Contacts of the helix formed by residues 18 - 32 (chain A) in PDB entry 3OPY
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 ASP 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A THR* 3.6 3.9 - - - -
17A ASN* 1.3 78.9 + - + +
19A ASP* 1.4 63.1 + - - +
20A ASN* 3.4 24.2 + - - +
21A LEU* 3.4 44.7 + - + +
22A PHE* 3.1 24.6 + - - +
110A LEU* 3.7 2.6 - - - +
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Residues in contact with ASP 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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17A ASN 3.6 4.4 + - - +
18A ASP* 1.4 71.2 + - - +
20A ASN* 1.3 69.1 + - - +
22A PHE* 3.1 3.7 + - - +
23A GLU* 2.9 47.8 + - - +
58A ILE* 5.8 2.2 - - + -
59A LYS* 5.6 0.5 - - - +
110A LEU* 3.4 31.7 - - + +
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Residues in contact with ASN 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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18A ASP* 3.3 18.8 + - - +
19A ASP* 1.3 84.3 - - - +
21A LEU* 1.4 60.2 + - - +
23A GLU* 4.2 3.5 - - - +
24A GLU* 3.0 42.5 + - - +
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Residues in contact with LEU 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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16A THR* 4.9 10.3 - - - -
18A ASP* 3.4 36.7 + - + +
19A ASP 3.2 0.2 - - - -
20A ASN* 1.4 73.9 - - - +
22A PHE* 1.3 56.1 + - - +
24A GLU* 3.6 8.7 + - + +
25A THR* 2.6 38.3 + - - -
163A PRO* 3.8 40.2 - - + -
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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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16A THR* 4.8 8.2 - - - -
18A ASP 3.1 13.8 + - - +
19A ASP* 3.1 8.3 + - - +
21A LEU* 1.3 76.6 - - - +
23A GLU* 1.4 78.0 + - - +
25A THR* 3.2 8.5 + - - -
26A PHE* 3.1 26.4 + - + +
59A LYS* 4.2 22.2 - - + -
61A ILE* 3.9 40.8 - - + -
108A ILE* 3.6 46.0 - - + +
109A LYS 4.2 4.5 - - - -
110A LEU* 3.6 40.4 - - + -
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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 ASP* 2.9 39.2 + - - +
20A ASN* 4.3 4.7 - - - +
22A PHE* 1.4 83.8 - - - +
24A GLU* 1.4 59.1 + - + +
26A PHE* 3.4 23.4 + - + +
27A ASN* 3.0 41.9 + - - +
61A ILE* 4.3 12.5 - - - +
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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 ASN* 3.0 35.0 + - - +
21A LEU* 3.9 10.9 - - + +
23A GLU* 1.4 75.2 - - + +
25A THR* 1.4 56.9 + - - +
27A ASN* 3.8 8.0 + - - +
28A PHE* 3.2 25.6 + - - +
162A ASP* 3.9 7.8 - - - +
163A PRO* 6.5 0.2 - - + -
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Residues in contact with THR 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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14A PHE* 5.2 8.1 - - + -
21A LEU 2.6 22.2 + - - -
22A PHE* 3.2 8.0 + - - -
24A GLU* 1.4 72.2 - - - +
26A PHE* 1.3 64.5 + - - +
28A PHE* 3.2 2.4 + - - +
29A TYR* 3.2 51.4 + - + +
108A ILE* 4.3 16.2 - - + -
162A ASP* 3.1 17.5 - - + +
163A PRO* 3.4 27.3 - - + +
164A MET* 5.7 3.1 - - + -
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Residues in contact with PHE 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* 3.1 14.4 + - + +
23A GLU* 3.4 27.8 - - + +
25A THR* 1.3 77.2 - - - +
27A ASN* 1.4 75.4 + - - +
29A TYR* 3.3 2.9 + - - +
30A THR* 2.6 46.2 + - + -
36A ALA* 4.1 10.5 - - + -
61A ILE* 3.7 40.6 - - + -
63A LEU* 3.7 24.9 - - + +
108A ILE* 4.0 14.1 - - + +
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Residues in contact with ASN 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* 3.0 28.2 + - - +
24A GLU* 4.1 8.4 - - - +
26A PHE* 1.4 94.9 - - - +
28A PHE* 1.4 59.1 + - - +
30A THR* 3.5 10.7 + - - +
31A LYS* 3.2 46.7 + - - +
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Residues in contact with PHE 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 11.4 + - - +
25A THR 3.3 7.9 - - - +
27A ASN* 1.4 76.4 - - - +
29A TYR* 1.3 99.1 + + - +
31A LYS* 3.5 10.6 + - - +
32A LEU* 3.4 42.7 + - + +
141A LEU* 4.4 16.8 - - + -
144A ILE* 5.7 8.4 - - + +
145A GLY* 5.3 11.4 - - - -
160A THR* 4.5 10.8 - - + -
161A ARG 3.8 24.2 - - - -
162A ASP* 3.3 29.6 - - + +
164A MET 5.8 0.2 - - - -
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Residues in contact with TYR 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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14A PHE* 3.5 20.9 - + - -
25A THR* 3.2 45.4 + - + +
28A PHE* 1.3 100.7 - + - +
30A THR* 1.4 59.1 + - - +
32A LEU* 3.0 22.3 + - + -
33A GLY 3.3 1.0 + - - -
34A PHE* 3.0 54.8 + + + +
63A LEU* 3.8 16.2 - - + -
106A VAL* 5.9 4.3 - - + -
108A ILE* 4.4 11.0 - - + -
129A PHE* 5.6 7.6 - + - -
162A ASP* 5.2 1.1 - - + +
164A MET* 4.5 7.6 + - - +
166A ASP* 2.9 26.7 + - + -
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Residues in contact with THR 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 PHE* 2.6 46.5 + - + -
27A ASN* 3.5 17.4 - - - +
28A PHE 3.3 0.2 - - - -
29A TYR* 1.4 76.5 - - - +
31A LYS* 1.3 61.1 + - + +
32A LEU 3.4 0.3 + - - -
33A GLY* 3.5 8.3 + - - -
34A PHE* 3.8 18.1 + - - +
63A LEU* 4.5 4.0 - - - +
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Residues in contact with LYS 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 ASN* 3.2 33.9 + - - +
28A PHE* 3.7 9.1 - - - +
29A TYR 3.3 0.2 - - - -
30A THR* 1.3 77.5 - - + +
32A LEU* 1.4 59.2 + - + +
33A GLY 3.4 3.4 + - - -
140A LYS* 3.9 14.9 - - - +
144A ILE* 5.1 18.8 - - + +
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Residues in contact with LEU 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 PHE* 3.4 51.1 + - + +
29A TYR* 3.0 19.6 + - + +
31A LYS* 1.4 77.4 - - + +
33A GLY* 1.3 56.6 + - - +
34A PHE* 3.6 10.7 - - + -
65A SER* 4.7 3.6 + - - -
137A LEU* 3.9 16.4 - - + +
140A LYS* 3.0 52.5 + - + +
141A LEU* 4.3 15.7 - - + +
144A ILE* 6.0 4.3 - - + -
160A THR* 5.9 0.9 - - + -
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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