Contacts of the helix formed by residues 780 - 788 (chain A) in PDB entry 4YZ9
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 780 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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776A GLY* 3.6 7.3 - - - -
777A LYS* 2.9 45.6 + - + +
779A LEU* 1.3 77.7 - - + +
781A ARG* 1.3 63.7 + - - +
782A GLN 3.5 0.9 - - - -
783A ALA* 3.9 7.3 + - - +
784A ASN* 2.9 38.3 + - - +
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Residues in contact with ARG 781 (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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733A GLY* 3.1 32.3 + - - -
735A GLU 2.8 19.9 + - - -
736A GLY* 3.6 16.4 - - - +
737A TRP* 3.9 9.9 - - - +
766A TYR* 6.1 2.6 - - - -
771A GLY 5.6 2.6 + - - -
773A HIS* 3.1 50.2 + - - +
775A PHE* 3.7 11.2 - - + +
776A GLY 3.2 17.6 + - - +
777A LYS* 2.9 22.3 - - - +
778A SER* 3.4 28.5 - - - +
779A LEU 3.4 2.0 - - - -
780A GLN* 1.3 78.5 - - - +
782A GLN* 1.3 65.3 + - - +
784A ASN* 3.1 4.5 + - - +
785A ILE* 2.9 27.4 + - - +
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Residues in contact with GLN 782 (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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735A GLU* 5.2 4.5 - - + +
736A GLY* 3.3 28.4 + - - +
737A TRP 4.2 0.9 + - - -
738A ILE* 3.5 36.0 + - - +
743A LEU* 3.4 37.4 - - + +
778A SER 4.8 1.2 + - - -
779A LEU 4.8 2.7 + - - +
780A GLN 3.5 0.2 - - - -
781A ARG* 1.3 78.9 - - - +
783A ALA* 1.3 61.7 + - - +
785A ILE* 3.3 20.9 + - - +
786A LEU* 3.5 18.7 + - + +
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Residues in contact with ALA 783 (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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779A LEU 5.4 2.1 + - - +
780A GLN* 3.9 9.0 + - - +
781A ARG 3.3 0.6 - - - -
782A GLN* 1.3 77.3 - - - +
784A ASN* 1.3 66.5 + - - +
786A LEU* 3.3 18.9 + - - +
787A LEU* 3.5 20.3 + - + +
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Residues in contact with ASN 784 (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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775A PHE* 2.9 23.7 + - + +
776A GLY* 4.9 0.4 - - - -
780A GLN* 2.9 36.5 + - - +
781A ARG 3.1 3.2 + - - +
783A ALA* 1.3 79.2 - - - +
785A ILE* 1.3 58.1 + - - +
787A LEU* 3.7 11.0 - - - +
788A GLY* 2.8 23.7 + - - -
789A ALA* 2.9 38.9 + - + +
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Residues in contact with ILE 785 (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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736A GLY* 3.1 31.6 - - - +
738A ILE 3.8 13.5 - - - +
740A PRO* 3.7 34.6 - - + +
758A PHE* 3.9 11.7 - - + -
775A PHE* 3.4 31.2 - - + -
781A ARG 2.9 18.7 + - - +
782A GLN* 3.6 26.9 - - - +
783A ALA 3.2 0.6 - - - -
784A ASN* 1.3 79.2 - - - +
786A LEU* 1.3 62.2 + - + +
788A GLY 3.5 6.1 + - - -
815A MET* 3.5 16.8 - - - +
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Residues in contact with LEU 786 (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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740A PRO* 4.0 24.3 - - + +
743A LEU* 3.9 33.9 - - + -
782A GLN* 3.5 15.2 + - + +
783A ALA* 3.3 11.4 + - - +
785A ILE* 1.3 79.2 - - + +
787A LEU* 1.3 58.6 + - + +
788A GLY 3.8 0.2 + - - -
815A MET* 4.8 4.9 - - - +
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Residues in contact with LEU 787 (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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783A ALA* 3.5 16.6 - - + +
784A ASN* 3.8 14.6 - - - +
786A LEU* 1.3 76.5 - - + +
788A GLY* 1.3 62.4 + - - +
789A ALA* 3.6 28.1 + - + +
815A MET* 5.0 1.1 - - - -
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Residues in contact with GLY 788 (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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775A PHE* 4.5 4.0 - - - -
784A ASN 2.8 10.2 + - - -
785A ILE 3.5 1.9 + - - -
786A LEU 3.4 4.2 + - - -
787A LEU* 1.3 79.8 - - - +
789A ALA* 1.3 57.1 + - - -
790A CYS* 3.7 7.7 + - - -
815A MET* 3.7 31.6 - - - +
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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