Contacts of the strand formed by residues 43 - 48 (chain B) in PDB entry 1Y8Q
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 HIS 43 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA 3.1 28.4 + - - -
17B GLY* 3.6 19.5 + - - -
18B GLY 3.7 12.7 + - - +
19B ARG* 3.6 18.7 - - + -
20B VAL* 3.0 24.4 + - - +
41B PHE* 5.4 1.2 - - - +
42B SER* 1.3 80.7 - - - +
44B ILE* 1.3 64.5 + - - +
88B ASN* 2.6 39.8 + - + +
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Residues in contact with ILE 44 (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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20B VAL* 3.3 20.6 - - + +
22B VAL* 4.4 7.4 - - + -
33B LEU* 3.8 26.9 - - + -
36B LEU* 3.9 26.7 - - + -
37B VAL* 3.9 23.6 - - + -
41B PHE* 4.2 15.5 - - + +
42B SER 3.8 2.0 + - - +
43B HIS* 1.3 83.0 - - - +
45B ASP* 1.3 76.6 + - - +
46B LEU 4.7 0.2 - - - +
87B ALA* 6.2 0.4 - - + -
88B ASN 3.3 7.2 + - - +
89B ILE* 3.2 18.9 - - + +
90B VAL* 3.0 23.4 + - - +
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Residues in contact with ASP 45 (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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19B ARG* 2.8 36.8 + - - +
20B VAL 2.9 6.9 + - - -
21B LEU* 3.6 11.8 - - + -
22B VAL* 2.8 27.2 + - - -
44B ILE* 1.3 82.9 - - - +
46B LEU* 1.3 60.4 + - - +
90B VAL* 3.4 13.7 - - - +
92B TYR* 2.7 35.9 + - + -
109B PHE* 3.3 27.5 - - + -
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Residues in contact with LEU 46 (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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22B VAL* 3.4 18.6 - - + +
24B GLY 3.7 20.0 - - - +
25B ALA* 3.9 12.6 - - + -
29B GLY* 5.8 0.2 - - - -
33B LEU* 3.5 41.3 - - + -
44B ILE 4.2 0.2 - - - -
45B ASP* 1.3 75.3 - - - +
47B ILE* 1.3 71.3 - - - +
73B ALA* 3.8 21.8 - - - +
76B ALA* 3.7 19.3 - - + -
77B LYS* 4.8 2.7 - - - +
89B ILE* 4.8 7.2 - - + -
90B VAL 3.0 9.1 + - - +
91B ALA* 3.4 4.6 - - + -
92B TYR* 2.9 28.5 + - - +
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Residues in contact with ILE 47 (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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21B LEU* 4.4 7.9 - - + -
22B VAL 3.1 4.6 + - - +
23B VAL* 3.7 35.4 - - + -
24B GLY* 2.8 33.3 + - - -
46B LEU* 1.3 76.7 - - - +
48B ASP* 1.3 64.0 + - - +
73B ALA* 4.7 0.4 - - - -
92B TYR* 3.4 17.9 - - + +
94B ASP 3.4 13.7 - - - +
96B ILE* 3.7 31.2 - - + +
101B TYR* 3.6 41.5 - - + +
105B PHE* 5.9 1.3 - - + -
802B ATP 4.2 1.4 + - + -
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Residues in contact with ASP 48 (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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25B ALA* 2.7 37.9 + - + +
47B ILE* 1.3 76.1 - - - +
49B LEU* 1.3 59.4 + - - +
50B ASP* 2.8 32.8 + - - +
72B LYS* 3.6 11.4 - - + +
73B ALA* 4.2 13.9 + - + +
92B TYR 3.1 8.9 + - - +
93B HIS* 3.2 7.6 - - - -
94B ASP 2.8 21.1 + - - -
802B ATP 2.7 41.8 + - - -
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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