Contacts of the helix formed by residues 839 - 843 (chain A) in PDB entry 4AY6
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 GLN 839 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A ILE* 5.8 3.1 - - - +
837A PHE 3.9 0.4 + - - -
838A ASN* 1.3 84.4 - - - +
840A LEU* 1.3 65.4 + - - +
841A TYR* 3.3 38.0 + - + -
842A LYS* 3.5 12.5 + - + +
843A ILE* 4.9 2.1 + - - +
868A PHE* 3.7 46.2 - - + +
1200A 12V 3.1 30.6 + - - +
1394E TYR* 3.6 36.7 - - - +
1395E DNP 4.0 4.8 + - - -
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Residues in contact with LEU 840 (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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465A ILE 4.5 3.6 - - - +
467A CYS* 3.4 28.0 - - - -
838A ASN 4.5 7.0 - - - +
839A GLN* 1.3 68.7 - - - +
841A TYR* 1.3 65.7 + - - +
842A LYS 3.0 3.6 + - - -
843A ILE* 3.0 33.4 + - + +
865A LEU* 4.8 7.4 - - + -
866A LEU 3.4 28.9 - - - +
867A ARG* 4.9 0.2 - - - -
868A PHE* 3.1 16.9 + - + +
869A PRO* 3.6 25.4 - - + +
872A GLY* 3.9 23.3 - - - -
873A GLU 4.4 1.1 - - - +
876A ILE* 5.0 5.8 - - + -
892A PHE* 4.6 13.0 - - + -
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Residues in contact with TYR 841 (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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461A HIS* 5.2 5.8 - - - +
464A GLN* 3.0 50.2 + - + +
465A ILE* 3.8 28.2 + - + +
498A HIS* 4.9 8.0 + + - -
499A HIS* 6.3 0.9 - + - -
501A MET* 5.8 2.2 - - - -
502A LEU* 3.8 34.0 - - + +
839A GLN* 3.5 49.2 + - + -
840A LEU* 1.3 78.1 - - - +
842A LYS* 1.3 78.7 + - + +
843A ILE 3.1 0.7 + - - +
916A LEU* 4.4 2.6 - - - +
917A CYS* 5.1 2.5 - - - -
1200A 12V 3.6 28.5 + - + +
1395E DNP 5.4 1.7 + - - -
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Residues in contact with LYS 842 (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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838A ASN* 2.9 35.1 + - + +
839A GLN 3.5 11.2 + - - +
840A LEU 3.0 1.4 - - - -
841A TYR* 1.3 110.4 - - + +
843A ILE* 1.3 57.8 + - - +
844A ASP 3.9 0.3 + - - -
847A THR* 4.6 1.0 + - - -
914A THR* 3.5 28.6 - - + +
916A LEU* 3.7 24.4 - - - +
917A CYS* 3.3 28.5 - - + +
918A ASN 3.2 16.1 + - - +
1200A 12V 2.5 46.4 + - - -
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Residues in contact with ILE 843 (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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464A GLN* 3.5 9.6 + - - -
467A CYS* 4.8 0.3 - - - -
469A TRP* 3.2 35.0 + - + -
836A ASN* 5.1 4.5 - - - +
838A ASN 5.9 0.2 - - - +
839A GLN 5.2 1.6 - - - +
840A LEU* 3.0 40.3 + - + +
841A TYR 3.5 9.3 - - - +
842A LYS* 1.3 78.0 - - + +
844A ASP* 1.3 68.0 + - - +
847A THR* 4.1 12.1 - - + -
848A LEU* 4.2 9.4 - - + +
851A TRP* 3.8 22.9 - - + -
865A LEU* 4.8 10.5 - - + -
876A ILE* 4.6 12.1 - - + -
914A THR* 3.7 20.0 - - + -
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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