Contacts of the strand formed by residues 58 - 65 (chain B) in PDB entry 2NUO
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 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 4.9 2.5 - - + -
21B ILE* 3.9 26.2 - - + -
52B PHE* 3.6 21.2 - - + -
57B TYR* 1.3 73.8 - - - +
59B SER* 1.3 58.7 + - - +
60B ASN 3.6 22.4 - - - +
61B MET* 4.1 11.2 - - + -
74B PHE* 3.8 27.8 - - + -
75B GLU 3.7 4.9 - - - +
76B THR* 4.3 1.1 - - - +
98B VAL* 3.4 8.1 - - + +
99B LYS* 3.5 1.7 - - - -
100B VAL* 3.1 59.2 + - + +
103B ILE* 4.4 6.5 - - + -
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 3.3 3.7 + - - -
58B ILE* 1.3 72.7 - - - +
60B ASN* 1.3 74.8 + - - +
75B GLU 3.0 4.5 + - - -
76B THR 3.1 21.3 + - - -
77B ASN* 3.7 19.9 - - - -
97B ASN* 3.1 13.7 + - - -
98B VAL* 3.0 41.8 + - - +
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Residues in contact with ASN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 3.6 2.4 - - - +
59B SER* 1.3 104.1 + - - +
61B MET* 1.3 61.3 + - - +
74B PHE* 3.3 5.7 - - - +
75B GLU* 2.9 53.6 + - + +
81B ARG* 4.9 6.3 - - - +
94B THR* 5.7 2.7 - - + -
95B LEU* 3.3 8.7 - - - +
96B SER* 3.4 9.8 + - - +
97B ASN* 3.2 16.0 + - - +
98B VAL* 4.8 0.7 - - - -
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Residues in contact with MET 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ILE* 4.1 9.9 - - + -
60B ASN* 1.3 76.7 - - - +
62B THR* 1.3 61.7 + - - +
63B ILE* 4.1 20.6 - - + -
72B ILE* 3.9 23.8 - - + -
73B SER 3.3 15.3 - - - +
74B PHE* 4.0 18.2 - - + +
81B ARG* 4.8 1.6 - - - +
93B ASN 4.0 0.5 - - - +
94B THR* 3.3 4.6 - - - +
95B LEU* 2.8 55.7 + - + +
100B VAL* 3.8 28.7 - - + -
103B ILE* 5.3 2.9 - - + -
116B ILE* 4.2 18.4 - - + -
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Residues in contact with THR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B MET* 1.3 71.8 - - - +
63B ILE* 1.3 67.2 + - - +
64B ARG* 5.0 5.4 - - + +
71B ASN* 4.0 1.2 - - - +
72B ILE* 3.5 3.3 - - - -
73B SER* 2.9 44.5 + - - +
81B ARG* 4.5 5.8 + - - +
92B ALA* 4.3 19.3 - - + -
93B ASN 3.5 6.3 - - - +
94B THR* 2.9 25.8 + - - +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.8 59.3 - - + -
61B MET* 4.1 19.3 - - + -
62B THR* 1.3 77.7 - - - +
64B ARG* 1.3 75.1 + - - +
65B SER* 4.3 0.8 + - - -
69B ILE* 4.1 14.8 - - + -
71B ASN 3.4 7.2 - - - +
72B ILE* 4.0 15.0 - - + -
91B SER 3.6 1.6 - - - +
92B ALA* 3.5 0.6 - - - -
93B ASN* 2.9 34.3 + - - +
95B LEU* 6.2 0.2 - - + -
114B LEU* 4.1 16.6 - - + -
116B ILE* 4.3 8.7 - - + -
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Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B THR* 4.3 6.3 - - + -
63B ILE* 1.3 76.7 - - - +
65B SER* 1.3 65.3 + - - +
69B ILE 3.7 0.7 - - - -
70B ASP* 2.8 24.2 + - + -
71B ASN* 3.0 30.7 + - + +
87B GLY 3.8 16.6 - - - -
88B SER* 3.3 20.5 + - - +
89B GLY 2.9 23.3 + - - +
90B GLY 3.0 23.4 + - - -
91B SER* 3.2 9.3 - - - +
92B ALA* 3.8 26.1 - - + +
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Residues in contact with SER 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 4.1 8.7 - - - +
8A GLY* 3.4 26.0 + - - -
63B ILE* 4.3 3.9 + - - +
64B ARG* 1.3 78.7 - - - +
66B GLY* 1.3 59.9 + - - +
68B TYR 3.2 13.2 - - - -
69B ILE* 3.9 10.5 - - - -
70B ASP* 3.3 8.0 + - - -
90B GLY* 3.3 1.3 - - - -
91B SER* 2.9 32.7 + - - +
93B ASN* 4.9 5.9 + - - -
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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