Contacts of the helix formed by residues 772 - 800 (chain C) in PDB entry 4RNP
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 HIS 772 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771C ALA* 3.8 27.8 - - - +
773C LYS* 3.8 28.3 - - - +
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Residues in contact with LYS 773 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772C HIS* 3.8 26.0 - - - +
774C GLN* 3.8 28.3 - - - +
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Residues in contact with GLN 774 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773C LYS* 3.8 29.2 - - - +
775C GLU* 3.8 26.7 - - - +
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Residues in contact with GLU 775 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774C GLN* 3.8 26.5 - - - +
776C SER* 3.8 29.2 - - - +
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Residues in contact with SER 776 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775C GLU* 3.8 26.9 - - - +
777C GLY* 3.8 29.4 - - - +
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Residues in contact with GLY 777 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776C SER* 3.8 29.8 - - - +
778C ILE* 3.8 26.7 - - - +
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Residues in contact with ILE 778 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777C GLY* 3.8 27.8 - - - +
779C ALA* 3.8 29.6 - - - +
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Residues in contact with ALA 779 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778C ILE* 3.8 29.4 - - - +
780C PRO* 3.8 28.3 - - - -
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Residues in contact with PRO 780 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779C ALA* 3.8 25.8 - - - -
781C ASN* 3.8 28.5 - - - -
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Residues in contact with ASN 781 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780C PRO* 3.8 25.6 - - - -
782C PHE* 3.8 29.2 - - - +
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Residues in contact with PHE 782 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781C ASN* 3.8 28.5 - - - +
783C VAL* 3.8 27.8 - - - +
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Residues in contact with VAL 783 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782C PHE* 3.8 25.4 - - - +
784C HIS* 3.8 29.2 - - - +
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Residues in contact with HIS 784 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783C VAL* 3.8 26.0 - - - +
785C SER* 3.8 28.5 - - - +
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Residues in contact with SER 785 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784C HIS* 3.8 29.4 - - - +
786C GLN* 3.8 26.0 - - - +
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Residues in contact with GLN 786 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785C SER* 3.8 27.8 - - - +
787C ASP* 3.8 29.2 - - - +
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Residues in contact with ASP 787 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786C GLN* 3.8 24.9 - - - +
788C GLY* 3.8 29.6 - - - +
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Residues in contact with GLY 788 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C ARG* 4.3 24.5 - - - +
787C ASP* 3.8 28.9 - - - +
789C SER* 3.8 25.1 - - - +
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Residues in contact with SER 789 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788C GLY* 3.8 28.3 - - - +
790C HIS* 3.8 27.6 - - - +
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Residues in contact with HIS 790 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789C SER* 3.8 28.9 - - - +
791C LEU* 3.8 25.1 - - - +
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Residues in contact with LEU 791 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790C HIS* 3.8 27.4 - - - +
792C ARG* 3.8 28.9 - - - +
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Residues in contact with ARG 792 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791C LEU* 3.8 29.2 - - - +
793C LYS* 3.8 24.5 - - - +
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Residues in contact with LYS 793 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792C ARG* 3.8 27.1 - - - +
794C THR* 3.8 29.6 - - - +
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Residues in contact with THR 794 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793C LYS* 3.8 26.0 - - - +
795C VAL* 3.8 29.2 - - - +
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Residues in contact with VAL 795 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794C THR* 3.8 28.9 - - - +
796C VAL* 3.8 26.0 - - - +
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Residues in contact with VAL 796 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795C VAL* 3.8 27.6 - - - +
797C TRP* 3.8 29.2 - - - +
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Residues in contact with TRP 797 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796C VAL* 3.8 29.2 - - - +
798C ALA* 3.8 27.4 - - - +
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Residues in contact with ALA 798 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797C TRP* 3.8 24.0 - - - +
799C HIS* 3.8 29.6 - - - +
----------------------------------------------------------
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Residues in contact with HIS 799 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798C ALA* 3.8 29.4 - - - +
800C GLU* 3.8 28.7 - - - +
803C GLY* 4.4 20.9 - - - +
804C ILE* 4.6 10.8 - - - +
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Residues in contact with GLU 800 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799C HIS* 3.8 25.6 - - - +
801C LYS* 3.8 29.8 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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