Contacts of the strand formed by residues 19 - 23 (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 ARG 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY 3.4 4.4 + - - +
18B GLY* 1.3 72.5 - - - -
20B VAL* 1.3 60.3 + - - +
43B HIS* 3.6 18.6 - - + +
45B ASP* 2.8 37.1 + - - +
90B VAL* 4.7 10.4 - - - +
92B TYR* 3.8 8.1 + - - -
105B PHE* 5.3 0.2 - - - -
108B GLN* 3.5 53.1 + - - +
109B PHE* 3.3 21.1 - - + -
110B ILE* 3.0 32.1 + - - +
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLY 4.6 0.9 - - - +
19B ARG* 1.3 76.1 - - - +
21B LEU* 1.3 58.8 + - - +
36B LEU* 4.1 7.4 - - + -
41B PHE* 4.3 23.1 - - + -
43B HIS 3.0 14.7 + - - +
44B ILE* 3.3 18.4 - - + -
45B ASP 2.9 23.6 + - - +
109B PHE* 3.5 6.1 - - - -
110B ILE* 4.5 3.8 - - + -
111B LEU* 3.3 41.7 - - + +
113B MET* 3.5 25.1 - - + -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 1.3 73.2 - - - +
22B VAL* 1.3 78.9 + - - +
23B VAL* 4.1 12.3 - - + -
45B ASP* 3.6 24.9 - - + +
46B LEU 4.5 0.4 - - - +
47B ILE* 4.4 13.0 - - + -
92B TYR* 5.4 0.7 - - + -
96B ILE* 4.9 1.1 - - + -
105B PHE* 4.1 14.6 - - + -
106B PHE* 3.8 31.2 - - + -
109B PHE* 3.5 33.8 - - + -
111B LEU 3.0 11.0 + - - +
112B VAL* 3.4 12.3 - - + -
113B MET* 2.9 29.1 + - - +
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 1.3 80.5 - - - +
23B VAL* 1.3 62.8 + - - +
24B GLY 3.6 19.3 - - - +
29B GLY* 4.6 9.6 - - - +
32B LEU* 4.0 22.4 - - + -
33B LEU* 4.9 4.7 - - + -
36B LEU* 3.6 30.3 - - + -
44B ILE* 4.4 8.1 - - + -
45B ASP 2.8 14.8 + - - +
46B LEU* 3.4 15.6 - - + +
47B ILE* 3.1 25.3 + - - +
113B MET* 3.5 11.7 - - + +
115B ALA* 5.0 1.3 - - + -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.1 24.2 - - + -
22B VAL* 1.3 72.5 - - - +
24B GLY* 1.3 60.8 + - - +
47B ILE* 3.7 18.8 - - + -
96B ILE* 3.8 27.4 - - + -
106B PHE* 5.2 0.4 - - + -
112B VAL* 4.3 7.6 - - + -
113B MET 3.1 8.6 + - - +
114B ASN* 3.6 20.2 - - - +
115B ALA* 2.9 32.9 + - - +
116B LEU* 3.5 24.3 - - + +
125B VAL* 4.4 5.2 - - + -
802B ATP 4.5 2.7 - - + -
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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
------------------------------------------------------------
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