Contacts of the helix formed by residues 808 - 826 (chain v) in PDB entry 6FF7
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 THR 808 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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807v TYR* 1.3 76.5 - - - +
809v GLU* 1.3 54.6 + - - +
810v ALA* 3.2 5.8 - - - -
811v THR* 3.1 14.8 + - - -
812v LYS* 2.8 32.2 + - - +
863v ALA* 4.1 10.1 - - - +
864v SER 5.8 3.8 - - - -
881v GLN* 6.0 3.6 - - - -
882v LEU 4.4 17.3 - - - -
883v GLU 4.9 9.2 - - - -
884v GLN* 5.5 6.1 - - - +
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Residues in contact with GLU 809 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808v THR* 1.3 71.5 - - - +
810v ALA* 1.3 59.2 + - - +
812v LYS* 3.5 11.0 - - + +
813v ALA* 2.9 27.5 + - - +
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Residues in contact with ALA 810 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808v THR* 3.2 4.5 - - - -
809v GLU* 1.3 77.8 - - - +
811v THR* 1.3 57.4 + - - +
813v ALA* 3.3 6.7 + - - +
814v GLN* 2.9 28.1 + - - +
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Residues in contact with THR 811 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807v TYR* 4.5 8.5 - - - -
808v THR* 3.1 19.6 + - - -
810v ALA* 1.3 75.3 - - - +
812v LYS* 1.3 59.6 + - - +
814v GLN* 3.7 7.9 - - - +
815v ARG* 2.8 31.2 + - - +
884v GLN* 5.3 13.2 - - - -
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Residues in contact with LYS 812 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807v TYR* 4.6 10.2 - - + +
808v THR 2.8 13.8 + - - +
809v GLU* 3.5 15.3 - - + +
810v ALA 3.2 0.2 - - - -
811v THR* 1.3 78.6 - - - +
813v ALA* 1.3 57.7 + - - +
815v ARG* 3.4 5.5 + - - +
816v LYS* 2.9 29.5 + - - +
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Residues in contact with ALA 813 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809v GLU 2.9 16.7 + - - +
810v ALA* 3.7 7.0 - - - +
812v LYS* 1.3 72.8 - - - +
814v GLN* 1.3 60.7 + - - +
816v LYS* 3.4 6.6 + - - +
817v GLN* 2.9 28.9 + - - +
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Residues in contact with GLN 814 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810v ALA 2.9 17.4 + - - +
811v THR* 3.8 8.5 - - - +
812v LYS 3.3 0.2 - - - -
813v ALA* 1.3 75.2 - - - +
815v ARG* 1.3 58.2 + - - +
817v GLN* 3.3 7.3 + - - +
818v GLN* 2.9 27.2 + - - +
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Residues in contact with ARG 815 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278v LEU* 4.7 20.0 - - + -
811v THR 2.8 19.0 + - - +
812v LYS* 3.8 5.8 - - - +
814v GLN* 1.3 75.0 - - - +
816v LYS* 1.3 59.9 + - - +
818v GLN* 3.2 8.4 + - - +
819v MET* 2.9 27.7 + - - +
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Residues in contact with LYS 816 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812v LYS 2.9 18.0 + - - +
813v ALA* 3.8 7.6 - - - +
815v ARG* 1.3 73.6 - - - +
817v GLN* 1.3 60.5 + - - +
819v MET* 3.3 8.5 + - - +
820v ALA* 2.9 28.4 + - - +
842v PHE 5.5 3.6 - - - +
843v LEU* 5.4 16.6 - - + +
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Residues in contact with GLN 817 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813v ALA 2.9 18.1 + - - +
814v GLN* 3.5 8.5 - - - +
816v LYS* 1.3 77.1 - - - +
818v GLN* 1.3 58.3 + - - +
820v ALA* 3.4 8.2 + - - +
821v GLU* 2.9 27.9 + - - +
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Residues in contact with GLN 818 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814v GLN 2.9 14.7 + - - +
815v ARG* 3.2 11.4 + - - +
817v GLN* 1.3 73.9 - - - +
819v MET* 1.3 59.9 + - - +
821v GLU* 3.1 8.9 + - - +
822v GLU* 2.9 29.6 + - - +
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Residues in contact with MET 819 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276v ASN* 5.0 21.8 - - + +
815v ARG 2.9 13.4 + - - +
816v LYS* 3.3 12.5 + - - +
818v GLN* 1.3 77.3 - - - +
820v ALA* 1.3 57.0 + - - +
822v GLU* 3.4 3.4 + - - +
823v MET* 3.0 30.8 + - - +
842v PHE* 6.3 2.5 - - + -
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Residues in contact with ALA 820 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816v LYS 2.9 17.1 + - - +
817v GLN* 3.6 8.3 - - - +
819v MET* 1.3 74.8 - - - +
821v GLU* 1.3 58.1 + - - +
823v MET* 3.3 1.7 + - - +
824v VAL* 2.9 31.5 + - - +
839v ALA* 3.8 36.1 - - + +
843v LEU* 5.6 5.2 - - + -
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Residues in contact with GLU 821 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817v GLN 2.9 15.0 + - - +
818v GLN* 3.1 13.2 + - - +
820v ALA* 1.3 77.0 - - - +
822v GLU* 1.3 58.4 + - - +
824v VAL* 3.4 3.9 + - - +
825v GLU* 2.9 31.3 + - - +
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Residues in contact with GLU 822 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818v GLN 2.9 15.2 + - - +
819v MET* 4.4 3.4 - - - +
821v GLU* 1.3 76.9 - - - +
823v MET* 1.3 57.3 + - - +
825v GLU* 3.7 7.4 - - - -
826v ALA* 3.1 31.4 + - + +
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Residues in contact with MET 823 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819v MET 3.0 19.3 + - - +
820v ALA* 3.9 6.5 - - - +
821v GLU 3.2 0.2 - - - -
822v GLU* 1.3 78.8 - - - +
824v VAL* 1.3 58.5 + - - +
825v GLU 3.3 0.2 - - - -
826v ALA* 4.5 9.9 + - - +
828v GLY* 5.8 0.9 - - - -
834v LEU 5.7 2.8 + - - -
835v ALA 4.7 10.0 - - - +
838v MET* 6.1 2.7 - - + -
839v ALA* 4.5 13.9 - - + +
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Residues in contact with VAL 824 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820v ALA 2.9 17.3 + - - +
821v GLU* 3.7 3.4 - - - +
823v MET* 1.3 75.6 - - - +
825v GLU* 1.3 59.8 + - - +
828v GLY* 4.3 14.9 - - - -
835v ALA 5.6 3.1 - - - -
836v ALA* 5.3 14.6 - - + +
839v ALA* 5.1 4.7 - - + +
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Residues in contact with GLU 825 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821v GLU 2.9 18.6 + - - +
822v GLU* 4.0 6.5 - - - -
823v MET 3.3 0.2 - - - -
824v VAL* 1.3 80.1 - - - +
826v ALA* 1.3 61.1 + - - +
827v ALA 3.0 9.2 + - - -
828v GLY 4.1 3.0 + - - -
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Residues in contact with ALA 826 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822v GLU* 3.1 19.4 + - + +
823v MET* 4.5 8.1 + - - +
824v VAL 3.8 0.4 - - - -
825v GLU* 1.3 71.2 - - - +
827v ALA* 1.3 72.3 + - - +
828v GLY* 3.6 0.4 - - - -
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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