Contacts of the helix formed by residues 12 - 30 (chain A) in PDB entry 4WNG
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 SER 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLY* 1.3 79.9 + - - +
13A MET* 1.3 66.8 + - - +
14A GLU* 3.8 18.7 - - - +
15A ALA* 3.3 26.3 + - - +
16A SER* 3.3 16.5 + - - -
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Residues in contact with MET 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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12A SER* 1.3 74.3 - - - +
14A GLU* 1.3 74.4 + - - +
16A SER* 3.5 5.5 + - - +
17A CYS 3.1 18.4 + - - -
46A VAL* 3.6 32.8 - - + +
47A GLY 3.6 17.1 - - - +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 3.8 16.6 - - - +
13A MET* 1.3 89.8 + - - +
15A ALA* 1.3 61.2 + - - +
17A CYS* 3.5 2.8 + - - +
18A LEU* 3.2 25.4 + - - +
48A THR* 3.5 18.4 + - - +
49A GLU* 3.0 52.2 + - - +
50A ASP* 4.2 3.0 + - + +
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Residues in contact with ALA 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 GLY* 4.5 9.2 - - - +
12A SER* 3.3 24.7 + - - +
13A MET 3.2 0.8 - - - -
14A GLU* 1.3 80.2 - - - +
16A SER* 1.3 62.0 + - - +
18A LEU* 3.4 11.2 + - - +
19A GLU* 3.1 34.0 + - + +
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Residues in contact with SER 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY* 5.5 0.7 - - - -
12A SER 3.3 12.8 + - - -
13A MET* 3.5 9.5 + - - +
15A ALA* 1.3 75.4 - - - +
17A CYS* 1.3 65.0 + - - +
19A GLU* 3.3 14.7 + - - +
20A LEU* 3.0 32.8 + - - +
46A VAL* 4.4 14.8 - - - -
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Residues in contact with CYS 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 MET 3.1 9.0 + - - +
14A GLU 3.6 5.4 - - - +
16A SER* 1.3 76.9 - - - +
18A LEU* 1.3 64.3 + - - +
20A LEU* 3.5 3.9 + - - +
21A ALA* 3.0 23.9 + - - +
43A ALA* 3.4 28.2 - - - +
46A VAL* 4.1 7.1 - - + +
47A GLY 3.3 19.5 - - - +
48A THR* 3.6 29.2 - - - -
53A THR* 4.6 3.8 - - + -
54A LEU* 5.4 0.4 - - - -
57A ILE* 3.8 19.1 - - - -
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU 3.2 11.5 + - - +
15A ALA* 3.4 13.7 - - - +
16A SER 3.3 0.2 - - - -
17A CYS* 1.3 79.8 - - - +
19A GLU* 1.3 52.1 + - + +
21A ALA* 3.0 6.0 + - - +
22A LEU* 2.8 43.6 + - + +
53A THR* 4.0 20.6 - - + +
1007B VAL* 4.0 27.1 - - + +
1011B PHE* 3.6 37.2 - - + -
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Residues in contact with GLU 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 ALA* 3.1 21.5 + - - +
16A SER* 3.3 16.4 + - - +
18A LEU* 1.3 79.0 - - + +
20A LEU* 1.3 63.4 + - + +
22A LEU* 3.2 12.2 + - + +
23A GLU* 3.1 21.8 + - - +
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Residues in contact with LEU 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 SER* 3.0 22.6 + - - +
17A CYS 3.7 4.0 - - - +
19A GLU* 1.3 77.3 - - + +
21A ALA* 1.3 56.8 + - - +
23A GLU* 3.3 4.7 + - - +
24A GLY* 2.9 22.7 + - - -
39A PHE* 3.6 41.4 - - + +
42A ALA* 3.7 12.1 - - + -
43A ALA* 3.7 26.0 - - + +
46A VAL* 3.5 31.6 - - + -
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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 CYS 3.0 14.3 + - - +
18A LEU* 3.4 9.4 - - - +
20A LEU* 1.3 76.6 - - - +
22A LEU* 1.3 58.4 + - - +
24A GLY* 3.0 2.3 + - - +
25A GLU* 2.8 34.7 + - - +
40A PHE* 3.5 12.2 - - + -
43A ALA* 4.1 2.9 - - + +
53A THR* 5.4 0.2 - - + -
57A ILE* 4.0 19.5 - - + -
1007B VAL* 3.7 28.3 - - + -
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Residues in contact with LEU 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 LEU* 2.8 19.6 + - + +
19A GLU* 3.6 14.1 - - + +
21A ALA* 1.3 77.0 - - - +
23A GLU* 1.3 56.5 - - - +
25A GLU* 3.3 11.3 + - + +
26A ARG* 2.9 28.6 + - - +
1007B VAL* 4.4 10.0 - - + +
1008B THR* 3.6 30.1 - - + -
1011B PHE* 6.1 3.8 - - + -
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Residues in contact with GLU 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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19A GLU 3.1 9.6 + - - +
20A LEU* 3.6 8.1 - - - +
22A LEU* 1.3 75.9 - - - +
24A GLY* 1.3 61.0 + - - +
26A ARG* 2.7 48.4 + - - +
27A LEU* 2.9 45.0 + - + +
39A PHE* 3.5 37.9 - - + -
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Residues in contact with GLY 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 LEU 2.9 12.8 + - - -
21A ALA 3.0 4.4 + - - -
23A GLU* 1.3 77.0 - - - +
25A GLU* 1.3 62.1 + - - +
27A LEU* 3.3 0.5 + - - -
28A CYS* 3.0 28.6 + - - +
36A GLY* 3.9 9.6 - - - -
39A PHE* 3.7 18.9 - - - +
40A PHE* 3.4 15.0 - - - -
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Residues in contact with GLU 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 2.8 20.5 + - - +
22A LEU* 3.7 10.7 - - + +
24A GLY* 1.3 72.1 - - - +
26A ARG* 1.3 61.8 + - - +
28A CYS* 3.4 3.4 + - - +
29A LYS* 3.1 43.4 + - + +
40A PHE* 3.4 6.0 - - + -
60A GLN* 2.9 34.9 + - - +
1006B SER* 2.5 23.1 + - - -
1007B VAL* 2.7 42.9 + - - +
1008B THR* 4.6 4.2 - - - +
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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
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22A LEU 2.9 18.2 + - - +
23A GLU* 2.7 44.5 + - - +
25A GLU* 1.3 77.0 - - - +
27A LEU* 1.3 80.7 + - - +
29A LYS* 3.4 9.5 + - - +
30A SER* 3.1 28.4 + - - -
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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
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23A GLU* 2.9 29.5 + - - +
24A GLY 3.9 2.9 - - - +
26A ARG* 1.3 98.0 - - - +
28A CYS* 1.3 60.7 + - - +
30A SER* 2.9 22.5 + - - +
32A ASP* 2.9 37.5 + - + +
35A ALA* 4.0 22.7 - - + +
36A GLY* 3.9 4.7 - - - +
39A PHE* 3.3 41.3 - - + -
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Residues in contact with CYS 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 GLY 3.0 20.0 + - - +
25A GLU* 3.9 5.8 - - - +
26A ARG 3.3 0.2 - - - -
27A LEU* 1.3 76.6 - - - +
29A LYS* 1.3 58.3 + - + +
31A GLY* 2.8 21.3 + - - -
32A ASP 4.2 5.4 - - - -
33A CYS* 4.0 30.0 - - - -
36A GLY* 3.9 14.6 - - - -
40A PHE* 3.7 20.9 - - + -
60A GLN* 5.4 1.8 - - - +
64A ALA* 4.2 12.3 - - - -
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Residues in contact with LYS 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 GLU* 3.1 36.7 + - + +
26A ARG* 3.8 8.0 - - - +
27A LEU 3.4 0.2 - - - -
28A CYS* 1.3 76.4 - - + +
30A SER* 1.3 58.0 + - - +
31A GLY* 3.0 5.7 + - - -
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Residues in contact with SER 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 ARG* 3.1 23.2 + - - -
27A LEU* 2.9 19.7 + - - +
28A CYS 3.2 0.4 - - - -
29A LYS* 1.3 74.7 - - - +
31A GLY* 1.3 57.0 + - - +
32A ASP* 3.7 10.2 + - - +
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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
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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