Contacts of the helix formed by residues 15 - 37 (chain C) in PDB entry 5W97
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.7 27.8 - - + -
14C SER* 1.3 90.2 - - - +
16C TRP* 1.3 77.6 + - + +
17C PRO 3.5 0.9 - - - -
18C LEU* 3.3 8.8 + - - +
19C THR* 3.2 21.7 + - - +
21J HIS* 3.7 31.2 - - + +
32J TYR* 3.5 34.5 - - + -
36J MET* 3.9 7.0 - - + -
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Residues in contact with TRP 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG* 4.9 2.5 - - - -
14C SER* 3.3 15.9 + - - -
15C PRO* 1.3 90.3 - - + +
17C PRO* 1.4 67.0 - - + +
19C THR* 3.3 16.4 + - + -
20C GLY* 2.8 25.5 + - - -
53C THR* 3.4 14.4 - - + +
56C GLN* 2.9 54.9 - - + +
57C TRP* 3.6 43.7 - + + -
59C ARG* 4.0 3.6 - - - -
60C ASP* 3.0 23.0 + - + -
21J HIS* 3.9 20.5 - + + +
32J TYR* 3.8 26.2 - + + -
35J THR* 4.3 13.7 - - + -
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Residues in contact with PRO 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG* 3.1 43.7 - - + +
99A ASN* 3.7 18.2 - - + +
100A MET* 3.5 36.3 - - + +
103A TRP* 4.8 1.8 - - + -
14C SER* 3.6 13.5 - - - +
16C TRP* 1.4 93.0 - - + +
18C LEU* 1.3 56.7 + - - +
20C GLY* 3.3 0.7 + - - -
21C ALA* 2.9 30.6 + - - +
57C TRP* 3.9 7.2 - - + -
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.1 45.1 + - + +
8A PHE* 4.3 11.9 - - + -
99A ASN* 4.9 0.6 - - - +
103A TRP* 4.2 35.7 - - + +
15C PRO* 3.3 11.7 + - + +
16C TRP 3.3 0.6 - - - -
17C PRO* 1.3 78.6 - - - +
19C THR* 1.3 58.8 + - + +
21C ALA* 3.2 5.5 + - + +
22C LEU* 2.8 57.8 + - + +
36J MET* 5.0 7.2 - - - -
40J LEU* 6.0 2.0 - - + -
101J CHD 4.7 8.5 - - - +
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Residues in contact with THR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PRO 3.2 13.9 + - - +
16C TRP* 3.3 22.1 + - + -
18C LEU* 1.3 74.2 - - + +
20C GLY* 1.3 61.8 + - - +
22C LEU* 3.8 2.4 - - + +
23C SER* 2.8 30.5 + - - -
53C THR* 2.6 25.5 + - - +
35J THR* 4.0 14.6 - - + -
36J MET* 3.8 32.3 - - + +
39J CYS* 3.7 23.9 - - + -
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Residues in contact with GLY 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A MET* 4.4 9.6 - - - -
607A PGV 4.0 14.8 - - - +
16C TRP 2.8 18.9 + - - -
17C PRO 3.7 1.3 - - - -
19C THR* 1.3 75.7 + - - +
21C ALA* 1.3 57.8 + - - +
23C SER* 2.8 21.0 + - - -
24C ALA* 3.0 16.8 + - - +
53C THR* 3.7 13.2 - - - -
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A MET* 4.5 2.2 - - + +
103A TRP* 3.3 41.7 - - + +
104A LEU* 3.7 17.9 - - + +
107A PRO* 4.1 8.2 - - + +
17C PRO 2.9 13.2 + - - +
18C LEU* 3.2 8.0 + - + +
20C GLY* 1.3 72.3 - - - +
22C LEU* 1.3 69.5 + - + +
24C ALA* 3.1 6.8 + - - +
25C LEU* 3.1 18.4 + - - +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TRP* 6.5 0.2 - - + -
107A PRO* 5.2 10.1 - - + -
18C LEU* 2.8 40.9 + - + +
19C THR* 4.0 4.5 - - + +
21C ALA* 1.3 78.2 - - + +
23C SER* 1.3 62.3 + - - +
25C LEU* 3.0 24.4 + - + +
26C LEU* 3.1 18.3 + - - +
36J MET* 6.2 1.1 - - - -
39J CYS* 3.9 25.6 - - + +
40J LEU* 4.2 18.6 - - + -
43J THR* 3.7 32.9 + - + +
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C THR 2.8 17.6 + - - -
20C GLY* 2.8 22.9 + - - -
21C ALA 3.1 0.2 - - - -
22C LEU* 1.3 77.9 - - - +
24C ALA* 1.3 54.9 + - - +
26C LEU* 3.3 5.1 + - - +
27C MET* 3.1 35.0 + - - +
46C GLY* 4.1 1.2 - - - -
49C THR* 3.2 29.8 - - - -
50C ASN* 3.7 30.6 + - - -
39J CYS* 4.9 0.4 - - - -
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LEU* 3.7 23.1 - - + -
152A LEU* 3.8 16.4 - - + -
607A PGV 4.0 15.2 - - + +
20C GLY 3.0 13.4 + - - +
21C ALA 3.3 9.9 - - - +
23C SER* 1.3 75.2 + - - +
25C LEU* 1.3 60.3 + - - +
27C MET* 4.0 10.5 - - - +
28C THR* 2.7 32.8 + - - +
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PRO* 3.9 28.5 - - + +
110A LEU* 4.0 28.7 - - + -
111A LEU* 4.1 28.3 - - + -
152A LEU* 4.2 3.7 - - - +
21C ALA 3.1 6.3 + - - +
22C LEU* 3.0 17.7 + - + +
24C ALA* 1.3 75.7 - - - +
26C LEU* 1.3 59.5 + - + +
28C THR* 2.9 15.8 + - - -
29C SER* 2.9 25.2 + - - +
43J THR* 4.4 22.9 - - + +
46J SER* 4.1 18.6 - - - +
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Residues in contact with LEU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU 3.1 14.9 + - - +
23C SER* 3.8 2.9 - - - +
24C ALA 3.3 0.4 - - - -
25C LEU* 1.3 78.8 - - + +
27C MET* 1.3 59.3 - - - +
29C SER* 4.0 3.3 + - - -
30C GLY* 2.8 26.0 + - - -
42C LEU* 3.5 21.3 - - + +
45C ILE* 3.9 22.7 - - + -
46C GLY* 3.5 13.9 - - - +
49C THR* 3.9 19.7 - - - +
38J LEU 4.3 2.9 - - - +
39J CYS* 4.3 13.7 - - - +
42J GLY* 3.3 38.6 - - - +
43J THR* 3.6 10.3 - - - +
46J SER* 4.3 6.3 - - - +
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Residues in contact with MET 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PGV 4.3 38.4 - - + -
23C SER* 3.1 28.6 + - - +
24C ALA* 4.0 9.4 - - - +
25C LEU 3.4 0.2 - - - -
26C LEU* 1.3 76.3 - - - +
28C THR* 1.3 57.1 + - - +
30C GLY* 3.6 0.2 - - - -
31C LEU* 2.9 35.2 + - + +
43C LEU* 3.9 12.8 - - + +
46C GLY* 3.6 17.7 - - - -
47C LEU* 3.7 24.0 - - + +
50C ASN* 3.6 38.1 - - + +
307C DMU 5.5 4.5 - - + -
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Residues in contact with THR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 3.6 13.4 - - - +
148A PHE* 3.6 43.8 - - + +
151A HIS* 5.6 0.7 - - + -
152A LEU* 3.8 23.1 - - + +
607A PGV 4.4 13.9 - - + -
24C ALA 2.7 24.3 + - - +
25C LEU* 2.9 15.6 + - - -
27C MET* 1.3 73.0 - - - +
29C SER* 1.3 62.0 + - - -
31C LEU* 3.4 3.8 + - - -
32C THR* 3.0 26.8 + - - -
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Residues in contact with SER 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 4.2 18.6 - - - +
145A LEU* 5.2 2.5 - - - -
25C LEU* 2.9 29.4 + - - +
26C LEU* 4.0 1.7 + - - -
28C THR* 1.3 73.9 + - - +
30C GLY* 1.3 57.7 + - - +
32C THR* 3.2 9.9 + - - -
33C MET* 2.9 30.3 + - - +
42C LEU* 3.4 22.2 - - - +
46J SER* 3.5 14.9 - - - -
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Residues in contact with GLY 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU 2.8 22.9 + - - -
27C MET 3.6 1.1 - - - -
29C SER* 1.3 77.5 + - - +
31C LEU* 1.3 56.6 + - - +
33C MET* 3.2 4.6 + - - +
34C TRP* 2.8 27.0 + - - +
39C SER 4.0 3.1 - - - +
42C LEU* 3.5 19.9 - - - +
43C LEU* 3.6 15.6 - - - +
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A PHE* 3.8 26.9 - - + -
607A PGV 4.0 25.4 - - + -
27C MET* 2.9 23.3 + - + +
28C THR 3.8 4.7 - - - +
30C GLY* 1.3 70.2 - - - +
32C THR* 1.3 60.7 + - - +
34C TRP* 3.6 25.7 - - + +
35C PHE* 2.9 43.0 + - + -
43C LEU* 4.1 18.3 - - + +
302C PEK 4.2 29.8 - - + -
307C DMU 4.8 11.0 - - + -
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ALA* 3.9 25.8 - - + +
144A ASP* 4.9 2.0 - - + -
145A LEU* 3.6 31.8 + - + +
148A PHE* 3.3 21.4 - - - -
28C THR 3.0 14.9 + - - -
29C SER* 3.4 9.2 - - - -
30C GLY 3.2 0.2 - - - -
31C LEU* 1.3 73.1 - - - +
33C MET* 1.3 68.1 + - - +
35C PHE* 3.4 2.3 + - - -
36C HIS* 3.1 33.8 + - + +
37C PHE* 4.3 6.6 - - + -
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Residues in contact with MET 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C SER 2.9 14.9 + - - +
30C GLY* 3.2 12.5 + - - +
32C THR* 1.3 77.1 - - - +
34C TRP* 1.3 63.8 + - - +
37C PHE* 3.0 61.4 + - + -
39C SER* 3.3 28.9 + - - +
42C LEU* 4.7 12.6 - - + +
45J TYR* 6.0 1.3 - - + +
49J CYS* 3.7 48.9 - - + +
52J TRP* 4.6 11.7 - - + -
53J ALA* 5.9 0.4 - - - -
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Residues in contact with TRP 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLY 2.8 15.4 + - - +
31C LEU* 3.6 19.5 - - + +
32C THR 3.2 0.4 - - - -
33C MET* 1.3 80.0 - - - +
35C PHE* 1.3 90.1 + + - +
36C HIS 3.4 0.2 + - - -
38C ASN* 3.5 19.6 + - - -
39C SER 3.3 11.9 + - - +
40C MET* 3.5 40.5 - - + +
43C LEU* 4.5 9.2 - - + -
302C PEK 4.3 22.4 - - + -
307C DMU 4.2 33.0 - - + -
61G SER* 3.2 30.8 + - - -
62G TRP* 3.8 37.2 - + + +
69G PHE* 5.1 0.4 - + - -
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Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASP* 5.2 0.9 - - - -
148A PHE* 4.5 6.3 - + - -
210A LEU* 4.3 22.9 - - + -
214A ASN* 3.5 50.9 - - + +
215A LEU* 4.5 15.7 - - + -
31C LEU* 2.9 29.8 + - + +
32C THR* 3.4 2.0 + - - -
34C TRP* 1.3 105.4 - + - +
36C HIS* 1.3 68.3 + + - +
302C PEK 3.8 25.1 - - + -
58G LYS* 2.9 23.3 + - - -
61G SER* 3.1 20.3 + - - -
62G TRP* 5.9 0.2 - + - -
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Residues in contact with HIS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY* 3.5 32.0 + - - -
141A ALA* 3.7 20.7 - - + +
144A ASP* 2.7 36.0 + - + -
213A ARG* 4.3 1.6 + - - -
214A ASN* 3.9 13.6 + - - -
32C THR* 3.1 19.4 + - + +
35C PHE* 1.3 81.3 - + + +
37C PHE* 1.3 82.8 + - + +
38C ASN 3.4 5.0 + - - -
58G LYS* 4.2 17.5 - - - +
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Residues in contact with PHE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 5.8 2.9 - - + -
119A GLU* 5.2 11.9 - - + -
141A ALA* 4.5 17.9 - - + -
32C THR* 4.3 8.7 - - + -
33C MET* 3.0 51.7 + - + +
36C HIS* 1.3 95.0 - - + +
38C ASN* 1.3 67.9 + - - +
39C SER* 3.1 7.8 + - - -
52J TRP* 3.9 27.1 - + + -
53J ALA* 3.9 24.7 - - + -
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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