Contacts of the helix formed by residues 793 - 807 (chain A) in PDB entry 4NC6
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 SER 793 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789A LYS 4.6 0.4 + - - -
790A ARG 3.6 2.5 + - - -
791A TYR 3.1 8.7 - - - +
792A ARG* 1.3 77.0 - - - +
794A GLU* 1.3 58.9 + - - +
795A GLU* 3.4 14.6 + - - +
796A ASN* 3.0 41.7 + - - +
797A ALA* 3.1 20.8 + - - +
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Residues in contact with GLU 794 (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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739A TYR* 3.5 55.3 + - + +
792A ARG 3.5 6.0 + - - +
793A SER* 1.3 67.5 + - - +
795A GLU* 1.3 71.2 + - + +
797A ALA* 3.2 1.7 + - - +
798A LYS* 2.9 43.7 + - - +
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Residues in contact with GLU 795 (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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793A SER* 3.3 9.6 + - - +
794A GLU* 1.3 94.0 + - + +
796A ASN* 1.3 64.3 + - - +
798A LYS* 3.7 17.2 - - - +
799A LYS* 3.0 28.2 + - + +
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Residues in contact with ASN 796 (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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790A ARG* 3.0 67.3 + - - +
791A TYR* 3.5 13.1 - - + -
793A SER* 3.0 22.9 + - - +
795A GLU* 1.3 77.7 - - - +
797A ALA* 1.3 57.9 + - - +
799A LYS* 3.5 7.3 + - - +
800A LEU* 3.0 29.3 + - - +
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Residues in contact with ALA 797 (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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739A TYR* 4.0 16.4 - - + -
740A MET* 3.5 40.6 - - + -
743A HIS* 6.0 0.2 - - - -
791A TYR* 3.8 8.0 - - + +
793A SER 3.1 15.5 + - - +
794A GLU 3.7 4.7 - - - +
795A GLU 3.2 0.2 - - - -
796A ASN* 1.3 75.3 - - - +
798A LYS* 1.3 63.8 + - - +
800A LEU* 3.3 2.8 + - - +
801A MET* 3.0 30.1 + - - +
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Residues in contact with LYS 798 (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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565A ASN 5.7 4.3 - - - +
739A TYR* 3.5 26.1 + - + +
743A HIS* 5.5 11.5 - - + +
794A GLU* 2.9 37.2 + - - +
795A GLU* 3.7 15.5 - - - +
797A ALA* 1.3 76.2 - - - +
799A LYS* 1.3 64.7 + - + +
801A MET* 3.3 5.1 + - - +
802A GLU* 3.1 24.4 + - - +
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Residues in contact with LYS 799 (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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790A ARG* 5.4 10.5 - - - +
795A GLU* 3.0 18.8 + - + +
796A ASN* 4.1 8.1 - - - +
798A LYS* 1.3 77.6 - - + +
800A LEU* 1.3 62.3 + - - +
802A GLU* 3.4 24.3 - - - +
803A LEU* 3.0 24.0 + - - +
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Residues in contact with LEU 800 (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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740A MET* 4.0 11.0 - - + -
759A VAL* 4.2 13.7 - - + +
762A GLY* 3.4 35.9 - - - +
763A LEU* 3.6 13.5 - - + +
766A THR* 3.7 9.6 - - + +
791A TYR* 3.7 30.7 - - + +
796A ASN 3.0 18.8 + - - +
797A ALA* 3.5 5.4 - - - +
799A LYS* 1.3 77.6 - - - +
801A MET* 1.3 76.3 + - - +
803A LEU* 3.3 3.9 + - + +
804A ALA* 2.9 26.3 + - + +
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Residues in contact with MET 801 (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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564A ARG 5.6 1.3 - - - -
740A MET* 3.9 13.2 - - + -
743A HIS* 3.7 39.9 - - + +
744A ILE* 3.8 33.0 - - + +
747A LEU* 3.2 31.6 - - + -
759A VAL* 4.0 14.8 - - + -
797A ALA 3.0 19.5 + - - +
798A LYS 3.3 2.7 + - - +
800A LEU* 1.3 90.3 - - - +
802A GLU* 1.3 67.5 + - - +
804A ALA* 3.6 4.1 - - + +
805A CYS* 3.0 29.8 + - - -
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Residues in contact with GLU 802 (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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564A ARG* 4.0 8.9 + - - +
798A LYS 3.1 12.9 + - - +
799A LYS* 3.4 33.3 - - - +
801A MET* 1.3 77.6 - - - +
803A LEU* 1.3 57.6 + - - +
805A CYS* 3.3 6.0 + - - +
806A ASN* 3.0 45.3 + - - +
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Residues in contact with LEU 803 (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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762A GLY* 3.9 15.3 - - - +
765A LYS* 4.4 11.0 - - + -
766A THR* 3.3 27.1 - - - +
799A LYS 3.0 17.7 + - - +
800A LEU* 3.7 4.7 - - + +
802A GLU* 1.3 73.6 - - - +
804A ALA* 1.3 56.1 + - - +
806A ASN* 3.1 11.7 + - + +
807A MET* 2.7 62.5 + - + +
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Residues in contact with ALA 804 (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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747A LEU* 5.6 0.7 - - + -
758A ASN* 3.2 55.6 + - + +
759A VAL* 3.9 17.7 - - + +
762A GLY* 4.8 3.1 - - - -
800A LEU* 2.9 17.9 + - + +
801A MET* 3.6 13.7 - - + +
803A LEU* 1.3 77.1 - - - +
805A CYS* 1.3 64.0 + - - +
807A MET* 3.3 2.7 + - - -
808A LYS 3.2 6.4 + - - -
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Residues in contact with CYS 805 (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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564A ARG* 3.6 49.3 + - + +
747A LEU* 3.9 32.5 - - - -
758A ASN* 4.9 0.7 - - - +
801A MET 3.0 22.0 + - - +
802A GLU 3.8 1.1 - - - +
804A ALA* 1.3 76.5 - - - +
806A ASN* 1.3 61.5 + - - +
808A LYS* 3.2 39.5 + - + +
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Residues in contact with ASN 806 (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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564A ARG* 2.6 24.4 + - - +
802A GLU* 3.0 36.4 + - - +
803A LEU* 3.5 13.3 - - + +
805A CYS* 1.3 79.4 - - - +
807A MET* 1.3 56.7 + - - +
808A LYS* 3.1 10.2 + - - +
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Residues in contact with MET 807 (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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705A TYR* 4.3 24.9 - - + -
706A ILE* 4.8 1.6 - - + -
758A ASN* 3.8 4.1 + - - +
761A LEU* 4.1 42.2 - - + +
762A GLY* 4.2 3.1 - - - -
765A LYS* 4.1 26.2 - - + -
803A LEU* 2.7 52.5 + - + +
804A ALA* 3.3 8.9 + - - +
806A ASN* 1.3 70.1 - - + +
808A LYS* 1.3 65.6 + - - +
809A ILE* 3.3 19.6 + - + +
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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