Contacts of the helix formed by residues 2 - 30 (chain D) in PDB entry 2B1F
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 VAL 2 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.6 18.8 - - + +
3D LYS* 1.3 70.3 + - + +
4D GLN* 3.3 14.6 + - - +
5D LEU* 3.2 20.3 + - + +
6D GLU* 2.7 60.5 + - - +
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Residues in contact with LYS 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D VAL* 1.3 83.0 - - + +
4D GLN* 1.3 78.0 + - - +
6D GLU* 3.5 15.7 + - - +
7D ASP* 2.9 29.3 + - - +
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Residues in contact with GLN 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ARG* 6.0 1.7 - - - +
26C LEU* 5.0 0.3 - - - +
29C LEU* 3.7 40.4 - - + +
2D VAL 4.0 13.5 + - - +
3D LYS* 1.3 95.0 + - - +
5D LEU* 1.3 59.8 + - + +
7D ASP* 3.4 8.5 + - - +
8D ALA* 3.0 27.4 + - - +
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Residues in contact with LEU 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.2 13.1 - - + +
29A LEU* 4.1 34.8 - - + +
30A VAL* 3.8 14.6 - - + +
5B LEU* 3.6 30.1 - - + -
26C LEU* 4.2 9.4 - - + -
29C LEU* 4.0 16.6 - - + -
2D VAL* 3.2 19.6 + - - +
4D GLN* 1.3 75.9 - - - +
6D GLU* 1.3 61.3 + - - +
8D ALA* 3.3 5.8 + - - +
9D VAL* 2.9 32.8 + - + +
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Residues in contact with GLU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 3.9 25.3 - - + +
2D VAL* 2.7 46.5 + - - +
3D LYS* 3.6 14.9 - - - +
4D GLN 3.3 0.2 - - - -
5D LEU* 1.3 76.3 - - - +
7D ASP* 1.3 62.6 + - - +
9D VAL* 3.3 6.5 + - - +
10D GLU* 3.0 35.7 + - - +
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Residues in contact with ASP 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ARG* 3.7 30.0 + - - +
3D LYS 2.9 18.1 + - - +
4D GLN* 3.5 9.2 - - - +
5D LEU 3.3 0.2 - - - -
6D GLU* 1.3 74.8 - - - +
8D ALA* 1.3 57.0 + - - +
10D GLU* 3.2 18.6 + - - +
11D GLU* 2.9 39.0 + - - +
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Residues in contact with ALA 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.1 8.5 - - + -
22C ALA* 4.1 10.3 - - + +
25C ARG* 6.0 3.4 - - + -
26C LEU* 3.6 33.7 - - + -
4D GLN 3.0 13.9 + - - +
5D LEU 3.5 9.0 - - - +
7D ASP* 1.3 76.5 + - - +
9D VAL* 1.3 63.6 + - - +
11D GLU* 3.3 7.4 + - - +
12D LEU* 2.9 29.8 + - - +
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Residues in contact with VAL 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 4.8 5.1 - - + +
26A LEU* 3.7 38.8 - - + +
27A LYS* 4.1 31.0 - - + +
30A VAL* 4.4 6.3 - - + -
5D LEU 2.9 19.8 + - - +
6D GLU* 3.3 9.4 + - - +
8D ALA* 1.3 75.0 - - - +
10D GLU* 1.3 60.3 + - + +
12D LEU* 3.1 7.8 + - - +
13D LEU* 2.9 40.7 + - + +
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Residues in contact with GLU 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLU* 3.0 21.5 + - - +
7D ASP* 3.5 24.1 + - - +
9D VAL* 1.3 77.0 - - + +
11D GLU* 1.3 63.3 + - + +
13D LEU* 3.2 14.2 + - + +
14D SER* 3.2 23.6 + - - -
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Residues in contact with GLU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C HIS* 2.9 48.6 + - - +
21C ASN* 3.2 33.1 + - + +
22C ALA* 4.0 9.9 - - + +
25C ARG* 4.7 8.4 + - - +
7D ASP* 2.9 31.2 + - - +
8D ALA* 3.3 8.7 + - - +
10D GLU* 1.3 75.9 - - - +
12D LEU* 1.3 59.2 + - - +
14D SER* 3.3 8.4 + - - -
15D ALA* 3.0 21.8 + - - +
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.7 19.6 - - + +
22A ALA* 4.7 0.4 - - + -
23A VAL* 3.4 30.2 - - + +
26A LEU* 3.5 32.1 - - + -
12B LEU* 3.7 28.7 - - + -
19C LEU* 4.3 14.6 - - - -
22C ALA* 3.5 22.7 - - + -
8D ALA 2.9 16.3 + - - +
9D VAL* 3.7 3.4 - - - +
11D GLU* 1.3 75.7 - - - +
13D LEU* 1.3 59.7 + - - +
15D ALA* 3.2 3.5 + - + +
16D ASN* 2.8 30.9 + - - +
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 4.2 14.6 - - + -
27A LYS* 4.2 24.5 - - - +
9D VAL* 2.9 30.4 + - + +
10D GLU* 3.2 14.8 + - + +
12D LEU* 1.3 72.1 - - - +
14D SER* 1.3 60.6 + - - +
16D ASN* 3.3 12.6 + - + +
17D TYR* 2.8 31.2 + - - +
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Residues in contact with SER 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C HIS* 3.6 30.7 + - - -
10D GLU 3.2 10.0 + - - -
11D GLU* 3.4 10.4 - - - -
13D LEU* 1.3 78.8 - - - +
15D ALA* 1.3 62.5 + - - +
17D TYR* 3.3 7.5 + - - +
18D HIS* 3.1 31.6 + - - -
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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
----------------------------------------------------------
19A LEU* 3.9 13.9 - - + -
15C ALA* 3.6 30.9 - - + +
18C HIS* 3.8 5.8 - - + +
19C LEU* 3.9 17.0 - - + +
11D GLU 3.0 13.8 + - - +
12D LEU* 3.5 11.9 - - - +
14D SER* 1.3 75.8 - - - +
16D ASN* 1.3 58.0 + - - +
18D HIS 3.3 1.6 + - - -
19D LEU* 3.0 28.9 + - - +
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Residues in contact with ASN 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 2.7 30.7 + - - -
19A LEU* 3.5 16.5 - - + +
20A GLU* 4.6 11.9 - - - +
23A VAL* 5.5 5.6 - - + +
12D LEU 2.8 21.1 + - - +
13D LEU* 3.7 15.9 - - + +
15D ALA* 1.3 69.7 - - - +
17D TYR* 1.3 64.5 + - - +
19D LEU* 3.5 1.1 + - - -
20D GLU* 2.9 47.7 + - - +
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Residues in contact with TYR 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU 2.8 18.2 + - - +
14D SER* 3.6 6.5 - - - +
15D ALA 3.2 0.2 - - - -
16D ASN* 1.3 78.6 - - - +
18D HIS* 1.3 98.9 + + - +
20D GLU* 3.3 4.5 + - - +
21D ASN* 2.9 55.3 + - - +
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Residues in contact with HIS 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 5.3 1.8 - - - -
11C GLU* 2.8 50.8 + - - +
14C SER* 3.7 30.9 - - - -
15C ALA 3.8 7.0 - - - +
18C HIS* 3.9 19.9 + + - -
14D SER* 3.1 22.9 + - - -
15D ALA 3.3 4.5 + - - +
17D TYR* 1.3 99.1 - + - +
19D LEU* 1.3 65.2 + - - +
21D ASN* 3.3 4.2 + - - +
22D ALA* 3.2 18.0 + - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.5 31.9 - - + +
15A ALA* 3.9 15.0 - - + +
16A ASN* 3.6 42.0 - - + +
19A LEU* 4.0 15.0 - - + -
15B ALA* 6.2 0.4 - - + -
19B LEU* 4.9 10.3 - - + -
12C LEU* 4.4 11.2 - - + -
15C ALA* 4.0 4.8 - - + +
19C LEU* 6.2 1.3 - - + -
15D ALA 3.0 17.4 + - - +
16D ASN 3.7 4.7 - - - +
18D HIS* 1.3 77.3 - - - +
20D GLU* 1.3 56.6 + - - +
22D ALA* 3.2 6.1 + - - +
23D VAL* 3.1 36.1 + - + +
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 3.0 23.0 + - - +
20A GLU* 4.1 6.8 - - - +
16D ASN* 2.9 47.3 + - - +
17D TYR* 3.9 4.2 - - - +
19D LEU* 1.3 73.0 - - + +
21D ASN* 1.3 60.7 + - - +
23D VAL* 3.7 8.4 - - + +
24D ALA* 2.9 32.3 + - - +
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Residues in contact with ASN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLU* 2.9 31.2 + - - +
17D TYR* 2.9 55.8 + - - +
18D HIS 3.4 9.9 - - - +
20D GLU* 1.3 75.4 - - - +
22D ALA* 1.3 62.9 + - - +
24D ALA* 3.5 3.7 + - - +
25D ARG* 3.1 50.0 + - - +
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Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.2 7.2 - - + -
8C ALA* 4.2 21.3 - - + +
11C GLU* 4.2 5.8 - - + +
12C LEU* 3.6 31.0 - - + -
18D HIS 3.2 6.6 + - - +
19D LEU 3.2 8.9 + - - +
21D ASN* 1.3 77.9 - - - +
23D VAL* 1.3 60.0 + - - +
25D ARG* 3.9 2.7 - - - +
26D LEU* 2.9 37.3 + - - +
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Residues in contact with VAL 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.8 6.3 - - + +
12A LEU* 3.7 33.0 - - + -
13A LEU* 3.9 29.2 - - + -
16A ASN* 5.6 1.8 - - + +
19D LEU* 3.1 24.7 + - + +
20D GLU* 3.7 10.8 - - + +
21D ASN 3.4 0.2 - - - -
22D ALA* 1.3 76.2 - - - +
24D ALA* 1.3 58.0 + - - +
26D LEU* 3.8 2.7 - - - +
27D LYS* 2.8 52.9 + - + +
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLU 2.9 18.3 + - - +
21D ASN* 3.9 4.5 - - - +
23D VAL* 1.3 79.2 - - - +
25D ARG* 1.3 64.0 + - + +
27D LYS* 3.7 7.6 + - - +
28D LYS* 3.3 40.7 + - - +
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Residues in contact with ARG 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLN* 4.9 5.3 - - - +
7C ASP* 4.6 16.2 + - - -
8C ALA* 6.2 2.7 - - + -
11C GLU* 4.1 7.5 + - - -
21D ASN* 3.1 49.6 + - - +
22D ALA* 4.2 2.5 - - - +
24D ALA* 1.3 80.5 - - + +
26D LEU* 1.3 64.0 + - + +
28D LYS* 3.2 28.7 + - + +
29D LEU* 3.2 18.9 + - - +
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Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.0 18.1 - - + +
8A ALA* 5.3 1.3 - - + -
9A VAL* 3.8 18.8 - - + -
12A LEU* 3.8 24.9 - - + -
26B LEU* 4.0 25.6 - - + -
4C GLN 4.5 4.5 - - - +
5C LEU* 4.1 17.3 - - + -
8C ALA* 3.7 23.6 - - + -
22D ALA 2.9 20.8 + - - +
23D VAL 4.0 0.7 - - - +
25D ARG* 1.3 71.9 - - + +
27D LYS* 1.3 61.2 + - - +
28D LYS 3.1 1.8 - - - -
29D LEU* 3.1 12.2 + - + +
30D VAL* 2.9 32.4 + - - +
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Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.8 28.4 - - + +
13A LEU* 4.4 15.2 - - - +
23D VAL* 2.8 34.2 + - + +
24D ALA* 3.8 7.9 - - - +
26D LEU* 1.3 75.6 - - - +
28D LYS* 1.3 62.6 + - + +
30D VAL* 3.4 24.5 + - + +
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Residues in contact with LYS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLN* 5.7 2.0 - - - +
24D ALA* 3.3 26.8 + - - +
25D ARG* 3.2 33.8 + - + +
26D LEU 3.1 0.6 - - - -
27D LYS* 1.3 77.9 - - + +
29D LEU* 1.3 63.3 + - - +
30D VAL 4.3 2.9 - - - -
----------------------------------------------------------
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 5.3 2.9 - - - -
5A LEU* 3.7 16.2 - - + +
1C LYS 4.2 11.0 - - - +
4C GLN* 3.3 48.6 + - + +
5C LEU* 3.6 32.1 - - + -
25D ARG 3.2 10.8 + - - +
26D LEU* 3.1 16.3 + - + +
28D LYS* 1.3 76.0 - - - +
30D VAL* 1.3 64.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 5.3 13.9 - - + +
5A LEU* 3.5 29.8 - - + +
6A GLU* 3.9 34.1 - - + +
9A VAL* 4.3 11.9 - - + -
26D LEU 2.9 21.4 + - - +
27D LYS* 3.6 18.8 - - + +
28D LYS 3.4 3.7 - - - -
29D LEU* 1.3 79.9 - - - +
----------------------------------------------------------
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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