Contacts of the strand formed by residues 819 - 823 (chain A) in PDB entry 3LZB
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 VAL 819 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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773A CYS* 3.3 2.8 - - - -
774A LEU* 2.6 52.1 + - + +
797A ILE* 3.9 22.9 - - + -
814A LEU* 4.2 15.7 - - + -
815A ALA 3.7 13.5 - - - +
816A ALA* 3.0 10.6 + - - +
817A ARG 3.5 0.2 - - - -
818A ASN* 1.3 81.6 - - - +
820A LEU* 1.3 58.9 + - - +
827A VAL* 3.7 31.0 - - + -
828A LYS 3.6 9.6 - - - +
829A ILE* 4.2 9.2 - - + +
879A THR* 4.7 0.9 - - + -
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Residues in contact with LEU 820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ITI 3.6 53.8 - - + +
751A CYS* 3.8 12.1 - - + -
769A MET* 3.4 35.2 - - + -
772A GLY* 3.6 4.9 - - - +
773A CYS* 4.6 3.8 - - + -
817A ARG 5.0 0.4 - - - +
818A ASN 4.9 1.1 - - - -
819A VAL* 1.3 76.0 - - - +
821A VAL* 1.3 61.0 + - - +
822A LYS 4.0 0.4 - - - -
827A VAL* 3.1 9.4 - - - +
828A LYS* 2.8 37.2 + - + +
830A THR* 3.5 38.6 - - + -
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Residues in contact with VAL 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769A MET* 3.7 14.5 - - - +
771A PHE* 3.3 38.7 - - + +
772A GLY 2.9 15.4 + - - +
773A CYS 3.9 2.9 - - - +
774A LEU* 3.7 39.0 - - + -
777A TYR* 4.2 13.7 - - + -
793A TRP* 5.9 0.4 - - + +
820A LEU* 1.3 76.2 - - - +
822A LYS* 1.3 57.7 + - - +
823A THR 3.1 30.1 - - - +
824A PRO* 3.9 9.4 - - + -
827A VAL* 4.0 8.1 - - + -
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Residues in contact with LYS 822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767A GLN* 2.9 29.1 + - - +
769A MET* 3.8 24.3 - - + -
770A PRO* 3.9 15.3 - - + +
771A PHE* 3.8 10.5 - - - -
820A LEU 4.0 1.8 + - - -
821A VAL* 1.3 74.2 - - - +
823A THR* 1.3 70.8 + - + +
826A HIS* 2.8 39.3 + - + +
828A LYS* 4.0 28.5 - - + +
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Residues in contact with THR 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771A PHE* 4.3 3.8 - - - -
821A VAL* 3.1 12.6 - - - +
822A LYS* 1.3 87.7 - - + +
824A PRO* 1.3 71.7 - - - +
825A GLN* 3.0 33.3 + - - +
826A HIS* 3.0 30.6 + - + +
827A VAL* 4.6 0.2 - - - +
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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