Contacts of the strand formed by residues 88 - 98 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87H SER 3.2 2.9 + - - +
88H ILE* 3.4 33.7 - - + -
89H ALA* 3.0 20.3 + - - +
90H ALA 4.9 2.2 - - - +
91H ALA* 4.0 19.7 - - + -
94H PHE* 4.1 7.9 - - + -
82I VAL* 5.4 0.8 - - - +
86I GLY 4.0 9.9 - - - +
87I SER* 1.3 84.9 + - - +
89I ALA* 1.3 57.8 + - - +
91I ALA* 4.2 9.4 - - + -
94I PHE* 4.0 31.4 - - + -
86J GLY 6.0 0.2 - - - +
88J ILE* 3.4 33.4 - - + +
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Residues in contact with ALA 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H ALA* 3.4 10.3 - - - +
90H ALA* 2.8 32.8 + - - +
79I GLN* 3.4 10.8 + - - +
82I VAL* 4.2 22.7 - - + +
87I SER 4.3 0.2 - - - -
88I ILE* 1.3 72.8 - - - +
90I ALA* 1.3 61.5 - - - +
79J GLN* 3.1 28.0 - - - +
82J VAL* 5.7 0.4 - - + -
87J SER* 5.3 0.4 + - - -
88J ILE 3.0 7.3 + - - -
89J ALA* 3.4 11.4 - - - +
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Residues in contact with ALA 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H ALA* 3.3 5.2 - - - -
77I VAL* 4.0 17.9 - - + -
89I ALA* 1.3 76.7 - - + +
91I ALA* 1.3 62.3 + - - +
92I THR* 5.7 1.8 - - + -
77J VAL* 3.8 30.5 - - + -
79J GLN* 4.7 1.6 - - - +
88J ILE* 4.9 1.8 - - - +
89J ALA 2.8 20.7 + - - +
90J ALA* 4.5 1.6 - - - -
91J ALA* 3.1 22.9 + - - +
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Residues in contact with ALA 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H ALA 3.1 7.5 + - - +
91H ALA* 3.3 5.0 - - - +
92H THR* 3.1 23.4 + - - +
88I ILE* 4.2 18.8 - - + -
90I ALA* 1.3 75.6 - - - +
92I THR* 1.3 63.5 + - - +
93I GLY 3.5 2.0 + - - -
94I PHE* 4.3 13.0 + - + -
88J ILE* 4.0 23.8 - - + -
91J ALA* 3.3 9.6 - - + +
94J PHE* 5.0 3.1 - - + -
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Residues in contact with THR 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H THR* 3.2 13.9 - - + +
69I ALA 5.9 0.2 - - - -
71I VAL* 3.6 16.1 - - + +
75I THR* 4.7 16.8 - - + -
90I ALA 5.7 0.9 - - - -
91I ALA* 1.3 71.1 - - - +
93I GLY* 1.3 60.4 + - - +
71J VAL* 3.0 25.0 - - + +
75J THR* 4.1 31.4 - - + +
91J ALA 3.1 9.6 + - - +
92J THR* 3.2 5.8 - - + -
93J GLY* 2.7 28.8 + - - -
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Residues in contact with GLY 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H ALA 5.2 0.9 - - - -
92H THR* 2.7 24.7 + - - -
93H GLY* 3.8 1.1 - - - -
69I ALA* 3.6 25.9 - - - +
71I VAL* 3.8 7.9 - - - -
91I ALA 3.5 1.8 + - - -
92I THR* 1.3 70.7 - - - +
94I PHE* 1.3 57.8 + - - +
93J GLY* 3.7 1.3 - - - -
94J PHE* 2.8 35.0 + - - +
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Residues in contact with PHE 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H ALA* 5.0 3.8 - - + -
92H THR 4.0 0.2 + - - -
93H GLY 2.8 22.0 + - - +
94H PHE* 3.3 43.7 - + + -
95H VAL* 3.1 18.4 + - - +
69I ALA* 4.2 1.1 - - - +
88I ILE* 4.0 24.5 - - + -
91I ALA* 4.3 10.8 - - + -
93I GLY* 1.3 71.9 - - - +
95I VAL* 1.3 65.6 + - - +
96I LYS* 4.2 26.7 - - + -
88J ILE* 4.1 11.9 - - + -
94J PHE* 3.3 47.1 - + + -
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Residues in contact with VAL 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H GLY* 3.9 14.1 - - - -
95H VAL* 3.3 27.6 - - + +
97H LYS* 6.6 0.2 - - + -
67I GLY 5.4 0.4 - - - +
68I GLY* 3.6 24.7 - - - +
69I ALA* 3.9 5.8 - - + +
94I PHE* 1.3 78.8 - - - +
96I LYS* 1.3 67.3 + - - +
97I LYS* 5.0 4.9 - - + +
94J PHE* 3.1 6.2 + - - +
95J VAL* 3.3 28.3 - - + +
96J LYS 3.1 21.8 + - - +
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Residues in contact with LYS 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H VAL 3.1 7.8 + - - +
96H LYS* 3.4 35.2 - - + +
97H LYS* 3.0 25.9 + - - +
98H ASP* 5.5 0.2 - - - +
94I PHE* 4.2 21.2 - - + -
95I VAL* 1.3 75.7 - - - +
97I LYS* 1.3 66.1 + - - +
98I ASP* 5.1 15.0 - - + +
96J LYS* 3.4 40.4 - - + +
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Residues in contact with LYS 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H LYS* 3.5 14.1 - - + +
95I VAL* 5.0 5.6 - - + +
96I LYS* 1.3 76.4 - - - +
98I ASP* 1.3 63.0 + - - +
99I GLN* 4.2 28.7 - - + +
100I LEU 4.2 11.5 + - - +
101I GLY* 5.1 0.8 - - - -
102I LYS* 6.3 0.6 - - - +
96J LYS 3.0 11.1 + - - +
97J LYS* 3.5 24.8 - - + +
98J ASP* 3.1 45.9 + - - +
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Residues in contact with ASP 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H LYS 2.8 10.0 + - - -
98H ASP* 3.3 19.7 - - - +
99H GLN 3.2 14.9 + - - -
100H LEU* 3.1 43.3 - - - +
96I LYS* 5.1 15.7 - - + -
97I LYS* 1.3 73.7 - - - +
99I GLN* 1.3 59.4 + - - +
98J ASP* 3.9 16.6 - - - +
100J LEU* 5.4 0.3 - - - +
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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