Contacts of the helix formed by residues 7 - 36 (chain D) in PDB entry 3ITX
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 7 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D PHE* 4.3 4.4 + - - -
5D ARG 4.1 2.0 + - - -
6D ILE* 1.3 73.1 - - - +
8D GLN* 1.3 66.6 + - - +
9D ASP* 3.0 22.7 - - - +
10D VAL* 2.9 26.2 + - + +
11D VAL* 3.2 10.4 + - - +
409D SER* 5.5 1.2 - - - -
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Residues in contact with GLN 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D PHE* 3.2 54.9 - - + +
6D ILE 3.2 2.6 + - - +
7D ALA* 1.3 71.2 - - - +
9D ASP* 1.3 57.4 + - - +
11D VAL* 3.2 10.0 + - - +
12D ALA* 2.9 30.2 + - - +
90D GLN* 5.2 1.1 - - - +
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Residues in contact with ASP 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ALA* 3.0 29.8 - - - +
8D GLN* 1.3 79.3 - - - +
10D VAL* 1.3 63.1 + - - +
12D ALA* 3.9 6.8 - - - +
13D ARG* 2.7 57.3 + - - +
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Residues in contact with VAL 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 4.6 3.4 - - + -
7D ALA* 2.9 20.2 + - + +
9D ASP* 1.3 89.5 - - - +
11D VAL* 1.3 66.2 + - - +
13D ARG* 3.7 13.3 - - - +
14D GLU* 3.0 32.5 + - + +
405D THR* 4.1 14.6 - - + +
408D ALA* 4.2 7.9 - - + +
409D SER* 4.1 34.1 - - - +
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Residues in contact with VAL 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 3.9 13.0 - - + -
7D ALA 3.2 13.0 + - - +
8D GLN* 3.5 10.3 - - - +
10D VAL* 1.3 77.6 - - - +
12D ALA* 1.3 62.7 + - - +
14D GLU* 3.4 1.0 + - - +
15D ASN* 3.0 31.8 + - - +
90D GLN* 3.8 22.4 - - - +
91D LEU* 4.3 6.1 - - + -
397D GLY 4.4 10.8 - - - +
398D GLY 3.8 24.9 - - - +
399D ALA* 4.7 3.8 - - + -
405D THR* 4.0 13.0 - - + -
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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
----------------------------------------------------------
8D GLN 2.9 17.2 + - - +
9D ASP* 3.9 7.0 - - - +
11D VAL* 1.3 76.4 - - - +
13D ARG* 1.3 56.0 + - - +
15D ASN* 3.3 6.1 + - - +
16D ASP* 2.8 45.4 + - - +
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Residues in contact with ARG 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ASP* 2.7 53.6 + - - +
10D VAL* 3.7 14.5 - - - +
12D ALA* 1.3 77.2 - - - +
14D GLU* 1.3 63.8 + - - +
16D ASP* 3.4 8.4 + - - +
17D ARG* 3.1 50.2 + - - +
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Residues in contact with GLU 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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10D VAL* 3.0 22.4 + - + +
11D VAL 4.0 1.6 - - - +
13D ARG* 1.3 82.4 + - - +
15D ASN* 1.3 66.5 + - - +
17D ARG* 2.9 35.4 + - - -
18D ARG* 2.8 64.4 + - - +
401D ASP 5.7 0.3 + - - -
404D ALA 5.0 0.3 - - - +
405D THR* 3.3 30.2 + - + +
408D ALA* 4.0 29.9 - - + +
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Residues in contact with ASN 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL* 3.0 25.3 + - - +
12D ALA* 3.7 5.9 - - - +
14D GLU* 1.3 76.5 - - - +
16D ASP* 1.3 59.7 + - - +
18D ARG 3.1 3.6 + - - -
19D ALA* 2.7 36.5 + - - +
394D ARG* 4.2 16.1 - - + +
398D GLY 3.1 18.8 - - - +
399D ALA* 3.4 9.3 - - - +
400D VAL* 2.8 46.9 - - + +
401D ASP 4.8 0.2 - - - +
405D THR* 4.7 1.0 + - - -
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Residues in contact with ASP 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ALA* 2.8 35.8 + - - +
13D ARG* 3.7 7.4 + - - +
15D ASN* 1.3 80.1 - - - +
17D ARG* 1.3 61.1 + - - +
18D ARG 3.2 0.7 + - - -
19D ALA* 3.4 19.6 + - - +
20D SER* 4.6 2.3 + - - -
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Residues in contact with ARG 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ARG* 3.1 34.2 + - - +
14D GLU* 2.9 43.0 + - - +
16D ASP* 1.3 77.4 - - - +
18D ARG* 1.3 73.8 + - + +
20D SER* 5.3 2.4 + - - -
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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
----------------------------------------------------------
14D GLU* 2.8 55.0 + - - +
15D ASN 3.1 3.9 + - - +
17D ARG* 1.3 94.4 - - + +
19D ALA* 1.3 64.5 + - - +
20D SER 3.3 3.5 + - - -
21D ALA* 3.5 9.9 + - + +
22D LEU* 3.1 23.4 + - - +
400D VAL* 4.0 20.9 - - + -
401D ASP* 3.6 29.7 + - - +
404D ALA* 3.3 26.9 - - - +
405D THR* 5.1 0.4 + - - -
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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
----------------------------------------------------------
15D ASN 2.7 16.2 + - - +
16D ASP* 3.4 16.8 + - - +
18D ARG* 1.3 77.3 - - - +
20D SER* 1.3 62.8 + - - +
22D LEU* 3.4 8.1 + - - +
23D LYS* 3.0 24.6 + - - +
394D ARG* 5.4 9.6 - - - +
400D VAL* 5.4 1.3 - - - -
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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
----------------------------------------------------------
16D ASP 4.6 2.3 + - - -
17D ARG 5.3 2.0 + - - -
18D ARG 3.3 0.8 - - - -
19D ALA* 1.3 78.2 - - - +
21D ALA* 1.3 63.2 + - - +
23D LYS* 3.2 11.4 + - - +
24D GLU* 3.1 27.4 + - - +
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 4.1 28.2 + - + +
18D ARG* 3.5 11.9 + - + +
19D ALA 3.4 0.2 - - - -
20D SER* 1.3 79.0 - - - +
22D LEU* 1.3 58.8 + - - +
24D GLU* 3.1 5.4 + - - +
25D ASP* 2.9 38.8 + - - +
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Residues in contact with LEU 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 17.5 + - - +
19D ALA* 3.7 6.1 - - - +
21D ALA* 1.3 76.1 - - - +
23D LYS* 1.3 55.4 + - - +
25D ASP* 3.3 5.7 + - + +
26D TYR* 2.7 41.5 + - + +
387D PRO* 3.6 33.9 - - + +
390D ALA* 3.8 11.9 - - + -
391D GLU* 3.5 35.0 - - + +
394D ARG* 4.2 8.3 - - - +
400D VAL* 3.9 32.5 - - + -
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Residues in contact with LYS 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 3.0 14.2 + - - +
20D SER* 3.2 13.2 + - - +
22D LEU* 1.3 75.2 - - - +
24D GLU* 1.3 79.1 + - - +
26D TYR* 3.9 4.4 - - - +
27D GLU* 2.9 70.5 + - + +
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Residues in contact with GLU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 3.7 32.2 + - - +
20D SER* 3.1 18.0 + - - +
21D ALA* 3.4 8.1 - - - +
23D LYS* 1.3 102.3 + - - +
25D ASP* 1.3 62.5 + - - +
27D GLU* 4.1 5.7 - - - +
28D ALA* 3.1 24.8 + - - +
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Residues in contact with ASP 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 2.9 27.8 + - - +
35A ARG* 2.9 26.2 + - - +
21D ALA* 2.9 25.2 + - - +
22D LEU* 3.9 6.4 + - + +
24D GLU* 1.3 74.1 - - - +
26D TYR* 1.3 60.5 + - - +
28D ALA* 3.4 5.4 + - - +
29D LEU* 3.0 30.8 + - - +
387D PRO* 3.7 24.6 - - + +
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Residues in contact with TYR 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 2.7 26.0 + - + +
23D LYS* 3.9 5.2 - - - +
25D ASP* 1.3 73.8 - - - +
27D GLU* 1.3 64.3 + - + +
29D LEU* 3.3 1.3 + - - -
30D GLY* 2.8 27.5 + - - -
40D ILE* 3.5 35.2 + - + +
41D GLU* 2.7 33.1 + - - -
44D THR* 2.8 28.3 + - - +
387D PRO* 3.6 27.5 - - + +
388D ILE* 4.1 5.8 - - - -
391D GLU* 3.7 27.1 - - + +
395D ARG* 3.9 9.2 + - - -
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Residues in contact with GLU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LYS* 2.9 58.6 + - + +
24D GLU* 4.2 6.6 - - - +
26D TYR* 1.3 81.8 - - + +
28D ALA* 1.3 58.5 + - - +
30D GLY* 3.7 2.4 - - - +
31D ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 4.0 26.5 - - + +
35A ARG* 6.3 0.4 - - - +
24D GLU 3.1 19.9 + - - +
25D ASP* 3.7 6.5 - - - +
26D TYR 3.2 0.2 - - - -
27D GLU* 1.3 78.3 - - - +
29D LEU* 1.3 57.2 + - - +
31D ALA* 3.2 7.5 + - - +
32D ASN* 3.0 27.6 + - - +
35D ARG* 4.7 2.1 + - - -
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ASP 3.0 18.1 + - - +
26D TYR* 3.8 3.4 - - - +
28D ALA* 1.3 73.8 - - - +
30D GLY* 1.3 62.1 + - - +
32D ASN* 3.2 10.9 + - + +
33D LEU* 2.8 48.3 + - + +
40D ILE* 4.1 6.3 - - + -
383D THR* 3.7 28.0 - - + -
384D ASP 3.6 21.8 - - - +
385D VAL* 4.2 2.2 - - - -
387D PRO* 4.2 14.4 - - + -
388D ILE* 3.8 33.2 - - + -
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Residues in contact with GLY 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D TYR 2.8 18.5 + - - -
27D GLU* 3.7 2.9 - - - -
29D LEU* 1.3 78.4 - - - +
31D ALA* 1.3 55.0 + - - +
33D LEU* 3.8 1.7 - - - +
34D ALA* 2.9 30.0 + - - +
38D VAL 4.7 0.7 - - - +
40D ILE* 3.7 29.4 + - - +
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLU 2.9 17.0 + - - +
28D ALA* 3.5 7.2 - - - +
30D GLY* 1.3 74.8 - - - +
32D ASN* 1.3 64.0 + - - +
34D ALA* 3.4 7.0 + - - +
35D ARG* 3.1 44.4 + - - +
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Residues in contact with ASN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASP* 3.0 31.5 + - - +
28D ALA 3.0 16.7 + - - +
29D LEU* 3.6 13.7 - - + +
31D ALA* 1.3 76.3 - - - +
33D LEU* 1.3 66.2 + - - +
35D ARG* 3.1 30.6 + - - +
36D ARG* 2.8 49.2 + - - +
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Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 2.8 35.4 + - + +
30D GLY* 3.8 4.0 - - - +
32D ASN* 1.3 74.4 - - - +
34D ALA* 1.3 60.8 + - - +
36D ARG* 2.8 47.8 + - - +
37D GLY 3.0 0.2 + - - -
38D VAL* 2.8 44.3 + - + +
40D ILE* 3.9 33.9 - - + +
43D VAL* 4.9 0.2 - - + -
355D LEU* 4.1 27.8 - - + -
388D ILE* 4.2 11.2 - - + -
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Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D GLY 2.9 17.7 + - - +
31D ALA* 3.6 8.3 - - - +
32D ASN 3.3 0.2 - - - -
33D LEU* 1.3 76.4 - - - +
35D ARG* 1.3 59.3 + - + +
37D GLY* 3.0 18.3 + - - -
38D VAL 3.3 11.2 + - - +
----------------------------------------------------------
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Residues in contact with ARG 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 6.2 0.2 - - - -
21A ALA* 4.5 24.0 - - + +
24A GLU* 3.6 37.6 + - - +
25A ASP* 2.8 30.7 + - - +
28D ALA 4.7 1.8 + - - -
31D ALA* 3.1 33.8 + - - +
32D ASN* 3.1 25.5 + - - +
34D ALA* 1.3 77.5 - - + +
36D ARG* 1.3 59.9 + - + +
37D GLY 3.3 1.6 + - - -
----------------------------------------------------------
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Residues in contact with ARG 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ASN* 2.8 42.4 + - - +
33D LEU* 2.8 23.6 + - - +
35D ARG* 1.3 80.5 - - + +
37D GLY* 1.3 59.9 + - - +
38D VAL* 3.3 12.2 + - + +
355D LEU* 4.4 12.1 + - - +
357D ASP* 5.7 1.0 - - - +
379D ARG* 3.2 22.5 + - - +
380D ALA* 4.2 5.1 - - - +
383D THR* 3.0 37.4 + - - +
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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