2 - - + -
307P PGV 3.6 27.4 - - + -
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Residues in contact with THR 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111N LEU* 3.7 13.6 - - - +
148N PHE* 3.4 37.7 - - + +
151N HIS* 5.6 0.2 - - + -
152N LEU* 4.1 18.4 - - + -
609N PGV 3.9 28.7 - - + -
24P ALA 3.0 19.0 + - - +
25P LEU* 3.1 10.2 + - - -
27P MET* 1.3 71.6 - - - +
29P SER* 1.3 64.8 + - - +
31P LEU* 3.3 1.8 + - - +
32P THR* 2.7 34.1 + - - -
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Residues in contact with SER 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111N LEU* 4.8 9.2 - - - +
145N LEU* 5.3 2.7 - - - +
25P LEU* 2.8 24.5 + - - +
26P LEU* 3.8 4.5 - - - -
28P THR* 1.3 80.7 + - - +
30P GLY* 1.3 57.4 + - - +
32P THR* 3.1 9.8 + - - -
33P MET* 2.9 30.5 + - - +
42P LEU* 3.9 16.3 - - - +
46W SER* 3.8 20.2 + - - -
49W CYS* 6.0 0.3 - - - +
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Residues in contact with GLY 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P LEU 2.7 21.3 + - - -
27P MET 3.5 2.0 - - - -
28P THR 3.2 0.2 - - - -
29P SER* 1.3 76.9 - - - +
31P LEU* 1.3 55.7 + - - +
33P MET* 3.2 3.8 + - - +
34P TRP* 2.9 28.4 + - - +
39P SER 4.0 1.2 - - - +
42P LEU* 3.5 8.5 - - - +
43P LEU* 3.4 29.3 - - - +
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Residues in contact with LEU 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148N PHE* 3.6 32.5 - - + -
609N PGV 4.2 12.6 - - + -
27P MET* 2.8 23.7 + - + +
29P SER 3.3 0.2 - - - -
30P GLY* 1.3 68.7 - - - +
32P THR* 1.3 57.4 + - - +
34P TRP* 3.2 29.3 + - + +
35P PHE* 2.7 47.8 + - + +
43P LEU* 4.1 16.6 - - + -
302P DMU 3.9 23.6 - - + -
305P PEK 4.2 25.6 - - + -
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Residues in contact with THR 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141N ALA* 3.8 23.3 - - + +
144N ASP* 4.8 4.3 - - + -
145N LEU* 3.8 33.2 - - + +
148N PHE* 3.1 18.8 - - - -
28P THR 2.7 22.2 + - - -
29P SER* 3.3 7.6 - - - -
31P LEU* 1.3 77.4 - - - +
33P MET* 1.3 58.6 + - - +
35P PHE* 4.5 4.7 - - - +
36P HIS* 2.9 39.0 + - + +
37P PHE* 4.3 5.1 - - + -
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Residues in contact with MET 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P SER 2.9 14.5 + - - +
30P GLY* 3.4 12.1 - - - +
32P THR* 1.3 77.5 - - - +
34P TRP* 1.3 57.6 + - - +
37P PHE* 2.8 64.5 + - + -
38P ASN 3.1 7.4 + - - -
39P SER* 3.4 23.3 + - - +
42P LEU* 4.5 16.8 - - + +
45W TYR* 5.7 2.2 - - + +
49W CYS* 3.7 44.9 - - + +
52W TRP* 4.8 10.5 - - + -
53W ALA* 5.9 0.4 - - - -
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Residues in contact with TRP 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P GLY 2.9 16.4 + - - +
31P LEU* 3.5 21.8 - - + +
33P MET* 1.3 80.2 - - - +
35P PHE* 1.3 88.7 + + - +
36P HIS 3.4 0.3 + - - -
38P ASN* 3.6 16.6 + - - +
39P SER 3.2 15.2 + - - +
40P MET* 3.5 17.0 - - + -
43P LEU* 4.5 11.0 - - + -
302P DMU 2.6 61.2 + + - -
305P PEK 3.8 30.1 - - + -
61T SER* 3.0 35.2 + - - -
62T TRP* 3.8 19.5 - + - -
69T PHE* 5.3 0.2 - + - -
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Residues in contact with PHE 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144N ASP* 5.2 1.3 - - + -
148N PHE* 4.9 3.6 - + - -
210N LEU* 4.2 23.6 - - + -
214N ASN* 3.2 48.7 - - + +
215N LEU* 4.3 16.4 - - + -
31P LEU* 2.7 31.3 + - + +
32P THR* 5.1 1.1 - - - -
34P TRP* 1.3 102.6 - + - +
36P HIS* 1.3 68.2 + - + +
38P ASN 5.0 0.2 - - - -
305P PEK 4.3 24.7 - - + -
58T LYS* 2.8 29.3 + - - -
61T SER* 3.4 17.5 + - - -
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Residues in contact with HIS 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135N ASN* 6.6 0.7 - - + -
140N GLY* 3.3 30.2 + - - -
141N ALA* 3.7 18.1 - - + +
144N ASP* 2.6 31.4 + - + -
213N ARG* 4.6 1.3 - - - -
214N ASN* 3.7 11.4 + - - -
32P THR* 2.9 25.3 + - + +
35P PHE* 1.3 86.7 + - + +
37P PHE* 1.3 86.4 + - + +
38P ASN 3.4 3.1 - - - -
58T LYS* 4.2 13.5 - - + +
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Residues in contact with PHE 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N VAL* 5.8 1.1 - - + -
119N GLU* 4.9 12.8 - - - -
141N ALA* 4.3 19.1 - - + -
145N LEU* 6.4 0.4 - - + -
32P THR* 4.3 4.5 - - + -
33P MET* 2.8 57.0 + - + +
36P HIS* 1.3 97.2 - - + +
38P ASN* 1.3 71.1 + - - +
39P SER* 3.3 6.6 + - - -
52W TRP* 3.7 27.6 - + + -
53W ALA* 3.8 26.5 - - + -
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Residues in contact with ASN 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P MET 3.1 2.8 + - - -
34P TRP* 3.6 17.1 + - - +
36P HIS 3.4 2.4 - - - -
37P PHE* 1.3 80.1 - - - +
39P SER* 1.3 57.4 + - - +
302P DMU 4.8 10.0 + - - -
61T SER* 4.0 19.2 - - - +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il