Contacts of the helix formed by residues 13 - 40 (chain A) in PDB entry 3DXR
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 GLN 13 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 1.3 73.6 - - - +
14A LYS* 1.3 65.8 + - - +
15A VAL 3.1 1.1 - - - -
16A VAL* 3.1 15.1 + - - +
17A GLU* 3.1 21.0 + - - +
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Residues in contact with LYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 4.5 5.8 - - + -
13A GLN* 1.3 79.5 - - - +
15A VAL* 1.3 63.3 + - + +
17A GLU* 3.4 7.8 + - - +
18A GLN* 3.1 22.3 + - - +
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.2 43.7 - - + +
14A LYS* 1.3 80.0 - - + +
16A VAL* 1.3 67.5 + - + +
18A GLN* 3.1 6.4 + - - +
19A LYS* 2.5 40.0 + - + +
19B ILE* 6.4 0.2 - - + -
22B ALA* 5.1 5.4 - - + -
23B GLU* 5.4 14.8 - - + +
26B LEU* 5.0 8.7 - - + -
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE 4.0 16.6 - - - +
13A GLN* 3.1 13.6 + - - +
15A VAL* 1.3 83.8 - - + +
17A GLU* 1.3 54.0 + - - +
19A LYS* 3.5 6.8 - - + +
20A GLN* 2.6 41.2 + - + +
26B LEU* 3.9 25.6 - - + -
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN 3.1 8.9 + - - +
14A LYS* 3.7 10.8 - - - +
15A VAL 3.3 0.2 - - - -
16A VAL* 1.3 80.3 - - - +
18A GLN* 1.3 58.5 + - - +
20A GLN* 3.6 7.1 - - - +
21A MET* 3.1 24.3 + - - +
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS 3.1 14.4 + - - +
15A VAL* 3.4 9.9 - - - +
17A GLU* 1.3 76.1 - - - +
19A LYS* 1.3 59.7 + - - +
21A MET* 2.9 9.6 + - - +
22A LYS* 2.8 29.1 + - - +
25A MET* 5.4 0.2 - - - +
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Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 2.5 24.0 + - + +
16A VAL* 3.6 7.2 - - + +
18A GLN* 1.3 73.2 - - - +
20A GLN* 1.3 58.1 + - - +
22A LYS* 3.4 8.6 + - - +
23A ASP* 2.8 29.3 + - - +
26B LEU* 5.7 10.5 - - + -
30B THR* 5.7 6.4 - - - +
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Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 2.6 26.6 + - + +
17A GLU* 3.6 8.7 - - - +
19A LYS* 1.3 70.6 - - - +
21A MET* 1.3 61.7 + - - +
23A ASP* 3.3 8.2 + - - +
24A PHE* 3.0 27.9 + - - +
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Residues in contact with MET 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU 3.1 11.6 + - - +
18A GLN* 2.9 11.4 + - - +
20A GLN* 1.3 80.3 - - - +
22A LYS* 1.3 60.8 + - - +
24A PHE* 3.3 6.9 + - - +
25A MET* 3.0 41.8 + - + +
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Residues in contact with LYS 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 GLN 2.8 15.0 + - - +
19A LYS* 3.6 9.0 - - - +
21A MET* 1.3 75.6 - - - +
23A ASP* 1.3 59.4 + - - +
25A MET* 3.3 17.3 + - + +
26A ARG* 3.0 25.1 + - - +
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS 2.8 18.4 + - - +
20A GLN* 3.4 10.1 - - - +
21A MET 3.2 0.2 - - - -
22A LYS* 1.3 76.5 - - - +
24A PHE* 1.3 57.7 + - - +
26A ARG* 2.8 28.3 + - - +
27A LEU* 3.2 7.6 + - - +
30B THR* 5.1 16.2 - - + +
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Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN 3.0 13.0 + - - +
21A MET* 3.7 10.1 - - - +
23A ASP* 1.3 71.5 - - - +
25A MET* 1.3 68.4 + - + +
26A ARG 2.9 5.2 + - - -
27A LEU* 3.4 16.2 + - + +
28A TYR* 3.3 29.8 + + + +
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Residues in contact with MET 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN 5.4 0.2 - - - +
21A MET* 3.0 36.4 + - + +
22A LYS* 3.6 17.0 - - + +
24A PHE* 1.3 81.6 - - + +
26A ARG* 1.3 62.4 + - - +
28A TYR* 4.0 9.9 - - + +
29A SER* 3.2 22.3 + - - -
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS 3.0 12.4 + - - +
23A ASP* 2.8 19.3 + - - +
24A PHE 2.9 0.8 - - - -
25A MET* 1.3 76.8 - - - +
27A LEU* 1.3 66.1 + - - +
29A SER* 3.0 6.7 + - - -
30A ASN* 2.8 37.5 + - - +
30B THR* 6.4 0.9 - - + -
34B ASN* 5.2 11.2 - - - +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP 3.2 6.6 + - - +
24A PHE* 3.4 18.6 + - + +
26A ARG* 1.3 76.4 - - - +
28A TYR* 1.3 58.0 + - - +
30A ASN* 2.9 9.8 + - + +
31A LEU* 2.6 39.9 + - + +
63A PHE* 3.6 31.6 - - + -
64A LEU* 3.7 27.6 - - + -
67A SER* 4.2 17.3 - - - +
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Residues in contact with TYR 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 PHE* 3.3 25.8 + + + +
25A MET* 4.0 9.9 - - + +
27A LEU* 1.3 79.9 - - - +
29A SER* 1.3 64.4 + - - +
31A LEU* 3.3 11.2 + - + +
32A VAL* 2.8 54.7 + - + +
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MET 3.2 18.4 + - - -
26A ARG* 3.0 6.3 + - - -
28A TYR* 1.3 88.5 - - - +
30A ASN* 1.3 59.7 + - - +
32A VAL* 3.2 7.3 + - - +
33A GLU* 2.9 29.9 + - - +
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Residues in contact with ASN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 2.8 38.8 + - - +
27A LEU* 3.5 8.6 - - + +
29A SER* 1.3 75.2 - - - +
31A LEU* 1.3 58.1 + - - +
33A GLU* 3.8 13.0 - - - +
34A ARG* 2.8 30.4 + - - +
63A PHE* 4.6 13.6 - - + -
34B ASN* 5.1 9.9 + - - +
38B ASN* 5.5 13.4 - - - +
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Residues in contact with LEU 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 LEU* 2.6 25.2 + - + +
28A TYR* 3.4 9.2 - - + +
30A ASN* 1.3 70.8 - - - +
32A VAL* 1.3 68.7 + - + +
34A ARG* 3.2 1.6 + - + +
35A CYS* 3.0 40.8 + - - -
60A SER* 4.0 17.5 - - - +
63A PHE* 3.2 42.3 - - + -
64A LEU* 4.1 30.1 - - + -
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 2.8 59.5 + - + +
29A SER* 3.4 7.4 - - - +
31A LEU* 1.3 78.8 - - + +
33A GLU* 1.3 58.8 + - - +
35A CYS* 3.8 2.4 - - - +
36A PHE* 2.9 36.5 + - + +
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Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER 2.9 15.7 + - - +
30A ASN* 3.8 13.4 - - - +
32A VAL* 1.3 74.9 - - - +
34A ARG* 1.3 61.6 + - - +
36A PHE* 4.0 5.0 - - - +
37A THR* 2.7 41.0 + - - +
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Residues in contact with ARG 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 ASN 2.8 20.3 + - - +
31A LEU* 3.5 7.9 - - - +
33A GLU* 1.3 77.7 - - - +
35A CYS* 1.3 57.7 + - - +
37A THR* 3.5 25.3 + - - +
38A ASP* 3.1 56.5 + - - +
59A CYS* 4.0 15.0 - - - -
63A PHE* 4.3 24.5 - - + -
41B TYR* 3.3 41.4 + - + +
42B LYS* 6.3 0.2 - - - +
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Residues in contact with CYS 35 (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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31A LEU* 3.0 32.7 + - - +
32A VAL* 4.1 2.9 - - - +
34A ARG* 1.3 75.5 - - - +
36A PHE* 1.3 62.8 + - - +
38A ASP* 3.9 0.9 - - - +
39A CYS* 3.0 34.6 + - - +
56A ILE* 4.2 22.2 - - + +
59A CYS* 2.0 52.7 - - + -
60A SER* 3.6 16.6 - - - -
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Residues in contact with PHE 36 (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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32A VAL* 2.9 24.6 + - + +
33A GLU* 4.0 5.6 - - - +
35A CYS* 1.3 77.8 - - - +
37A THR* 1.3 68.7 + - - +
40A VAL* 3.2 56.2 + - + +
43A PHE* 4.0 28.5 - + - -
48A LEU* 5.9 1.3 - - + -
56A ILE* 6.1 0.2 - - - -
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Residues in contact with THR 37 (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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33A GLU* 2.7 29.7 + - - +
34A ARG* 3.5 24.2 - - - +
36A PHE* 1.3 86.8 - - - +
38A ASP* 1.3 61.1 + - - +
40A VAL 4.9 3.8 - - - +
41A ASN* 6.1 0.9 - - - +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG* 3.1 53.1 + - - +
35A CYS* 4.5 2.5 - - - +
37A THR* 1.3 81.2 - - - +
39A CYS* 1.3 64.6 + - - +
41A ASN* 6.2 0.6 - - - +
55A CYS* 4.1 5.4 - - - -
59A CYS* 4.8 6.2 - - + -
41B TYR* 3.7 12.1 + - - -
47B THR* 4.4 16.2 + - - +
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Residues in contact with CYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS 3.0 20.8 + - - +
38A ASP* 1.3 82.4 - - - +
40A VAL* 1.3 60.6 + - + +
41A ASN* 3.4 12.1 + - - +
52A GLU* 3.6 17.3 - - - +
55A CYS* 2.0 66.3 - - + +
56A ILE* 3.4 17.9 - - + -
59A CYS* 4.2 9.6 - - - -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.2 58.1 + - + +
37A THR 4.9 3.3 - - - +
39A CYS* 1.3 77.6 - - + +
41A ASN* 1.3 57.8 + - - +
42A ASP 4.4 4.0 - - - +
43A PHE* 3.4 28.1 - - + -
48A LEU* 3.9 26.2 - - + -
52A GLU* 3.4 19.1 - - + +
56A ILE* 4.4 13.5 - - + -
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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) + - + + + + + -
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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