Contacts of the helix formed by residues 12 - 31 (chain A) in PDB entry 2GUT
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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4A MET* 3.7 22.4 - - - +
9A ASP* 3.2 22.4 + - - +
10A TRP 3.1 1.9 - - - +
11A ARG* 1.3 80.0 - - - +
13A THR* 1.3 66.5 + - - +
14A ALA* 3.2 12.1 + - - +
15A PHE* 3.1 17.8 + - - +
16A ARG* 3.2 13.7 + - - +
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Residues in contact with THR 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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11A ARG 3.8 2.2 + - - -
12A SER* 1.3 72.0 + - - +
14A ALA* 1.3 55.0 + - - +
16A ARG* 4.1 9.1 - - - +
17A GLN* 2.7 45.7 + - + +
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Residues in contact with ALA 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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4A MET* 4.5 18.6 - - + -
12A SER* 3.2 9.2 + - - +
13A THR* 1.3 78.1 - - - +
15A PHE* 1.3 63.0 + - - +
17A GLN* 3.7 9.8 - - - +
18A LYS* 3.0 36.1 + - + +
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Residues in contact with PHE 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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4A MET* 5.3 12.7 - - + -
7A GLU* 5.5 16.6 - - + -
9A ASP 3.9 8.5 - - - +
10A TRP* 3.7 42.6 - - + +
12A SER* 3.1 15.7 + - - +
14A ALA* 1.3 79.7 - - - +
16A ARG* 1.3 69.4 + - - +
18A LYS* 3.7 3.4 - - - +
19A LEU* 3.1 47.7 + - + +
52A ARG* 5.3 1.8 - - + -
55A TYR* 5.0 7.0 - + - -
56A LEU* 4.0 32.5 - - + -
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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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10A TRP 4.4 0.8 + - - -
11A ARG 6.0 0.4 - - - -
12A SER 3.2 10.6 + - - +
13A THR* 4.1 9.3 - - - +
15A PHE* 1.3 81.4 - - - +
17A GLN* 1.3 54.6 + - - +
19A LEU* 3.3 6.8 + - - +
20A VAL* 2.7 57.9 + - + +
39A LYS* 5.3 13.6 - - - +
42A GLU* 5.4 2.7 - - + +
43A SER* 4.8 20.7 - - - +
46A PHE* 4.2 37.6 - - + +
55A TYR* 4.5 10.5 - - + +
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Residues in contact with GLN 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 THR* 2.7 33.8 + - + +
14A ALA* 3.7 8.4 + - - +
16A ARG* 1.3 73.5 - - - +
18A LYS* 1.3 88.9 + - - +
20A VAL* 2.9 19.1 + - - +
21A SER* 3.1 20.6 + - - -
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Residues in contact with LYS 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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3A ALA* 3.8 28.7 - - + +
4A MET* 6.1 3.9 - - - -
14A ALA* 3.0 24.1 + - + +
15A PHE* 3.7 4.2 - - - +
17A GLN* 1.3 96.1 - - - +
19A LEU* 1.3 71.6 + - + +
21A SER* 3.1 13.0 + - - -
22A GLN* 3.2 22.7 + - + +
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Residues in contact with LEU 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 PHE* 3.1 29.2 + - + +
16A ARG 3.6 5.6 - - - +
18A LYS* 1.3 83.7 - - + +
20A VAL* 1.3 61.5 + - - +
22A GLN* 3.1 23.1 + - + +
23A ILE* 3.0 21.2 + - + +
55A TYR* 3.1 40.8 - - + +
56A LEU* 4.1 20.4 - - + -
59A VAL* 3.9 20.2 - - + -
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Residues in contact with VAL 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* 2.7 46.6 + - + +
17A GLN* 3.2 11.4 - - - +
19A LEU* 1.3 73.0 - - - +
21A SER* 1.3 64.7 + - - +
24A GLU* 3.1 23.8 + - + +
38A SER* 5.4 0.7 - - - -
39A LYS* 4.7 24.0 - - + +
42A GLU* 2.9 49.8 - - + +
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Residues in contact with SER 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 GLN* 3.1 20.2 + - - -
18A LYS* 3.1 10.3 + - - -
20A VAL* 1.3 76.8 - - - +
22A GLN* 1.3 67.5 + - - +
24A GLU* 3.2 7.6 + - - +
25A ASP* 2.8 31.5 + - - +
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Residues in contact with GLN 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 LYS* 3.3 20.1 - - + +
19A LEU* 3.1 17.4 + - + +
21A SER* 1.3 87.3 + - - +
23A ILE* 1.3 56.5 + - - +
25A ASP* 3.1 9.8 + - - +
26A ALA* 2.9 31.2 + - - +
63A ILE* 3.8 18.6 - - + +
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU 3.0 25.0 + - - +
20A VAL 3.9 0.2 - - - +
22A GLN* 1.3 76.1 - - - +
24A GLU* 1.3 60.0 + - - +
26A ALA* 4.1 1.4 - - - +
27A MET* 3.2 29.8 + - + +
38A SER* 3.5 5.8 - - - +
41A MET* 5.1 6.3 - - + -
42A GLU* 3.2 44.9 - - + +
45A VAL* 6.2 0.9 - - + -
55A TYR* 3.9 6.1 - - - +
59A VAL* 3.4 35.4 - - + -
62A LEU* 3.3 27.9 - - + +
63A ILE* 3.9 15.0 - - + -
66A PHE* 5.2 0.4 - - + -
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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 VAL* 3.1 20.0 + - + +
21A SER* 3.5 8.4 - - - +
22A GLN 3.2 0.2 - - - -
23A ILE* 1.3 75.5 - - - +
25A ASP* 1.3 64.6 + - - +
27A MET* 4.0 3.5 - - + +
28A ARG* 3.1 29.7 + - - +
38A SER* 3.1 28.7 + - - +
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Residues in contact with ASP 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 SER* 2.8 19.0 + - - +
22A GLN* 3.1 11.4 + - - +
24A GLU* 1.3 75.6 - - - +
26A ALA* 1.3 66.0 + - - +
28A ARG* 3.3 10.9 + - - +
29A LYS* 3.2 38.6 + - - +
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Residues in contact with ALA 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 GLN 2.9 15.3 + - - +
23A ILE 4.1 3.1 - - - +
25A ASP* 1.3 76.7 - - - +
27A MET* 1.3 51.9 + - - +
29A LYS* 3.5 4.0 + - - +
30A ALA* 2.7 37.4 + - - +
63A ILE* 3.7 39.3 - - + +
66A PHE* 4.3 5.2 - - + +
67A ARG* 4.8 10.4 - - + +
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Residues in contact with MET 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 ILE* 3.2 16.2 + - + +
24A GLU* 4.0 3.8 - - + +
26A ALA* 1.3 76.8 - - - +
28A ARG* 1.3 66.8 + - - +
30A ALA* 2.9 7.5 + - - +
31A GLY* 2.9 21.3 + - - -
32A VAL* 3.4 26.3 + - + +
33A ALA* 6.2 0.9 - - - -
37A SER* 4.5 1.1 - - - -
38A SER* 3.3 39.9 - - - +
41A MET* 3.5 31.2 - - + -
66A PHE* 3.2 32.0 - - + -
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Residues in contact with ARG 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* 3.1 22.4 + - - +
25A ASP* 3.3 12.1 + - - +
27A MET* 1.3 81.5 - - - +
29A LYS* 1.3 66.8 + - + +
31A GLY* 3.2 10.9 + - - -
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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 ASP* 3.2 28.2 + - - +
26A ALA* 4.1 3.6 - - - +
28A ARG* 1.3 82.8 - - + +
30A ALA* 1.3 60.6 + - - +
31A GLY* 3.2 1.1 + - - -
70A HIS* 3.1 34.5 + - + +
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Residues in contact with ALA 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 ALA 2.7 20.3 + - - +
27A MET 2.9 7.8 + - - +
29A LYS* 1.3 79.5 - - - +
31A GLY* 1.3 64.3 + - - +
32A VAL* 4.1 4.8 - - + +
66A PHE* 3.6 45.1 - - + +
67A ARG* 5.3 0.9 - - - +
69A ILE* 5.1 3.1 - - - +
70A HIS* 3.4 27.4 + - - +
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Residues in contact with GLY 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 MET 2.9 7.7 + - - -
28A ARG 3.2 8.4 + - - -
29A LYS 3.2 4.9 - - - -
30A ALA* 1.3 82.3 - - - +
32A VAL* 1.3 61.2 + - - +
69A ILE* 5.7 1.0 - - - +
70A HIS* 5.2 1.3 - - - -
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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