Contacts of the helix formed by residues 10 - 32 (chain D) in PDB entry 3J41
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 TRP 10 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PHE* 1.3 100.3 - + + +
11D ARG* 1.3 65.2 + - + +
12D ALA 3.3 0.2 - - - -
13D ILE* 3.4 34.7 - - + +
14D CYS* 2.9 34.4 + - - -
88D CYS* 5.5 5.2 - - - -
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Residues in contact with ARG 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C LEU* 2.6 51.8 + - + +
223C LEU* 2.7 48.1 + - - +
224C PHE 2.9 22.0 + - - -
225C PRO* 3.3 35.0 - - + +
226C ARG* 5.6 4.8 - - - +
9D PHE 3.3 4.6 - - - +
10D TRP* 1.3 79.7 - - + +
12D ALA* 1.3 57.8 + - - +
14D CYS* 3.3 7.7 + - - +
15D ALA* 2.9 26.2 + - - +
62D ILE* 4.1 10.7 - - + +
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Residues in contact with ALA 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PHE* 3.7 14.4 - - - +
10D TRP 3.3 0.2 - - - -
11D ARG* 1.3 78.7 - - - +
13D ILE* 1.3 59.0 + - - +
15D ALA* 3.1 5.1 + - - +
16D GLU* 2.9 34.2 + - - +
62D ILE* 3.5 23.0 - - - +
63D SER* 3.5 16.1 - - - -
85D ARG* 4.5 10.8 - - - +
89D TYR* 3.6 14.4 - - + +
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Residues in contact with ILE 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PHE* 3.0 48.6 + - + +
10D TRP* 3.4 35.4 - - + +
11D ARG 3.3 0.2 - - - -
12D ALA* 1.3 76.6 - - - +
14D CYS* 1.3 61.6 + - - +
16D GLU* 3.5 4.8 + - - -
17D PHE* 3.0 26.4 + - + +
88D CYS* 3.8 23.3 - - + +
89D TYR* 4.6 11.4 - - + -
92D ALA* 3.5 19.4 - - + +
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Residues in contact with CYS 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C LEU* 4.4 16.2 - - + -
10D TRP* 2.9 28.7 + - - -
11D ARG* 3.5 9.9 - - - +
12D ALA 3.2 0.2 - - - -
13D ILE* 1.3 77.1 - - - +
15D ALA* 1.3 60.6 + - - +
17D PHE* 3.2 6.3 + - - +
18D PHE* 2.8 53.3 + - + -
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Residues in contact with ALA 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C LEU* 5.9 2.7 - - + -
11D ARG 2.9 13.9 + - - +
12D ALA* 3.1 13.4 + - - +
14D CYS* 1.3 77.2 - - - +
16D GLU* 1.3 57.2 + - - +
17D PHE 3.2 0.2 + - - -
18D PHE* 3.9 3.2 - - - +
19D ALA* 2.8 35.6 + - - +
59D VAL* 3.8 27.2 - - + +
62D ILE* 4.2 8.7 - - + -
63D SER* 3.6 15.3 - - - +
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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
----------------------------------------------------------
12D ALA 2.9 19.3 + - - +
13D ILE* 3.7 5.6 - - - +
14D CYS 3.3 0.2 - - - -
15D ALA* 1.3 76.4 - - - +
17D PHE* 1.3 60.2 + - - +
19D ALA* 4.3 3.1 - - - +
20D SER* 2.5 33.1 + - - -
59D VAL* 5.1 0.2 - - - +
63D SER* 2.6 24.4 + - - +
65D ALA* 3.3 3.6 + - - -
66D HIS 2.9 20.3 + - - -
67D VAL* 2.6 28.9 + - - -
89D TYR* 3.7 31.0 - - + +
92D ALA* 4.2 12.9 - - + +
93D GLN* 3.1 14.8 - - + +
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Residues in contact with PHE 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ILE* 3.0 18.6 + - + +
14D CYS* 3.5 7.2 - - - +
15D ALA 3.1 0.2 - - - -
16D GLU* 1.3 78.7 - - - +
18D PHE* 1.3 94.3 + + - +
21D LEU* 3.1 29.8 + - + +
92D ALA* 3.5 28.0 - - + +
95D LEU* 3.8 17.5 - - + -
96D GLY* 3.5 28.8 - - - -
99D ALA* 4.4 14.4 - - + -
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Residues in contact with PHE 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LEU* 5.9 1.6 - - + -
218C LEU* 3.5 39.9 - - + -
222C LEU* 4.8 4.7 - - + -
14D CYS* 2.8 45.6 + - + +
15D ALA* 4.1 3.1 - - - +
17D PHE* 1.3 96.7 - + - +
19D ALA* 1.3 58.5 + - - +
21D LEU* 3.2 14.8 + - + +
22D PHE* 2.9 54.8 + + + -
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Residues in contact with ALA 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ALA 2.8 22.6 + - - +
18D PHE* 1.3 73.1 - - - +
20D SER* 1.3 53.1 + - - +
22D PHE* 4.4 0.7 - - - -
23D TYR* 2.8 35.5 + - - +
55D LEU* 3.2 24.9 - - + +
59D VAL* 4.0 19.4 - - + +
67D VAL* 3.2 26.7 - - + -
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Residues in contact with SER 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D GLU 2.5 24.4 + - - -
17D PHE 3.7 3.6 - - - -
19D ALA* 1.3 73.9 - - - +
21D LEU* 1.3 60.5 + - - +
24D VAL* 3.0 37.7 + - - +
67D VAL* 3.4 22.5 - - - +
93D GLN* 3.3 40.9 - - - +
96D GLY* 3.9 2.0 - - - -
97D ALA* 3.9 4.3 - - - -
186D ALA* 5.8 1.3 - - - -
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C PHE* 3.6 32.8 - - + -
17D PHE* 3.1 29.0 + - + +
18D PHE* 3.5 19.5 - - + +
20D SER* 1.3 77.9 - - - +
22D PHE* 1.3 62.1 + - + +
25D PHE* 2.7 40.0 + - + +
96D GLY 3.0 16.3 + - - +
99D ALA* 4.0 15.9 - - + -
100D GLY* 3.5 25.0 - - - +
103D VAL* 4.9 6.7 - - + -
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Residues in contact with PHE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C PHE* 4.0 24.5 - + - -
139C LEU* 3.7 33.4 - - + -
140C GLN* 4.9 7.0 - - + -
143C LEU* 3.9 25.6 - - + -
218C LEU* 4.1 8.3 - - + -
18D PHE* 2.9 42.9 + + + +
21D LEU* 1.3 84.0 - - + +
23D TYR* 1.3 59.3 + - - +
25D PHE* 4.2 1.3 - - - -
26D PHE* 2.8 61.1 + + + +
51D ALA* 5.8 0.2 - - - -
55D LEU* 3.8 28.3 - - + -
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Residues in contact with TYR 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ALA 2.8 23.9 + - - +
20D SER 3.7 1.8 - - - +
22D PHE* 1.3 72.6 - - - +
24D VAL* 1.3 69.5 + - + +
26D PHE* 4.4 0.3 - - - +
27D GLY* 2.9 27.9 + - - -
48D PHE* 4.0 17.4 - + - -
51D ALA* 4.6 8.1 - - + +
52D LEU* 4.1 23.3 - - + +
55D LEU* 3.5 18.1 - - + +
67D VAL* 3.6 21.8 - - + -
68D ASN* 5.3 1.0 + - - -
141D PHE* 5.7 0.7 - - - -
168D LEU* 3.2 43.3 - - + +
172D HIS* 5.1 0.5 - - - -
182D GLY 5.1 2.1 + - - -
184D ASN* 3.6 31.8 + - - +
187D ARG* 3.9 19.1 - - + +
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D SER* 3.0 19.3 + - - +
21D LEU 4.1 0.9 - - - +
23D TYR* 1.3 86.1 - - + +
25D PHE* 1.3 62.6 + - - +
27D GLY* 5.0 0.2 - - - -
28D LEU* 2.8 70.7 + - + +
48D PHE* 5.6 0.4 - - - -
97D ALA* 3.4 41.7 - - + +
101D ALA 4.0 3.6 - - - +
186D ALA* 5.7 0.4 - - + -
187D ARG* 4.2 14.8 - - + +
190D ALA* 4.0 8.5 - - + -
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Residues in contact with PHE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C VAL* 5.1 9.0 - - + -
136C PHE* 3.9 33.2 - + + -
174C PHE* 3.4 39.0 - + - -
21D LEU* 2.7 27.5 + - + +
22D PHE* 3.6 4.5 - - - +
24D VAL* 1.3 73.9 - - - +
26D PHE* 1.3 78.2 + + - +
29D GLY* 3.1 24.6 + - - -
100D GLY* 3.4 26.6 - - - +
103D VAL* 3.9 21.1 - - + -
104D LEU* 3.5 33.7 - - + +
107D VAL* 5.2 4.9 - - + -
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Residues in contact with PHE 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C PHE* 3.4 18.8 - - + -
137C LEU* 3.6 25.8 - - + -
140C GLN* 3.3 39.5 - - + -
170C LEU* 4.0 34.0 - - + +
171C GLY* 4.9 1.1 - - - -
174C PHE* 3.8 25.7 - + + +
22D PHE* 2.8 48.5 + + + +
23D TYR 4.4 0.9 - - - +
25D PHE* 1.3 89.2 - + - +
27D GLY* 1.3 64.6 + - - +
30D ALA* 3.0 26.9 + - - +
47D ALA* 4.8 1.4 - - - +
51D ALA* 4.6 4.5 - - + -
55D LEU* 6.2 0.2 - - + -
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Residues in contact with GLY 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D TYR 2.9 20.1 + - - -
26D PHE* 1.3 78.2 - - - +
28D LEU* 1.3 60.1 + - - +
30D ALA* 3.4 4.3 + - - +
31D SER* 2.8 26.7 + - - -
44D VAL* 5.1 0.2 - - - +
47D ALA* 5.2 1.1 - - - -
48D PHE* 3.4 38.9 - - - -
51D ALA* 5.1 1.2 - - - +
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL* 2.8 46.6 + - + +
27D GLY* 1.3 73.3 - - - -
29D GLY* 1.3 59.2 + - - +
31D SER* 2.8 18.7 + - - -
32D LEU* 3.0 19.2 + - - +
48D PHE* 4.4 0.7 - - + -
101D ALA* 3.9 18.8 - - + -
104D LEU* 4.0 13.2 - - + -
116D LEU* 3.3 21.5 - - + +
117D ALA* 4.1 4.7 - - + -
187D ARG* 3.5 45.8 - - + +
191D PRO* 3.8 17.7 - - + -
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Residues in contact with GLY 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C PHE* 3.5 24.0 - - - +
177C TYR* 5.5 4.5 - - - -
178C TYR* 4.3 6.1 + - - -
25D PHE 3.1 21.0 + - - -
27D GLY 3.3 0.2 - - - -
28D LEU* 1.3 78.4 - - - +
30D ALA* 1.3 59.8 + - - +
31D SER 3.4 0.7 + - - -
32D LEU* 3.5 21.1 + - - +
104D LEU* 3.8 13.0 - - - +
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C LEU* 5.8 0.2 - - + -
173C LEU* 4.0 21.7 - - + +
174C PHE* 3.8 7.8 - - + +
177C TYR* 5.2 5.1 - - - -
26D PHE 3.0 18.8 + - - +
27D GLY 4.0 1.8 - - - +
28D LEU 3.2 0.2 - - - -
29D GLY* 1.3 75.1 - - - +
31D SER* 1.3 58.0 + - - +
32D LEU 3.5 0.9 - - - -
33D ARG* 3.0 20.7 + - - -
43D GLN* 4.9 6.7 - - + +
44D VAL* 3.6 8.0 - - + +
47D ALA* 3.6 27.6 - - + -
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Residues in contact with SER 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLY 2.8 17.2 + - - -
28D LEU 2.8 10.6 + - - -
30D ALA* 1.3 78.9 - - - +
32D LEU* 1.3 65.9 + - - +
33D ARG* 3.3 5.5 + - - +
40D HIS* 3.8 15.7 - - - -
44D VAL* 3.2 33.1 - - - +
48D PHE* 3.4 6.4 - - - -
117D ALA* 3.5 21.9 - - - +
176D MET* 5.8 0.9 - - - -
187D ARG* 5.0 1.4 + - - -
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C TYR* 5.2 5.4 - - - -
178C TYR* 3.6 23.8 - - - +
28D LEU 3.0 23.6 - - - +
29D GLY* 3.7 17.1 - - - +
30D ALA 3.5 1.6 - - - -
31D SER* 1.3 77.2 - - - +
33D ARG* 1.3 79.2 + - - +
104D LEU* 4.1 13.2 - - + -
108D THR* 3.6 17.9 - - + +
112D VAL* 3.4 30.8 - - + +
113D ARG* 4.3 5.6 - - - +
116D LEU* 4.3 10.1 - - + -
117D ALA* 4.2 20.2 - - - +
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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
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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) + - + + + + + -
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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