Contacts of the helix formed by residues 8 - 34 (chain A) in PDB entry 3U5V
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 ASN 8 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A HIS* 1.3 82.2 - - - +
9A ALA* 1.3 64.4 + - - +
10A LEU* 3.3 15.0 + - - +
11A GLU* 2.8 48.1 + - - +
12A ARG* 3.1 11.2 + - - +
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASN* 1.3 72.2 - - - +
10A LEU* 1.3 62.3 + - - +
12A ARG* 3.2 29.6 + - - +
13A LYS* 2.9 25.7 + - - +
16A ARG* 5.2 0.9 + - - -
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASN* 3.2 16.2 + - - +
9A ALA* 1.3 77.5 - - - +
11A GLU* 1.3 61.7 + - + +
13A LYS* 3.2 21.7 + - + +
14A ARG* 2.9 53.9 + - + +
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A HIS 2.6 35.7 + - - +
8A ASN* 2.8 42.0 + - - +
10A LEU* 1.3 79.8 - - + +
12A ARG* 1.3 58.1 + - - +
14A ARG* 4.0 5.1 - - - +
15A ARG* 3.0 29.6 + - - +
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Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A HIS* 2.5 37.5 + - - +
8A ASN* 3.1 10.1 + - - +
9A ALA* 3.4 34.0 - - - +
11A GLU* 1.3 73.2 - - - +
13A LYS* 1.3 65.6 + - - +
15A ARG* 3.3 7.0 + - - +
16A ARG* 3.0 46.6 + - - +
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Residues in contact with LYS 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ALA 2.9 18.1 + - - +
10A LEU* 3.5 19.1 - - + +
12A ARG* 1.3 77.0 - - - +
14A ARG* 1.3 65.8 + - - +
16A ARG* 3.2 23.8 + - - +
17A ASP* 3.0 49.7 + - - +
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Residues in contact with ARG 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 2.9 41.6 + - + +
11A GLU* 4.0 5.8 - - - +
13A LYS* 1.3 80.9 - - + +
15A ARG* 1.3 57.7 + - - +
17A ASP* 3.7 14.0 + - - +
18A ILE* 2.9 51.4 + - + +
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Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU 3.0 19.5 + - - +
12A ARG* 3.5 8.5 - - - +
13A LYS 3.2 0.2 - - - -
14A ARG* 1.3 78.0 - - - +
16A ARG* 1.3 59.3 + - + +
18A ILE* 3.4 18.5 + - - +
19A ASN* 3.0 49.4 + - - +
41A LYS* 2.7 20.9 - - - +
701A NO3 2.6 46.2 + - - -
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ALA 5.2 0.6 + - - -
12A ARG* 3.0 40.7 + - - +
13A LYS* 3.2 27.1 + - - +
15A ARG* 1.3 77.5 - - + +
17A ASP* 1.3 61.7 + - - +
19A ASN* 3.4 7.1 + - - +
20A GLU* 3.0 31.6 + - - +
23A ARG* 5.1 2.2 + - - +
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 3.0 39.9 + - - +
14A ARG* 3.3 15.7 + - - +
16A ARG* 1.3 79.4 - - - +
18A ILE* 1.3 58.4 + - + +
20A GLU* 3.4 13.3 + - - +
21A ALA* 3.0 28.8 + - - +
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Residues in contact with ILE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 2.9 39.4 + - + +
15A ARG* 3.7 36.6 - - - +
17A ASP* 1.3 75.7 - - + +
19A ASN* 1.3 61.0 + - - +
21A ALA* 3.2 7.2 + - - +
22A PHE* 2.9 46.1 + - + -
701A NO3 3.8 10.8 - - - +
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Residues in contact with ASN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ARG* 3.0 42.9 + - - +
16A ARG* 3.8 6.5 - - - +
18A ILE* 1.3 75.5 - - - +
20A GLU* 1.3 61.9 + - - +
22A PHE* 3.2 7.8 + - - +
23A ARG* 3.0 47.7 + - - +
41A LYS* 3.0 34.3 + - - +
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ARG 3.0 18.5 + - - +
17A ASP* 3.6 14.8 - - - +
19A ASN* 1.3 78.0 - - - +
21A ALA* 1.3 60.3 + - - +
23A ARG* 3.2 24.8 + - + +
24A GLU* 3.0 43.2 + - + +
27A ARG* 4.9 1.5 + - - +
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASP 3.0 16.4 + - - +
18A ILE* 3.2 7.4 + - - +
20A GLU* 1.3 72.9 - - - +
22A PHE* 1.3 64.6 + - - +
24A GLU* 3.4 11.7 + - - +
25A LEU* 3.0 26.0 + - - +
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Residues in contact with PHE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 2.9 33.8 + - + -
19A ASN* 3.3 11.2 - - - +
21A ALA* 1.3 77.4 - - - +
23A ARG* 1.3 50.3 + - + +
25A LEU* 3.3 7.0 + - + +
26A GLY* 2.8 34.0 + - - -
41A LYS* 3.5 56.8 - - + -
44A ILE* 3.7 29.8 - - + +
45A LEU* 3.8 31.2 - - + -
701A NO3 3.4 27.1 - - - -
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Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ARG* 5.1 2.2 + - - +
19A ASN* 3.0 39.1 + - - +
20A GLU* 3.2 35.4 + - - +
22A PHE* 1.3 75.9 - - + +
24A GLU* 1.3 57.7 + - - +
26A GLY* 3.3 1.4 + - - -
27A ARG* 3.0 58.6 + - + +
44A ILE* 5.4 2.0 - - - -
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU* 3.0 41.5 + - + +
21A ALA* 3.7 8.6 - - - +
23A ARG* 1.3 76.8 - - - +
25A LEU* 1.3 61.4 + - - +
27A ARG* 3.5 25.9 + - - +
28A MET* 3.2 27.6 + - + +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA 3.0 17.0 + - - +
22A PHE* 3.8 6.7 - - + +
24A GLU* 1.3 76.7 - - - +
26A GLY* 1.3 56.4 + - - +
28A MET* 3.2 24.4 + - + +
29A CYS* 2.9 41.4 + - - -
44A ILE* 3.9 17.9 - - + +
45A LEU* 5.1 11.4 - - + -
48A ALA* 3.9 23.1 - - + -
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Residues in contact with GLY 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE 2.8 21.2 + - - -
23A ARG* 3.7 2.0 - - - -
25A LEU* 1.3 73.3 - - - +
27A ARG* 1.3 55.4 + - - +
29A CYS* 3.3 0.9 + - - -
30A GLN* 3.0 26.0 + - - +
39A GLN* 3.0 30.7 + - - -
44A ILE* 3.9 17.9 - - - +
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Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU* 4.9 1.6 + - - +
23A ARG* 3.0 41.3 + - - +
24A GLU* 3.6 35.3 + - - +
25A LEU 3.4 0.2 - - - -
26A GLY* 1.3 74.8 - - - +
28A MET* 1.3 61.0 + - - +
30A GLN* 3.4 7.9 + - - +
31A MET* 3.1 35.9 + - + +
39A GLN* 5.2 0.2 - - - -
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Residues in contact with MET 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 3.2 18.9 + - + +
25A LEU* 3.4 26.9 - - + +
26A GLY 3.2 0.2 - - - -
27A ARG* 1.3 78.0 - - - +
29A CYS* 1.3 63.2 + - - +
31A MET* 3.2 17.6 + - + +
32A HIS* 3.1 46.4 + - + +
51A VAL* 5.9 3.4 - - + -
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Residues in contact with CYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 2.9 28.6 + - - +
26A GLY* 3.7 4.9 - - - +
28A MET* 1.3 77.3 - - - +
30A GLN* 1.3 58.2 + - - +
32A HIS* 3.2 0.5 + - - -
33A LEU* 2.9 35.8 + - - +
39A GLN* 4.3 0.4 - - - +
44A ILE* 4.1 4.5 - - - -
47A GLN* 3.8 26.0 - - + +
48A ALA* 3.5 41.1 - - - -
51A VAL* 4.1 14.8 - - + -
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Residues in contact with GLN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY 3.0 17.1 + - - +
27A ARG* 3.6 8.5 - - - +
29A CYS* 1.3 78.3 - - - +
31A MET* 1.3 56.8 + - + +
33A LEU* 5.6 0.4 - - - +
34A LYS* 2.7 39.8 + - - +
35A SER* 3.5 16.5 + - - +
36A ASP* 3.1 39.7 + - - +
37A LYS 4.5 4.9 + - - -
39A GLN* 4.2 19.4 - - - +
47A GLN* 4.6 2.4 - - - +
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Residues in contact with MET 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG* 3.1 26.1 + - + +
28A MET* 3.2 19.0 + - + +
30A GLN* 1.3 77.9 - - + +
32A HIS* 1.3 63.7 + - + +
34A LYS* 2.8 33.5 + - - +
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Residues in contact with HIS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A MET* 3.1 45.6 + - + +
29A CYS 3.2 3.8 + - - +
31A MET* 1.3 84.5 - - + +
33A LEU* 1.3 64.0 + - + +
34A LYS* 4.7 1.1 - - - +
51A VAL* 3.8 29.3 - - + +
55A LEU* 4.1 29.2 - - + +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A CYS 2.9 17.4 + - - +
30A GLN* 5.2 0.7 - - - -
32A HIS* 1.3 80.0 - - + +
34A LYS* 1.3 74.6 + - - +
35A SER* 3.3 13.8 + - - +
47A GLN* 3.7 45.8 - - + +
50A GLN* 4.2 22.0 - - + -
51A VAL* 3.8 22.9 - - + +
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLN* 2.7 35.6 + - - +
31A MET* 2.8 37.0 + - - +
32A HIS 4.7 1.1 - - - +
33A LEU* 1.3 76.5 - - - +
35A SER* 1.3 62.2 + - - +
36A ASP* 3.4 4.6 + - - +
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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