Contacts of the helix formed by residues 775 - 788 (chain A) in PDB entry 5XA0
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 TYR 775 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773A LEU* 2.5 25.9 + - - +
774A PRO* 1.3 81.5 - - + +
776A ASP* 1.3 69.1 + - - +
777A LEU* 3.2 9.0 + - + +
778A ARG 3.7 2.2 + - - +
960A PRO 5.2 11.4 - - - -
967A VAL* 6.5 1.1 - - - -
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Residues in contact with ASP 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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773A LEU* 5.9 1.1 - - - -
774A PRO 3.8 1.0 + - - -
775A TYR* 1.3 74.5 - - - +
777A LEU* 1.3 65.4 + - - +
779A ALA* 3.0 20.0 + - - +
780A SER* 3.1 10.6 + - - -
960A PRO* 5.3 14.7 - - + +
963A GLU* 6.2 1.3 - - + +
967A VAL* 6.1 5.7 - - + +
970A THR* 6.4 2.0 - - - -
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Residues in contact with LEU 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A TYR* 3.2 7.5 - - + +
776A ASP* 1.3 76.7 - - - +
778A ARG* 1.3 66.2 + - - +
780A SER* 2.7 22.9 + - - -
781A PHE* 3.0 11.8 + - - +
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Residues in contact with ARG 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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768A MET* 5.3 2.0 - - - +
769A SER* 4.3 8.7 + - - +
772A ASN 4.3 4.7 - - - +
773A LEU* 3.3 29.8 - - - +
774A PRO* 5.5 0.4 - - + -
775A TYR* 3.7 1.6 + - - +
776A ASP 3.1 0.4 + - - -
777A LEU* 1.3 78.0 - - - +
779A ALA* 1.3 63.6 + - - +
781A PHE* 3.5 15.8 + - - +
782A CYS* 4.0 3.1 + - - +
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Residues in contact with ALA 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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769A SER* 3.0 32.0 - - - +
773A LEU* 4.3 10.7 - - + +
775A TYR 4.5 0.8 + - - -
776A ASP* 3.0 9.8 + - - +
778A ARG* 1.3 77.3 - - - +
780A SER* 1.3 67.2 + - - +
782A CYS* 3.0 15.9 + - - +
783A ARG* 3.1 9.5 + - - +
974A ILE* 5.6 10.5 - - + -
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Residues in contact with SER 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 ASP* 3.1 8.3 + - - -
777A LEU* 2.7 26.8 + - - -
779A ALA* 1.3 71.6 - - - +
781A PHE* 1.3 55.3 + - - -
783A ARG* 2.7 36.3 + - - +
784A LEU* 3.0 6.9 + - - +
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Residues in contact with PHE 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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777A LEU 3.0 8.9 + - - +
778A ARG* 3.8 11.0 - - - +
779A ALA 3.2 0.2 - - - -
780A SER* 1.3 76.7 - - - +
782A CYS* 1.3 62.6 + - - +
784A LEU* 3.2 17.0 + - - +
785A MET* 3.2 13.3 + - - +
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Residues in contact with CYS 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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765A LEU* 3.7 26.5 - - + +
766A ARG* 5.6 0.7 - - - -
768A MET* 6.4 0.4 - - + -
769A SER* 4.6 11.0 - - - +
778A ARG 4.0 2.5 + - - +
779A ALA* 3.0 12.5 + - - +
781A PHE* 1.3 79.1 - - - +
783A ARG* 1.3 62.5 + - - +
785A MET* 3.7 6.3 + - - +
786A LEU* 2.9 25.1 + - - +
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Residues in contact with ARG 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 ALA 3.1 6.7 + - - +
780A SER* 2.7 29.2 + - - +
782A CYS* 1.3 68.2 - - - +
784A LEU* 1.3 65.3 + - - +
786A LEU* 2.9 9.0 + - - +
787A HIS* 2.8 22.3 + - - +
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Residues in contact with LEU 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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780A SER 3.0 9.9 + - - +
781A PHE* 3.2 9.6 + - - +
783A ARG* 1.3 72.8 - - - +
785A MET* 1.3 68.4 + - - +
787A HIS* 2.7 24.0 + - - +
788A MET* 3.2 5.9 + - - +
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Residues in contact with MET 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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781A PHE 3.2 9.4 + - - +
782A CYS* 4.0 9.2 - - - +
784A LEU* 1.3 76.7 - - - +
786A LEU* 1.3 65.6 + - - +
788A MET* 2.9 25.3 + - - +
789A HIS* 5.4 0.2 - - - +
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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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782A CYS 2.9 19.3 + - - +
783A ARG* 2.9 8.8 + - - +
785A MET* 1.3 76.4 - - - +
787A HIS* 1.3 62.7 + - - +
788A MET 3.3 0.7 + - - -
789A HIS* 3.5 19.5 - - - +
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Residues in contact with HIS 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A ARG 2.8 10.9 + - - +
784A LEU* 2.7 24.0 + - - +
786A LEU* 1.3 73.4 - - - +
788A MET* 1.3 55.2 + - - +
789A HIS* 2.9 10.0 + - - +
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Residues in contact with MET 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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784A LEU 3.2 4.1 + - - +
785A MET* 2.9 16.8 + - - +
787A HIS* 1.3 76.1 - - - +
789A HIS* 1.3 57.0 + - - +
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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