Contacts of the strand formed by residues 10 - 19 (chain A) in PDB entry 2OXP
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 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A HIS* 3.3 39.5 + - + +
9A LYS* 1.3 78.6 - - - +
11A PRO* 1.3 71.4 - - + +
27A TYR* 2.7 36.9 + - + -
28A LYS* 3.7 13.9 + - - -
73A GLU* 3.1 8.8 - - - -
74A VAL* 2.8 43.1 + - + +
76A PHE* 3.7 18.4 + - - -
81A ARG* 4.7 2.4 + - - -
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Residues in contact with PRO 11 (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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9A LYS 4.6 1.3 - - - +
10A GLU* 1.3 88.0 - - + +
12A ALA* 1.3 61.8 + - - +
26A MET 4.9 0.2 - - - +
27A TYR* 4.1 15.1 - - - -
28A LYS* 5.1 2.4 + - - +
72A ILE 3.9 5.8 - - - +
73A GLU* 4.6 5.3 - - + +
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Residues in contact with ALA 12 (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 PRO* 1.3 76.1 - - - +
13A THR* 1.3 64.2 + - - +
25A LEU* 4.1 14.1 - - + -
26A MET 3.4 15.5 - - - +
27A TYR* 4.8 2.7 - - + -
72A ILE* 3.1 32.5 + - + +
74A VAL* 3.9 28.9 - - + -
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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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12A ALA* 1.3 75.4 + - - +
14A LEU* 1.3 75.2 + - - +
15A ILE* 3.4 1.3 + - + -
25A LEU* 3.3 7.7 - - - -
26A MET* 2.8 52.8 + - + +
72A ILE* 5.0 0.7 - - - -
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Residues in contact with LEU 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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12A ALA 4.3 0.2 - - - -
13A THR* 1.3 83.8 - - - +
15A ILE* 1.3 72.4 + - - +
16A LYS* 3.5 20.4 - - - +
17A ALA* 4.3 3.1 - - + +
23A VAL* 3.9 24.2 - - + -
25A LEU* 4.0 8.7 - - + +
66A ASP* 3.9 17.9 - - + +
67A GLU* 3.7 35.9 - - + +
72A ILE* 4.4 15.9 - - + +
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Residues in contact with ILE 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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13A THR* 3.4 1.8 + - + +
14A LEU* 1.3 79.3 - - - +
16A LYS* 1.3 73.7 + - + +
24A LYS* 3.0 26.4 + - + +
25A LEU 3.7 3.6 - - - -
26A MET* 3.7 45.1 - - + +
31A PRO* 3.5 32.3 - - + -
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Residues in contact with LYS 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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14A LEU* 3.5 9.3 - - - +
15A ILE* 1.3 88.3 - - + +
17A ALA* 1.3 66.8 + - - +
18A ILE* 4.6 10.3 - - - -
23A VAL* 3.7 0.9 - - - +
24A LYS* 2.9 63.9 + - + +
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Residues in contact with ALA 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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14A LEU* 4.3 4.8 - - + +
16A LYS* 1.3 84.0 - - - +
18A ILE* 1.3 63.6 + - - +
19A ASP 5.1 1.1 - - - +
22A THR 5.0 0.2 - - - -
23A VAL* 4.5 10.1 - - - -
59A SER 5.7 0.4 - - - +
62A THR* 6.5 0.4 - - + -
63A LYS* 3.7 48.5 - - + +
66A ASP* 6.4 0.9 - - + -
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Residues in contact with ILE 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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16A LYS* 4.1 10.8 - - - +
17A ALA* 1.3 81.4 - - - +
19A ASP* 1.3 69.6 + - - +
22A THR* 3.3 25.4 + - + +
23A VAL 3.8 5.4 - - - -
24A LYS* 3.6 34.8 - - + +
33A THR* 3.8 29.8 - - + +
44A THR* 5.5 0.2 + - - -
59A SER* 4.8 0.7 + - - -
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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 ALA* 5.1 1.0 - - - +
18A ILE* 1.3 89.4 + - + +
20A GLY* 1.3 67.0 + - - +
21A ASP* 3.3 10.4 - - - +
22A THR* 3.0 42.1 + - - +
41A THR* 5.0 1.7 + - - -
42A PRO 5.3 3.7 - - - +
43A GLU* 5.5 2.3 - - - -
44A THR* 4.3 19.6 + - + +
59A SER* 3.3 24.9 - - - +
62A THR* 3.9 10.3 - - - +
300A THP 5.8 0.2 + - - -
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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