Contacts of the strand formed by residues 820 - 823 (chain B) in PDB entry 1L8A
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 TYR 820 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813A THR* 4.9 9.7 + - - +
729B LEU* 4.6 10.1 - - + -
761B PHE* 3.4 13.5 - - - -
797B ALA* 3.3 22.4 - - + -
799B ALA* 3.6 22.5 - - + +
808B ALA 2.7 30.9 + - - -
809B GLU* 4.2 4.0 - - + +
811B VAL* 3.4 14.5 - - + +
812B ARG* 3.2 54.4 - - + +
815B VAL* 4.0 25.4 - - + -
818B ASP 4.2 1.4 + - - -
819B ASP* 1.3 78.7 + - - +
821B ARG* 1.3 61.5 + - - +
822B VAL* 3.5 17.8 + - + +
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Residues in contact with ARG 821 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A GLU 5.4 0.9 + - - -
775A ASN* 4.8 5.3 + - - +
776A MET* 3.4 43.0 - - - +
797B ALA 2.8 10.0 + - - +
798B VAL* 3.1 11.7 - - + +
799B ALA 2.8 25.6 + - - +
819B ASP* 4.1 6.7 - - - +
820B TYR* 1.3 72.2 - - - +
822B VAL* 1.3 62.2 + - - +
823B LEU* 6.1 1.3 - - + -
850B VAL 4.0 0.4 + - - -
851B ALA* 3.1 45.7 + - + +
854B GLY* 3.8 19.6 + - - -
855B GLU* 3.3 26.9 - - + +
858B LYS* 3.6 27.9 - - - +
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Residues in contact with VAL 822 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B ALA* 3.4 4.7 - - + +
805B LYS* 3.3 47.4 - - + +
808B ALA* 3.6 13.2 - - + -
809B GLU* 3.8 26.6 - - + +
820B TYR* 3.5 44.3 + - + +
821B ARG* 1.3 76.2 - - - +
823B LEU* 1.3 80.6 - - - +
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Residues in contact with LEU 823 (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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776A MET* 4.0 29.2 - - + -
798B VAL* 4.3 10.1 - - + -
799B ALA 2.7 13.3 + - - +
800B SER* 3.6 25.5 - - - +
801B THR* 3.8 4.7 + - - -
803B TYR 4.6 0.7 - - - +
805B LYS* 3.8 7.7 - - - +
808B ALA* 5.2 0.5 - - - +
821B ARG* 5.9 1.6 - - + -
822B VAL* 1.3 92.1 - - - +
824B GLY* 1.3 59.3 + - - +
842B GLU* 3.6 24.9 - - + +
843B VAL* 4.0 2.2 - - + -
847B TYR* 3.7 6.7 - - + +
848B VAL* 3.7 46.9 - - + +
851B ALA* 4.5 2.2 - - + -
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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