Contacts of the strand formed by residues 818 - 821 (chain D) in PDB entry 4X52
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 818 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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787D TYR* 3.7 16.6 - - + +
801D ASN* 5.9 0.4 - - - +
802D PHE* 3.7 37.5 - - + +
803D ASP 4.1 3.1 - - - +
804D SER* 3.7 27.4 - - - +
806D LEU 6.1 1.1 - - - -
817D GLY* 1.3 70.6 - - - -
819D TYR* 1.3 63.1 + - - +
820D PHE* 3.5 36.1 - - + -
877D PHE 3.2 6.6 - - - +
878D VAL* 3.3 1.4 - - - -
879D ILE* 2.8 45.0 + - + +
880D PHE 5.9 0.2 - - - -
881D GLN 5.2 1.1 - - - +
882D LYS* 4.8 20.2 - - + +
885D VAL* 5.2 2.9 - - + -
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Residues in contact with TYR 819 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786D PHE 4.2 1.6 - - - +
787D TYR* 3.3 26.7 - - + -
808D GLU* 3.8 35.3 - - + +
810D ASN* 4.4 11.9 - - + -
812D ASN* 3.1 20.2 - - - -
814D TYR* 2.8 47.4 + + - -
815D GLY 2.8 27.7 + - - -
817D GLY 3.3 16.8 - - - -
818D ILE* 1.3 75.3 - - - +
820D PHE* 1.3 60.9 + - - +
821D ALA 4.3 0.4 + - - -
827D SER* 5.1 2.6 + - - -
876D VAL* 3.8 22.9 - - + -
877D PHE 3.5 3.4 - - - -
878D VAL* 3.7 17.7 - - + -
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Residues in contact with PHE 820 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785D LEU* 3.7 24.0 - - + -
786D PHE 3.3 11.4 - - - -
787D TYR* 4.0 13.5 - + + -
802D PHE* 3.6 29.6 - + + -
818D ILE* 3.5 39.0 - - + -
819D TYR* 1.3 73.0 - - - +
821D ALA* 1.3 61.6 + - - +
843D ALA* 3.8 17.7 - - + -
845D VAL* 3.9 6.3 - - + -
876D VAL* 3.4 3.9 - - - +
877D PHE* 2.8 40.6 + - + +
879D ILE* 3.8 16.6 - - + -
885D VAL* 3.5 37.0 - - + -
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Residues in contact with ALA 821 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785D LEU* 3.6 7.8 - - - -
786D PHE* 2.8 31.8 + - + +
819D TYR 4.3 0.6 - - - -
820D PHE* 1.3 72.4 - - - +
822D LYS* 1.3 63.4 + - - +
823D ASP 3.4 20.9 - - - +
826D TYR* 3.8 17.5 - - + -
827D SER* 3.7 26.4 + - - +
875D SER 3.4 6.5 - - - +
876D VAL* 4.4 2.0 - - + +
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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