Contacts of the strand formed by residues 88 - 97 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C SER 3.2 2.9 + - - +
88C ILE* 3.4 33.7 - - + -
89C ALA* 3.0 20.5 + - - +
90C ALA 4.9 1.8 - - - +
91C ALA* 4.0 19.1 - - + -
94C PHE* 4.1 7.6 - - + -
82D VAL* 5.4 1.5 - - - +
86D GLY 4.0 9.9 - - - +
87D SER* 1.3 84.4 + - - +
89D ALA* 1.3 58.5 + - - +
91D ALA* 4.2 9.6 - - + -
94D PHE* 4.0 31.2 - - + -
86E GLY 6.0 0.4 - - - +
87E SER* 5.8 0.2 - - - -
88E ILE* 3.4 34.1 - - + +
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Residues in contact with ALA 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA* 3.4 10.9 - - - +
90C ALA* 2.8 32.2 + - - +
79D GLN* 3.4 9.2 + - - +
82D VAL* 4.2 23.4 - - + +
88D ILE* 1.3 72.3 - - - +
90D ALA* 1.3 62.1 + - - +
79E GLN* 3.1 28.0 - - - +
82E VAL* 5.7 0.2 - - + -
87E SER* 5.3 0.4 + - - -
88E ILE 3.0 7.5 + - - +
89E ALA* 3.4 11.4 - - - +
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Residues in contact with ALA 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ALA* 3.3 4.9 - - - -
77D VAL* 4.0 18.4 - - + -
89D ALA* 1.3 76.4 - - + +
91D ALA* 1.3 62.3 + - - +
92D THR* 5.7 1.8 - - + -
77E VAL* 3.8 30.5 - - + -
79E GLN* 4.7 2.0 - - - +
88E ILE* 4.9 1.6 - - - +
89E ALA 2.8 19.7 + - - +
90E ALA* 3.3 2.1 - - - -
91E ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ALA 3.1 7.7 + - - +
91C ALA* 3.3 4.5 - - - +
92C THR* 3.1 24.2 + - - +
88D ILE* 4.2 18.6 - - + -
90D ALA* 1.3 74.8 - - - +
92D THR* 1.3 63.5 + - - +
93D GLY 3.5 2.0 + - - -
94D PHE* 4.3 13.3 + - + -
88E ILE* 4.0 23.8 - - + -
91E ALA* 3.3 10.5 - - + +
94E PHE* 5.0 3.1 - - + -
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Residues in contact with THR 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C THR* 3.2 13.2 - - + +
69D ALA 5.9 0.2 - - - -
71D VAL* 3.6 16.1 - - + +
75D THR* 4.7 16.4 - - + -
90D ALA* 5.7 1.1 - - + -
91D ALA* 1.3 72.1 - - - +
93D GLY* 1.3 61.0 + - - +
71E VAL* 3.0 26.1 - - + +
75E THR* 4.1 31.9 - - + +
91E ALA 3.1 9.2 + - - +
92E THR* 3.2 5.8 - - + -
93E GLY* 2.7 27.7 + - - -
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Residues in contact with GLY 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ALA 5.2 0.2 - - - -
92C THR* 2.7 25.4 + - - -
93C GLY* 3.8 1.3 - - - -
69D ALA* 3.6 26.7 - - - +
71D VAL* 3.8 8.1 - - - -
91D ALA 3.5 2.2 + - - -
92D THR* 1.3 69.4 - - - +
94D PHE* 1.3 57.7 + - - +
93E GLY* 3.7 1.1 - - - -
94E PHE* 2.8 35.6 + - - +
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Residues in contact with PHE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ALA* 5.1 0.2 - - - +
91C ALA* 5.0 3.6 - - + -
93C GLY 2.8 23.1 + - - +
94C PHE* 3.3 44.8 - + + -
95C VAL* 3.1 18.2 + - - +
69D ALA* 4.2 0.9 - - - +
88D ILE* 4.0 24.9 - - + -
91D ALA* 4.3 11.9 - - + -
93D GLY* 1.3 73.1 - - - +
95D VAL* 1.3 65.1 + - - +
96D LYS* 4.2 27.6 - - + -
88E ILE* 4.1 12.1 - - + -
94E PHE* 3.3 48.2 - + + -
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C GLY* 3.9 15.0 - - - -
95C VAL* 3.3 27.6 - - + +
97C LYS* 6.4 1.1 - - + -
67D GLY 5.4 0.4 - - - +
68D GLY* 3.6 24.7 - - - +
69D ALA* 3.8 6.1 - - + +
94D PHE* 1.3 79.5 - - - +
96D LYS* 1.3 62.9 + - - +
97D LYS* 4.4 20.4 - - + -
94E PHE* 3.1 6.4 + - - +
95E VAL* 3.3 29.6 - - + +
96E LYS 3.1 21.8 + - - +
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Residues in contact with LYS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C VAL 3.1 7.6 + - - +
96C LYS* 3.4 33.3 - - + +
97C LYS 3.0 24.3 + - - -
99C GLN* 6.3 0.2 - - - +
94D PHE* 4.2 21.4 - - + -
95D VAL* 1.3 75.5 - - - +
97D LYS* 1.3 65.4 + - - +
98D ASP* 3.7 25.5 + - - +
96E LYS* 3.4 40.5 - - + +
98E ASP* 6.6 0.2 - - - -
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Residues in contact with LYS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C LYS* 4.2 22.4 - - + +
67D GLY 5.9 2.7 - - - +
95D VAL* 4.2 16.8 - - + -
96D LYS* 1.3 74.4 - - - +
98D ASP* 1.3 63.6 + - - +
99D GLN* 3.5 29.1 - - + +
95E VAL* 6.1 3.6 - - + -
96E LYS 3.0 10.7 + - - +
97E LYS* 4.0 42.9 - - + +
98E ASP* 3.3 24.6 + - - +
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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