Contacts of the helix formed by residues 762 - 769 (chain B) in PDB entry 5PYC
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 762 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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760B GLY* 4.4 5.5 + - - -
761B HIS* 1.3 86.9 + - - +
763B GLU* 1.3 65.2 + - - +
764B SER* 3.9 16.8 - - - +
765B GLU* 3.3 12.9 + - + +
766B VAL* 3.2 19.9 + - - +
874B ILE* 4.3 1.3 - - - -
875B GLN* 3.0 38.7 + - - +
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Residues in contact with GLU 763 (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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761B HIS 4.1 0.4 + - - -
762B GLN* 1.3 71.8 - - - +
764B SER* 1.3 63.3 + - - +
766B VAL* 3.1 2.6 + - - +
767B LEU* 2.9 38.1 + - + +
838B ARG* 3.0 43.7 + - - -
865B GLU* 4.9 0.2 - - - +
868B PHE* 3.8 18.5 - - + -
874B ILE* 3.6 25.6 - - + +
875B GLN* 5.4 1.2 - - - +
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Residues in contact with SER 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B GLN* 3.9 13.0 - - - +
763B GLU* 1.3 76.2 - - - +
765B GLU* 1.3 63.3 + - - +
767B LEU* 3.7 8.5 + - - +
768B MET* 3.5 27.4 + - - +
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Residues in contact with GLU 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761B HIS* 3.6 20.8 - - - +
762B GLN* 3.3 15.5 + - + +
763B GLU 3.2 0.4 - - - -
764B SER* 1.3 83.1 + - - +
766B VAL* 1.3 66.9 + - - +
768B MET* 3.1 16.4 + - - +
769B ARG* 2.9 52.5 + - - +
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Residues in contact with VAL 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761B HIS* 3.9 8.3 - - + -
762B GLN 3.2 7.6 + - - +
763B GLU 3.1 7.5 + - - +
765B GLU* 1.3 77.5 - - - +
767B LEU* 1.3 65.1 + - - +
769B ARG* 3.0 51.3 + - - +
830B VAL* 3.5 9.9 - - + +
868B PHE* 4.0 18.6 - - + -
872B PHE* 3.5 39.9 - - + +
874B ILE* 3.6 21.5 - - + -
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Residues in contact with LEU 767 (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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763B GLU* 2.9 40.9 + - + +
764B SER* 4.1 9.0 - - - +
766B VAL* 1.3 76.8 - - - +
768B MET* 1.3 62.1 + - + +
769B ARG 3.5 0.9 + - - -
829B ARG* 3.8 1.7 - - - +
830B VAL* 3.6 6.5 + - + -
831B GLU* 2.8 56.8 + - + +
834B VAL* 3.7 37.9 - - + -
835B GLN* 6.2 2.5 - - + +
838B ARG* 4.6 5.6 - - - +
868B PHE* 3.9 13.5 - - + -
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Residues in contact with MET 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764B SER 3.5 15.0 + - - +
765B GLU* 3.1 12.6 + - - +
767B LEU* 1.3 80.9 - - + +
769B ARG* 1.3 62.1 + - - +
770B GLN* 3.5 5.0 + - - +
829B ARG* 3.7 45.3 + - - +
831B GLU* 4.7 14.6 - - - +
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Residues in contact with ARG 769 (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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761B HIS* 3.3 28.3 + - - -
765B GLU* 2.9 45.6 + - - +
766B VAL* 3.0 29.7 + - - +
768B MET* 1.3 74.8 - - - +
770B GLN* 1.3 67.2 + - - +
775B GLU* 3.6 33.5 + - + -
778B LYS* 4.8 8.9 - - - +
829B ARG* 3.3 3.9 - - - -
830B VAL* 3.0 33.8 + - + +
872B PHE* 4.1 16.0 + - - +
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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