Contacts of the helix formed by residues 780 - 787 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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775B PHE 4.1 0.2 - - - +
776B GLY* 4.1 5.0 - - - -
777B LYS* 3.1 48.4 + - + +
779B LEU* 1.3 78.2 - - + +
781B ARG* 1.3 59.6 + - - +
782B GLN 3.4 1.8 - - - -
783B ALA* 3.5 9.2 + - - +
784B ASN* 3.0 45.0 + - - +
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Residues in contact with ARG 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735B GLU 4.4 3.4 + - - -
736B GLY* 3.6 28.0 - - - +
737B TRP* 4.0 21.9 - - - +
766B TYR* 5.8 3.8 - - - -
771B GLY 5.2 5.3 + - - -
773B HIS* 3.2 33.2 - - + +
775B PHE* 3.5 24.1 - - + +
776B GLY 2.9 30.1 + - - +
777B LYS* 2.9 7.7 + - - +
778B SER* 3.2 46.2 - - - +
779B LEU 3.5 0.4 - - - -
780B GLN* 1.3 75.8 - - - +
782B GLN* 1.3 62.6 + - - +
784B ASN 3.4 0.5 + - - -
785B ILE* 2.9 32.9 + - - +
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Residues in contact with GLN 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735B GLU* 3.7 12.2 - - + +
736B GLY* 2.7 37.1 + - - +
738B ILE* 3.2 43.0 + - + +
739B ALA 4.7 0.4 + - - -
740B PRO* 5.3 0.6 - - - +
743B LEU* 4.6 22.0 - - + +
778B SER 4.8 1.0 + - - -
779B LEU 4.8 3.5 + - - +
780B GLN 3.4 0.4 - - - -
781B ARG* 1.3 77.8 - - - +
783B ALA* 1.3 64.9 + - - +
785B ILE* 3.2 30.2 + - - +
786B LEU* 3.3 16.8 + - + +
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Residues in contact with ALA 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779B LEU 5.2 2.3 + - - +
780B GLN* 3.5 12.7 + - + +
781B ARG 3.4 0.4 - - - -
782B GLN* 1.3 79.0 - - - +
784B ASN* 1.3 62.1 + - - +
786B LEU* 3.2 20.4 + - - +
787B LEU* 3.3 25.9 + - + +
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Residues in contact with ASN 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775B PHE* 3.0 30.7 + - + +
776B GLY* 5.1 0.2 - - - -
780B GLN* 3.0 38.9 + - - +
781B ARG 3.7 2.7 - - - +
782B GLN 3.3 0.2 - - - -
783B ALA* 1.3 76.8 - - - +
785B ILE* 1.3 56.5 + - - +
787B LEU* 3.3 9.1 + - - +
788B GLY* 3.0 9.0 + - - -
789B ALA* 3.0 56.7 + - - +
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Residues in contact with ILE 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736B GLY 3.0 31.2 - - - +
738B ILE 3.6 20.6 - - - +
740B PRO* 3.8 25.0 - - + +
758B PHE* 3.8 14.4 - - + -
773B HIS* 4.8 0.2 - - + -
775B PHE* 3.4 33.3 - - + -
781B ARG 2.9 20.4 + - - +
782B GLN* 3.4 25.1 - - - +
783B ALA 3.1 0.8 - - - -
784B ASN* 1.3 78.5 - - - +
786B LEU* 1.3 62.7 + - + +
787B LEU 3.5 0.2 + - - -
788B GLY* 3.5 2.1 + - - -
815B MET* 3.2 21.5 - - - +
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Residues in contact with LEU 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740B PRO* 4.6 18.2 - - + +
743B LEU* 4.0 37.0 - - + -
782B GLN* 3.3 13.0 + - + +
783B ALA* 3.2 13.5 + - - +
785B ILE* 1.3 80.4 - - + +
787B LEU* 1.3 62.9 + - + +
815B MET* 3.4 15.5 - - - +
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Residues in contact with LEU 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783B ALA* 3.3 25.4 + - + +
784B ASN* 3.3 11.2 + - - +
785B ILE 3.3 0.4 - - - -
786B LEU* 1.3 80.8 - - + +
788B GLY* 1.3 63.0 + - - +
789B ALA* 3.3 7.7 + - + +
815B MET* 4.5 1.3 - - - -
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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