Contacts of the helix formed by residues 771 - 780 (chain A) in PDB entry 1R4X
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 ASN 771 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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769A LYS* 3.3 4.2 - - - +
770A LEU* 1.3 77.5 - - + +
772A PHE* 1.3 64.1 + - - +
773A GLU* 3.3 11.3 + - - +
774A ALA* 3.0 32.6 + - + +
775A ALA* 3.2 18.7 + - - +
814A GLU* 3.5 4.1 - - - +
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Residues in contact with PHE 772 (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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769A LYS* 4.5 9.1 + - + -
770A LEU 3.9 0.6 - - - -
771A ASN* 1.3 73.5 - - - +
773A GLU* 1.3 59.9 + - - +
775A ALA* 3.1 5.2 + - - +
776A TRP* 2.9 63.4 + + + -
813A CYS* 4.1 20.4 - - + -
814A GLU* 2.8 19.6 + - - +
829A LEU* 3.7 44.4 - - + -
830A LEU 3.4 30.5 - - - -
831A ALA* 4.8 2.5 - - + -
841A LEU* 4.2 14.1 - - + -
842A VAL 3.7 18.2 - - - -
843A ARG* 4.7 3.4 - - + -
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Residues in contact with GLU 773 (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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771A ASN* 3.3 7.5 + - - +
772A PHE* 1.3 81.5 - - - +
774A ALA* 1.3 61.1 + - - +
776A TRP* 3.3 9.5 + - + +
777A ASP* 3.0 41.7 + - - +
814A GLU* 4.3 2.0 + - - +
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Residues in contact with ALA 774 (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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771A ASN* 3.0 33.7 + - + +
773A GLU* 1.3 75.2 - - - +
775A ALA* 1.3 58.3 + - - +
777A ASP* 3.4 7.7 + - - +
778A GLU* 2.9 32.7 + - - +
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Residues in contact with ALA 775 (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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769A LYS* 3.8 33.4 - - + +
771A ASN 3.2 8.8 + - - +
772A PHE* 3.1 9.3 + - + +
774A ALA* 1.3 81.9 - - - +
776A TRP* 1.3 61.2 + - - +
778A GLU* 3.3 12.4 + - - +
779A VAL* 3.0 29.3 + - + +
839A ASP* 5.7 0.9 - - - +
841A LEU* 3.6 14.6 - - + -
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Residues in contact with TRP 776 (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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772A PHE* 2.9 42.4 + + + +
773A GLU* 3.4 14.6 - - + +
775A ALA* 1.3 75.2 - - - +
777A ASP* 1.3 71.3 + - - +
779A VAL* 3.5 1.0 + - - +
780A GLY 3.1 10.0 + - - -
784A GLU* 3.7 3.1 + - - -
841A LEU* 3.6 41.9 - - + +
843A ARG* 3.7 34.5 - - + +
857A THR* 3.6 44.9 - - + -
859A ARG* 3.0 72.6 + - + +
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Residues in contact with ASP 777 (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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773A GLU* 3.0 41.9 + - - +
774A ALA* 3.8 6.5 - - - +
776A TRP* 1.3 86.7 - - - +
778A GLU* 1.3 64.2 + - - +
780A GLY* 3.2 13.5 + - - -
859A ARG* 4.2 5.9 + - - +
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Residues in contact with GLU 778 (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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769A LYS* 5.9 1.6 + - - -
774A ALA* 2.9 20.6 + - - +
775A ALA* 3.5 11.7 - - - +
777A ASP* 1.3 75.6 - - - +
779A VAL* 1.3 65.4 + - + +
839A ASP* 5.3 4.4 - - - +
861A LEU* 5.2 2.1 - - - +
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Residues in contact with VAL 779 (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 ALA* 3.0 16.7 + - + +
776A TRP 3.8 3.8 - - - +
778A GLU* 1.3 80.3 - - + +
780A GLY* 1.3 69.0 + - - +
782A GLU* 5.2 1.4 + - - +
839A ASP* 4.5 20.9 - - + +
841A LEU* 3.9 17.0 - - + -
859A ARG* 3.9 6.1 - - + -
860A SER* 3.5 43.0 - - - +
861A LEU* 3.6 29.1 - - + +
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Residues in contact with GLY 780 (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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776A TRP 3.1 9.5 + - - -
777A ASP 3.2 11.5 + - - -
778A GLU 4.5 0.4 - - - -
779A VAL* 1.3 84.8 - - - +
781A ASP* 1.3 59.7 + - - -
782A GLU 3.6 2.9 + - - -
783A PHE 5.0 0.5 + - - -
859A ARG* 3.3 33.4 - - - +
860A SER 4.9 3.1 - - - +
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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