Contacts of the helix formed by residues 18 - 29 (chain A) in PDB entry 2OCA
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 GLU 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ASP* 4.4 7.1 + - + +
17A CYS* 1.3 83.0 - - - +
19A GLU* 1.3 60.5 + - - +
20A SER* 3.8 12.6 - - - +
21A THR* 2.9 18.3 + - - +
22A PHE* 2.8 25.2 + - - +
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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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17A CYS 3.7 1.6 + - - -
18A GLU* 1.3 72.5 + - - +
20A SER* 1.3 61.3 + - - +
22A PHE* 3.5 7.8 + - - +
23A HIS* 3.1 52.3 + - + -
58A ARG* 4.6 15.3 - - - +
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Residues in contact with SER 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 GLU* 3.8 9.3 - - - +
19A GLU* 1.3 77.6 - - - +
21A THR* 1.3 78.7 + - - +
23A HIS* 3.2 14.8 + - - +
24A GLU* 3.3 21.8 + - - +
77A TYR* 4.6 5.0 + - - -
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Residues in contact with THR 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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2A ASP* 4.7 3.5 + - - +
3A ILE* 3.5 39.5 - - + -
17A CYS* 3.8 12.3 - - + +
18A GLU* 2.9 23.5 + - - +
20A SER* 1.3 85.4 + - - +
22A PHE* 1.3 63.4 + - - +
24A GLU* 3.2 11.5 + - - +
25A LEU* 3.0 23.5 + - + +
71A PHE* 4.2 5.2 - - + -
77A TYR* 3.9 27.4 + - + -
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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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15A ILE* 5.9 1.1 - - + -
17A CYS* 3.5 13.8 - - - -
18A GLU 2.8 12.3 + - - +
19A GLU* 3.6 8.3 - - - +
21A THR* 1.3 77.9 - - - +
23A HIS* 1.3 72.8 + + - +
25A LEU* 3.4 4.3 + - + +
26A ARG* 2.9 45.8 + - - +
54A LEU* 3.8 23.1 - - + -
55A ASP 3.6 22.7 - - - -
56A TYR* 3.5 26.5 - + - -
58A ARG* 3.4 65.3 - - + +
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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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19A GLU* 3.1 43.2 + - + +
20A SER* 3.2 9.7 + - - +
22A PHE* 1.3 89.0 - + - +
24A GLU* 1.3 65.7 + - + +
26A ARG* 3.5 16.0 + - - +
27A ASP* 3.3 25.5 + - - +
56A TYR* 3.8 28.3 + + - -
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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 SER* 3.3 15.9 + - - +
21A THR* 3.2 7.9 + - - +
23A HIS* 1.3 77.8 - - + +
25A LEU* 1.3 59.3 + - - +
27A ASP* 3.2 6.9 + - - +
28A PHE* 2.9 26.0 + - - +
71A PHE* 3.8 7.9 - - + -
75A PHE* 3.6 33.4 - - + -
77A TYR* 2.4 40.6 + - - -
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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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3A ILE* 4.0 21.1 - - + -
15A ILE* 4.2 30.1 - - + -
17A CYS* 4.3 4.7 - - - -
21A THR* 3.0 20.5 + - + +
22A PHE* 3.6 4.9 - - + +
24A GLU* 1.3 78.2 - - - +
26A ARG* 1.3 56.4 + - - +
28A PHE* 3.0 4.6 + - + +
29A PHE* 2.9 58.4 + - + -
54A LEU* 3.7 12.1 - - + -
68A ILE* 3.8 10.1 - - + -
71A PHE* 3.5 37.9 - - + -
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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 PHE* 2.9 36.8 + - + +
23A HIS* 3.7 18.7 - - - +
24A GLU 3.3 0.4 - - - -
25A LEU* 1.3 76.0 - - - +
27A ASP* 1.3 62.1 + - - +
29A PHE 3.9 8.7 - - - +
30A SER* 3.9 0.2 - - - -
52A ARG* 3.6 54.8 + - + +
54A LEU* 2.6 54.0 + - + +
55A ASP* 3.7 15.4 + - - +
56A TYR* 4.2 25.2 + - - -
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Residues in contact with ASP 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* 3.3 16.5 + - - +
24A GLU* 3.2 6.5 + - - +
25A LEU 3.1 0.4 - - - -
26A ARG* 1.3 76.6 - - - +
28A PHE* 1.3 64.2 + - - +
30A SER* 2.6 24.3 + - - -
50A ARG* 4.4 6.6 + - - -
52A ARG* 3.2 26.3 + - - +
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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 2.9 13.9 + - - +
25A LEU* 3.2 13.0 - - - +
27A ASP* 1.3 79.6 - - - +
29A PHE* 1.3 88.5 + + - +
30A SER 2.9 12.8 + - - +
67A GLN* 3.5 32.1 - - + -
70A LYS* 4.1 30.3 - - + -
71A PHE* 3.7 38.4 - + + -
74A ASN* 5.5 6.3 - - + -
75A PHE* 5.3 8.7 - + + -
270A MET* 4.2 5.7 - - - +
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Residues in contact with PHE 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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15A ILE* 5.3 1.3 - - + -
25A LEU* 2.9 46.6 + - + +
26A ARG 3.9 4.1 - - - +
28A PHE* 1.3 94.1 - + - +
30A SER* 1.3 59.1 + - - +
52A ARG* 3.7 1.4 - - - -
53A LEU* 3.0 30.3 + - + +
54A LEU* 4.3 11.8 + - + -
60A LEU* 3.6 35.2 - - + -
64A LEU* 4.0 27.6 - - + -
67A GLN* 3.8 23.1 - - + -
68A ILE* 3.8 19.1 - - + -
270A MET* 3.6 16.6 - - + -
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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