Contacts of the strand formed by residues 88 - 97 (chain A) in PDB entry 2N0A
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 ILE 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A VAL* 5.5 0.8 - - - +
86A GLY 3.9 9.0 - - - +
87A SER* 1.3 87.2 + - - +
89A ALA* 1.3 63.5 + - - +
91A ALA* 4.2 14.4 - - + +
94A PHE* 4.0 38.6 - - + -
86B GLY 6.0 0.2 - - - +
87B SER* 5.8 0.2 - - - -
88B ILE* 3.4 33.2 - - + +
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Residues in contact with ALA 89 (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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77A VAL* 5.5 0.9 - - - +
79A GLN* 3.4 23.2 + - - +
82A VAL* 4.2 24.8 - - + +
88A ILE* 1.3 75.2 - - - +
90A ALA* 1.3 61.0 + - - +
91A ALA 4.3 0.4 + - - -
79B GLN* 3.1 28.5 - - - +
82B VAL* 5.7 0.7 - - + -
87B SER* 5.3 0.2 + - - -
88B ILE 3.0 7.7 + - - -
89B ALA* 3.4 11.2 - - - +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 4.0 18.8 - - + -
89A ALA* 1.3 76.5 - - + +
91A ALA* 1.3 61.3 + - - +
92A THR* 4.4 1.6 - - + -
77B VAL* 3.8 30.5 - - + -
79B GLN* 4.7 2.2 - - - +
88B ILE* 4.9 2.0 - - - +
89B ALA 2.8 20.8 + - - +
90B ALA* 4.5 1.6 - - - -
91B ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 91 (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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88A ILE* 4.2 19.8 - - + +
89A ALA 4.3 0.6 - - - -
90A ALA* 1.3 75.0 - - - +
92A THR* 1.3 64.5 + - - +
93A GLY 3.5 4.2 + - - -
94A PHE* 4.3 14.6 + - + +
88B ILE* 4.0 23.6 - - + -
91B ALA* 3.3 10.3 - - + +
94B PHE* 5.0 3.6 - - + -
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Residues in contact with THR 92 (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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71A VAL* 3.5 23.3 - - + -
75A THR* 4.7 16.8 - - + +
90A ALA 5.7 1.1 - - - -
91A ALA* 1.3 71.3 - - - +
93A GLY* 1.3 59.9 + - - +
71B VAL* 3.0 26.0 - - + +
75B THR* 4.1 32.5 - - + +
91B ALA 3.1 9.6 + - - +
92B THR* 3.2 5.8 - - + -
93B GLY* 2.7 28.2 + - - -
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Residues in contact with GLY 93 (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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69A ALA* 3.6 25.6 - - - +
71A VAL* 3.4 16.1 - - - +
91A ALA 3.5 3.8 + - - -
92A THR* 1.3 70.2 - - - +
94A PHE* 1.3 59.0 + - - +
93B GLY* 3.8 1.7 - - - -
94B PHE* 2.8 34.5 + - - +
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Residues in contact with PHE 94 (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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69A ALA* 4.2 1.6 - - - +
88A ILE* 4.0 34.5 - - + -
91A ALA* 4.3 9.2 + - + +
93A GLY* 1.3 73.3 - - - +
95A VAL* 1.3 67.6 + - - +
96A LYS* 4.2 26.9 - - + -
88B ILE* 4.1 15.9 - - + -
94B PHE* 3.3 46.9 - + + -
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Residues in contact with VAL 95 (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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67A GLY 5.4 0.2 - - - +
68A GLY* 3.6 29.8 - - - +
69A ALA* 3.9 6.3 - - + +
94A PHE* 1.3 80.8 - - - +
96A LYS* 1.3 62.9 + - - +
97A LYS* 4.2 32.0 + - + +
94B PHE* 3.1 7.3 + - - +
95B VAL* 3.3 26.9 - - + +
96B LYS 3.1 21.8 + - - +
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Residues in contact with LYS 96 (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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94A PHE* 4.2 22.2 - - + -
95A VAL* 1.3 75.4 - - - +
97A LYS* 1.3 67.7 + - - +
98A ASP* 3.8 25.7 + - + -
100A LEU* 5.6 4.5 - - - +
103A ASN* 3.0 33.5 + - - +
96B LYS* 3.4 40.7 - - + +
98B ASP* 5.6 2.7 - - + -
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Residues in contact with LYS 97 (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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67A GLY 4.6 13.7 + - - -
68A GLY* 5.7 0.4 - - - -
95A VAL* 4.2 23.6 - - + +
96A LYS* 1.3 73.2 - - - +
98A ASP* 1.3 59.7 + - - +
99A GLN 3.9 1.3 - - - -
100A LEU* 6.3 0.7 - - - -
95B VAL* 6.3 0.2 - - + -
96B LYS 3.0 10.8 + - - +
97B LYS* 4.4 33.7 - - + +
98B ASP* 2.8 30.5 + - - +
99B GLN* 3.2 18.1 + - + +
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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