Contacts of the strand formed by residues 88 - 93 (chain B) in PDB entry 1YRP
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 ASP 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 5.8 2.8 - - - +
43B PHE* 4.3 29.0 - - + +
44B ILE 3.4 6.7 + - - +
45B LYS* 3.3 39.3 + - - +
46B LYS* 4.3 1.6 - - - -
84B GLU* 3.6 1.6 - - - +
85B ASN* 2.7 47.3 + - - +
87B THR* 1.3 95.6 + - - +
89B VAL* 1.3 64.9 + - - +
90B VAL* 4.3 5.0 + - + +
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Residues in contact with VAL 89 (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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4B PHE* 3.8 25.1 - - + -
42B LYS 3.5 1.7 - - - +
43B PHE* 3.7 1.0 - - - -
44B ILE* 2.8 40.4 + - + +
46B LYS* 4.1 16.8 - - + +
58B ARG* 4.7 2.0 - - + +
61B ILE* 3.9 24.0 - - + -
82B ILE* 5.4 0.2 - - + -
83B PHE 3.5 12.3 - - - +
84B GLU* 3.8 30.1 - - + +
88B ASP* 1.3 73.0 - - - +
90B VAL* 1.3 62.7 + - - +
91B LEU* 4.2 18.2 - - + -
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Residues in contact with VAL 90 (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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9B VAL* 4.0 29.2 - - + -
41B ALA* 4.2 15.7 - - + -
42B LYS 3.4 8.7 - - - +
43B PHE* 3.9 39.5 - - + -
82B ILE* 3.6 1.4 - - - -
83B PHE* 3.0 49.7 + - + +
84B GLU* 5.1 1.1 - - - +
85B ASN* 5.4 6.3 - - - +
88B ASP* 4.6 8.1 - - + +
89B VAL* 1.3 77.0 - - - +
91B LEU* 1.3 65.7 + - - +
92B ILE* 3.5 4.1 + - + -
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Residues in contact with LEU 91 (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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40B ALA 3.6 0.2 - - - +
41B ALA* 3.4 1.0 - - - -
42B LYS* 2.8 50.1 + - + +
44B ILE* 3.6 21.1 - - + -
61B ILE* 5.4 1.6 - - + -
64B GLU* 3.8 27.6 - - + +
65B VAL* 3.7 18.6 - - + -
68B LEU* 3.9 19.7 - - + -
79B LEU* 3.7 10.8 - - + -
81B ASP 3.9 2.7 - - - -
82B ILE* 3.4 26.2 - - + -
89B VAL* 4.2 11.9 - - + -
90B VAL* 1.3 70.5 - - - +
92B ILE* 1.3 63.4 + - - +
93B LEU* 3.5 7.8 + - + +
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Residues in contact with ILE 92 (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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9B VAL* 4.1 10.8 - - + -
13B TYR* 3.8 58.6 - - + +
30B CYS* 4.1 5.2 - - - -
39B TYR* 3.9 21.5 - - + -
40B ALA 3.8 0.9 - - - -
41B ALA* 3.8 25.1 - - + -
79B LEU* 3.6 5.2 - - - +
80B HIS* 3.1 28.7 + - + -
81B ASP* 3.0 21.0 + - + +
83B PHE* 4.0 17.7 - - + -
90B VAL* 3.5 2.4 + - + +
91B LEU* 1.3 70.5 - - - +
93B LEU* 1.3 59.9 + - - +
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Residues in contact with LEU 93 (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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27B VAL* 6.2 1.6 - - + -
39B TYR* 3.4 14.7 - - - -
40B ALA* 2.7 41.0 + - + +
42B LYS* 3.7 38.8 - - + +
64B GLU* 5.9 0.2 - - - +
68B LEU* 4.2 18.2 - - + -
77B ILE* 4.4 17.0 - - + -
78B THR 3.6 13.0 - - - +
79B LEU* 3.7 24.5 - - + -
80B HIS 5.3 1.1 - - - -
91B LEU* 3.9 7.6 - - + +
92B ILE* 1.3 75.6 - - - +
94B GLU* 1.3 66.2 + - - +
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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