Contacts of the helix formed by residues 805 - 810 (chain A) 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 LYS 805 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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803A TYR 3.5 0.6 + - - -
804A MET* 1.3 71.5 - - - +
806A LEU* 1.3 58.9 + - - +
807A PHE 3.0 0.9 + - - -
808A ALA 3.0 4.0 + - - +
809A GLU* 2.8 42.7 + - - +
822A VAL* 3.2 32.1 - - + +
823A LEU* 3.9 4.3 - - - +
824A GLY* 3.4 29.8 - - - +
826A ASP* 2.6 27.9 + - - +
841A PHE 5.9 0.2 - - - -
842A GLU* 5.2 2.8 + - - -
882A ASN* 4.7 10.3 + - - +
883A PRO* 5.9 1.0 - - - +
769B GLN* 3.5 28.1 + - + +
773B ARG* 4.3 30.3 - - - +
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Residues in contact with LEU 806 (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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647A ILE* 4.1 15.2 - - + +
804A MET* 3.0 11.9 + - + +
805A LYS* 1.3 76.9 - - - +
807A PHE* 1.3 63.7 + - - +
809A GLU* 3.6 14.4 - - + +
810A GLN* 2.9 26.0 + - - +
826A ASP* 5.0 0.6 + - - -
650B LEU* 3.6 38.8 - - + -
769B GLN* 4.2 9.1 - - - +
806B LEU* 3.8 37.5 - - + -
810B GLN* 3.7 32.3 - - + +
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Residues in contact with PHE 807 (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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646A HIS* 3.5 42.0 - + + -
647A ILE* 3.7 16.5 - - + +
650A LEU* 5.2 0.2 - - + -
659A ASP* 4.2 11.0 - - + -
731A SER* 3.8 15.5 - - - -
760A SER* 5.3 2.0 - - - -
761A PHE* 3.1 38.9 - + + +
762A THR* 3.7 18.2 - - - -
801A THR* 3.4 25.6 - - + -
803A TYR* 3.8 22.2 - + + -
804A MET 3.0 15.5 + - - +
806A LEU* 1.3 77.7 - - - +
808A ALA* 1.3 56.1 + - - +
810A GLN* 2.8 36.8 + - - +
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Residues in contact with ALA 808 (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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761A PHE* 3.6 33.4 - - + -
799A ALA* 4.0 7.0 - - + -
801A THR* 4.6 9.8 - - - +
804A MET 4.4 0.2 + - - -
805A LYS 3.0 2.8 + - - -
807A PHE* 1.3 76.2 - - - +
809A GLU* 1.3 65.0 + - - +
810A GLN 3.1 2.7 - - - -
811A VAL* 3.3 12.4 - - - +
820A TYR* 2.7 25.3 + - - +
822A VAL* 3.7 21.8 - - + -
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Residues in contact with GLU 809 (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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805A LYS* 2.8 24.6 + - - +
806A LEU* 3.2 14.5 + - + +
808A ALA* 1.3 79.3 - - - +
810A GLN* 1.3 60.8 + - - +
811A VAL 3.1 0.2 - - - -
812A ARG* 3.0 21.8 + - - +
820A TYR* 4.3 4.3 - - + +
822A VAL* 3.7 24.3 - - + +
769B GLN* 3.0 28.7 + - - +
809B GLU 5.4 3.8 - - - +
810B GLN* 4.0 11.4 - - - +
813B THR* 4.0 16.8 + - - +
814B TYR* 3.0 32.7 + - - -
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Residues in contact with GLN 810 (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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650A LEU* 3.9 18.3 - - - +
761A PHE* 3.5 12.4 - - - +
762A THR* 3.1 37.1 + - - +
765A ALA* 3.2 27.4 - - + +
806A LEU* 2.9 11.3 + - - +
807A PHE* 2.8 33.5 + - - +
809A GLU* 1.3 76.7 - - - +
811A VAL* 1.3 61.6 + - + +
812A ARG 3.4 0.4 + - - -
813A THR* 5.1 0.9 + - - -
814A TYR* 3.9 10.2 - - - -
806B LEU* 3.7 29.2 - - + +
809B GLU* 4.0 10.8 - - - +
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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