Contacts of the helix formed by residues 814 - 824 (chain A) in PDB entry 5FB0
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 TRP 814 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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795A PHE 3.4 8.5 - - - +
796A ALA 3.1 17.9 - - - +
797A SER* 3.3 19.3 - - - +
798A GLU* 3.5 50.5 - - + +
799A PRO* 3.4 18.4 - - + -
812A PRO* 3.9 28.0 - - + -
813A MET* 1.3 83.5 - - - +
815A LEU* 1.3 67.0 + - - +
816A ASN* 3.8 6.3 - - + +
817A LYS* 3.3 58.5 + - + +
818A VAL* 3.3 16.5 + - - +
840A ILE* 3.8 8.5 - - - -
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Residues in contact with LEU 815 (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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783A LEU* 3.6 27.4 - - + +
786A VAL* 4.2 10.1 - - + -
787A TYR* 3.1 27.4 + - + +
792A SER* 3.4 44.4 - - - +
795A PHE* 2.8 26.8 + - + +
796A ALA* 3.6 6.7 - - + +
814A TRP* 1.3 72.0 - - - +
816A ASN* 1.3 59.0 + - - +
818A VAL* 3.1 6.7 + - - +
819A LYS* 2.9 24.1 + - - +
837A MET* 3.9 19.1 - - + -
840A ILE* 4.0 9.4 - - + +
860A VAL* 6.0 0.7 - - + -
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Residues in contact with ASN 816 (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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787A TYR* 2.9 24.5 + - - -
796A ALA* 3.0 33.9 + - - +
797A SER* 3.7 12.3 + - - +
814A TRP* 3.9 6.7 - - + +
815A LEU* 1.3 75.6 - - - +
817A LYS* 1.3 57.0 + - - +
819A LYS* 3.3 14.6 + - + +
820A THR* 2.9 32.5 + - - +
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Residues in contact with LYS 817 (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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811A LYS* 5.2 4.9 - - - +
812A PRO 4.9 2.7 - - - +
813A MET* 3.4 34.1 - - + +
814A TRP* 3.3 53.3 + - + +
815A LEU 3.1 1.2 - - - -
816A ASN* 1.3 75.9 - - - +
818A VAL* 1.3 61.7 + - - +
820A THR* 3.3 7.0 + - - -
821A SER* 2.9 45.3 + - - +
836A ASP* 4.8 2.0 + - - -
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Residues in contact with VAL 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A LEU* 4.1 4.5 - - + -
813A MET* 3.6 21.3 - - + -
814A TRP 3.5 13.5 - - - +
815A LEU* 3.1 7.0 + - - +
817A LYS* 1.3 73.6 - - - +
819A LYS* 1.3 60.8 + - - +
821A SER* 4.1 0.3 - - - -
822A LEU* 2.9 33.8 + - - +
827A TYR* 3.7 13.7 - - + +
833A PHE* 3.5 38.1 - - + -
836A ASP* 3.8 15.9 - - + -
837A MET* 4.0 19.5 - - + -
840A ILE* 4.5 3.1 - - + -
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Residues in contact with LYS 819 (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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727A HIS* 3.1 30.4 + - + +
728A CYS* 4.5 6.1 + - - +
729A HIS 5.1 0.2 - - - -
730A ILE* 3.8 37.7 - - + +
732A SER* 6.0 1.1 - - - +
783A LEU* 3.8 13.8 - - + +
787A TYR* 3.8 30.5 + - - +
815A LEU 2.9 13.3 + - - +
816A ASN* 3.4 17.0 + - + +
818A VAL* 1.3 76.8 - - - +
820A THR* 1.3 58.7 + - - +
822A LEU* 3.9 1.9 - - - +
823A ASN* 2.9 34.1 + - + +
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Residues in contact with THR 820 (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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816A ASN* 2.9 18.5 + - - +
817A LYS* 3.7 8.5 - - - -
818A VAL 3.3 0.4 - - - -
819A LYS* 1.3 77.9 - - - +
821A SER* 1.3 64.9 + - - +
823A ASN* 3.2 7.9 + - + +
824A GLU* 3.0 47.2 + - + +
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Residues in contact with SER 821 (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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817A LYS* 2.9 33.6 + - - +
820A THR* 1.3 76.6 - - - +
822A LEU* 1.3 59.2 + - - +
824A GLU* 3.4 1.2 + - - -
825A GLN 3.1 4.0 + - - -
826A MET* 2.7 51.7 + - - +
827A TYR* 3.6 28.0 + - - -
836A ASP* 5.3 0.3 + - - -
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Residues in contact with LEU 822 (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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730A ILE* 5.2 2.9 - - + -
771A MET* 4.2 13.5 - - + -
776A GLN* 2.9 59.1 + - - +
779A CYS* 4.0 8.1 - - + +
780A GLU* 3.6 39.2 - - + +
783A LEU* 4.5 8.7 - - + -
818A VAL* 2.9 19.5 + - + +
819A LYS* 4.1 3.1 - - - +
821A SER* 1.3 73.4 - - - +
823A ASN* 1.3 65.2 + - - +
825A GLN* 3.2 6.8 + - - +
827A TYR* 3.5 23.2 - - + -
833A PHE* 4.1 18.6 - - + -
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Residues in contact with ASN 823 (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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730A ILE* 6.4 2.5 - - + -
731A PRO* 5.3 6.5 - - + +
732A SER* 4.7 21.2 + - - -
776A GLN* 5.2 0.6 + - - +
780A GLU* 5.3 3.8 - - - -
819A LYS* 2.9 22.6 + - + +
820A THR* 3.5 7.0 + - - +
822A LEU* 1.3 77.6 - - - +
824A GLU* 1.3 72.3 + - - +
825A GLN* 3.2 12.5 + - - +
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Residues in contact with GLU 824 (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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820A THR* 3.0 38.3 + - - +
821A SER* 5.0 0.5 - - - -
822A LEU 3.4 0.2 - - - -
823A ASN* 1.3 85.5 + - - +
825A GLN* 1.3 70.7 + - - +
826A MET* 3.3 29.9 + - + +
736C ASN* 4.4 2.8 + - - -
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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
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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