Contacts of the strand formed by residues 40 - 46 (chain A) in PDB entry 2OZ6
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A GLU* 1.3 94.3 - - + +
41A LEU* 1.3 61.3 + - - +
42A PHE* 3.9 1.2 - - - -
73A GLY 3.1 2.6 - - - +
87A ARG* 2.8 34.9 + - - +
101A GLU* 2.3 44.2 + - + +
102A ILE 3.2 11.9 - - - -
103A SER* 3.7 16.8 - - - +
104A TYR* 3.4 10.4 - - - +
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Residues in contact with LEU 41 (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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40A THR* 1.3 72.1 - - - +
42A PHE* 1.3 68.6 + - - +
71A PHE* 3.9 24.5 - - + -
72A PHE 3.7 4.7 - - - +
73A GLY 3.2 19.3 - - - +
74A GLU* 3.9 23.8 - - + -
77A LEU* 4.4 7.0 - - + -
100A ALA 3.8 0.2 - - - +
101A GLU* 3.6 2.1 - - - +
102A ILE* 2.8 47.3 + - + +
104A TYR* 3.9 8.1 - - + -
107A PHE* 4.0 48.0 - - + -
121A LEU* 4.5 4.3 - - + -
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Residues in contact with PHE 42 (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 ARG* 6.3 0.9 - - + -
25A TYR* 4.5 7.6 - - - -
31A ILE* 3.8 21.5 - - + -
32A ILE* 3.8 16.4 - - + -
40A THR* 3.9 4.0 - - - -
41A LEU* 1.3 79.1 - - - +
43A PHE* 1.3 62.6 + - - +
44A ILE 4.3 0.2 - - - -
71A PHE* 3.1 13.2 - - - -
72A PHE* 2.8 73.4 + + + +
73A GLY* 4.6 0.2 - - - -
87A ARG* 3.6 25.6 - - - -
99A VAL* 3.4 25.8 - - + -
100A ALA 3.4 4.9 - - - +
101A GLU* 3.4 39.9 - - + -
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Residues in contact with PHE 43 (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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8A MET* 4.8 10.1 - - + -
13A LEU* 3.3 34.8 - - + -
16A LEU* 4.9 4.9 - - + -
17A LEU* 4.5 7.0 - - + -
42A PHE* 1.3 74.5 - - - +
44A ILE* 1.3 71.9 + - - +
45A ILE* 3.2 20.2 + - + -
69A GLY* 3.5 34.8 - - - -
70A ASP 3.4 7.6 - - - -
71A PHE* 3.3 40.2 - + + -
99A VAL* 3.7 3.0 - - - -
100A ALA* 2.9 39.3 + - + +
102A ILE* 4.7 7.0 - - + -
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Residues in contact with ILE 44 (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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43A PHE* 1.3 73.7 - - - +
45A ILE* 1.3 63.0 + - - +
46A LYS 3.9 14.6 - - - +
47A GLY 3.4 23.3 - - - +
48A SER* 5.1 0.2 - - - -
49A VAL* 3.9 26.0 - - + +
66A LEU* 3.7 26.5 - - + +
67A ASN 3.4 19.3 - - - +
68A SER* 3.6 8.1 - - - -
69A GLY* 2.8 29.5 + - - -
70A ASP* 2.9 17.9 + - + +
72A PHE* 3.7 20.2 - - + -
97A CYS* 5.3 2.2 - - - -
98A GLU 4.1 3.6 - - - +
99A VAL* 4.4 5.4 - - + -
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Residues in contact with ILE 45 (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* 4.0 26.7 - - + -
22A ARG* 4.0 18.6 - - - -
43A PHE* 3.2 16.4 + - + +
44A ILE* 1.3 74.9 - - - +
46A LYS* 1.3 65.6 + - + +
68A SER* 3.9 9.6 - - - -
69A GLY 5.0 0.3 + - - -
98A GLU* 2.9 36.5 + - + +
99A VAL 4.1 0.9 - - - -
100A ALA* 3.8 25.1 - - + +
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Residues in contact with LYS 46 (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 ARG* 5.7 2.2 - - - +
44A ILE* 3.5 4.6 - - - +
45A ILE* 1.3 86.1 - - + +
47A GLY* 1.3 64.8 + - - +
68A SER* 4.0 6.1 - - - +
96A GLU* 3.7 18.6 + - - +
97A CYS* 3.3 4.3 - - - -
98A GLU* 2.8 41.4 + - + +
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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