Contacts of the helix formed by residues 19 - 32 (chain A) in PDB entry 1MOX
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 THR 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLN* 3.6 2.7 - - - +
18A GLY* 1.3 74.4 - - - +
20A PHE* 1.3 59.6 + - - +
21A GLU* 3.6 7.8 + - - +
22A ASP* 2.8 45.4 + - - +
23A HIS* 2.8 27.2 + - - +
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Residues in contact with PHE 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 GLN* 3.4 34.1 - - - +
19A THR* 1.3 73.3 - - - +
21A GLU* 1.3 59.9 + - - +
23A HIS* 3.2 6.5 + - - +
24A PHE* 2.8 30.3 + - - +
45A TYR* 3.6 21.5 - + + +
47A GLN* 3.4 52.5 - - + -
50A TYR* 4.7 6.1 - - + +
22C ARG* 6.4 0.2 - - - -
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Residues in contact with GLU 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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19A THR* 3.3 7.2 + - - +
20A PHE* 1.3 76.4 - - - +
22A ASP* 1.3 70.7 + - - +
24A PHE* 3.0 6.5 + - - +
25A LEU* 2.9 44.8 + - + +
50A TYR* 3.6 28.2 + - + +
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Residues in contact with ASP 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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17A LEU 3.6 14.6 - - - +
18A GLY* 4.3 3.6 - - - -
19A THR* 2.8 42.6 + - - +
21A GLU* 1.3 72.9 - - - +
23A HIS* 1.3 65.6 + - - +
25A LEU* 2.9 26.9 + - - +
26A SER* 3.1 11.6 + - - -
36C SER* 5.5 7.3 - - - -
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Residues in contact with HIS 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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12A ASN* 5.7 3.4 - - + -
15A THR 3.7 17.0 - - - -
16A GLN* 3.9 5.6 - - + -
17A LEU* 3.2 44.0 + - + +
19A THR 2.8 22.7 + - - +
20A PHE* 3.3 7.0 - - - +
22A ASP* 1.3 73.3 - - - +
24A PHE* 1.3 64.3 + - - +
26A SER* 3.4 6.1 - - - -
27A LEU* 3.2 23.1 + - + +
44A THR* 2.6 48.5 + - - -
45A TYR* 3.7 18.7 - + + -
46A VAL* 5.6 2.2 - - + -
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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
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20A PHE 2.8 16.0 + - - +
21A GLU 3.0 7.2 + - - +
23A HIS* 1.3 74.9 - - - +
25A LEU* 1.3 71.1 + - + +
26A SER 3.1 1.8 - - - -
27A LEU* 3.2 7.6 + - + +
28A GLN* 3.0 48.0 + - - +
46A VAL* 4.3 19.5 - - + -
50A TYR* 3.3 48.0 - + + -
51A ASP 3.5 19.7 - - - -
52A LEU* 3.7 24.9 - - + -
54A PHE* 4.2 13.2 - + - -
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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 GLU* 3.3 35.0 - - + +
22A ASP* 2.9 16.4 + - - +
24A PHE* 1.3 86.8 - - + +
26A SER* 1.3 57.9 + - - +
28A GLN* 3.9 20.3 - - - +
29A ARG* 3.0 49.5 + - - +
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Residues in contact with SER 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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17A LEU* 3.5 28.9 - - - +
22A ASP 3.1 9.8 + - - -
23A HIS* 3.4 12.6 - - - -
25A LEU* 1.3 77.0 - - - +
27A LEU* 1.3 64.8 + - - +
29A ARG* 3.4 18.8 + - - +
30A MET* 3.0 32.2 + - - +
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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
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23A HIS* 3.2 13.2 + - + +
24A PHE* 3.2 11.5 + - + +
26A SER* 1.3 79.3 - - - +
28A GLN* 1.3 58.8 + - - +
30A MET* 2.9 20.2 + - - -
31A PHE* 3.1 51.2 + - + +
42A GLU 3.7 17.5 - - - +
43A ILE* 4.3 19.5 - - + -
44A THR 5.3 2.0 - - - +
46A VAL* 4.0 27.4 - - + -
52A LEU* 4.2 16.4 - - + -
54A PHE* 4.0 9.2 - - + -
55A LEU* 5.5 2.0 - - + -
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Residues in contact with GLN 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* 3.0 33.7 + - + +
25A LEU* 4.0 23.5 - - - +
27A LEU* 1.3 77.5 - - - +
29A ARG* 1.3 58.5 + - - +
32A ASN* 3.1 32.2 + - - +
51A ASP 4.9 1.4 + - - -
54A PHE* 3.5 39.4 - - + +
1E NAG 3.5 19.7 - - - +
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Residues in contact with ARG 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* 3.0 42.2 + - - +
26A SER* 3.7 20.0 + - - +
27A LEU 3.1 0.2 - - - -
28A GLN* 1.3 79.8 - - - +
30A MET* 1.3 74.6 + - + +
31A PHE 3.5 0.7 + - - -
32A ASN* 4.2 6.2 + - - +
49C LEU* 5.6 12.7 - - - +
1E NAG 4.5 23.2 - - + +
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Residues in contact with MET 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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7A CYS* 3.8 15.2 - - - +
8A GLN* 4.9 17.2 + - + +
9A GLY 4.5 10.0 + - - +
10A THR* 4.2 22.4 - - + -
26A SER* 3.0 21.3 + - - +
27A LEU* 2.9 6.7 + - - +
29A ARG* 1.3 89.9 - - + +
31A PHE* 1.3 81.8 + - + +
409A HIS* 5.7 4.3 - - + +
711A PT 2.3 33.4 - - - -
49C LEU* 4.6 15.7 - - + -
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Residues in contact with PHE 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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7A CYS* 3.8 13.0 - - - -
9A GLY* 3.9 24.0 - - - -
10A THR* 4.2 16.8 - - + -
27A LEU* 3.1 43.5 + - + +
28A GLN 4.1 0.7 - - - -
30A MET* 1.3 92.1 - - + +
32A ASN* 1.3 69.3 + - - +
33A ASN 3.6 1.8 - - - -
34A CYS* 3.3 20.9 + - + +
37A VAL* 4.1 15.0 - - + -
40A ASN 3.9 12.6 - - - -
41A LEU* 3.8 30.7 - - + -
42A GLU 4.6 3.1 - - - -
54A PHE* 3.9 20.2 - + + +
55A LEU* 4.9 3.8 - - + -
57A THR* 4.6 0.5 + - - -
58A ILE* 4.6 8.6 - - + +
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Residues in contact with ASN 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 GLN* 3.1 18.4 + - - +
29A ARG 4.2 5.5 + - - +
30A MET 3.9 0.6 - - - -
31A PHE* 1.3 78.0 - - - +
33A ASN* 1.3 68.3 + - - +
34A CYS 3.5 0.9 + - - -
54A PHE* 3.4 35.2 - - - +
57A THR* 3.8 3.3 + - - +
1E NAG 1.4 74.7 + - + +
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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