Contacts of the helix formed by residues 822 - 832 (chain q) 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 ASP 822 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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763q ASN* 5.3 11.2 - - + -
821q VAL* 1.3 75.3 - - - +
823q PRO* 1.3 65.9 - - - +
824q MET* 4.4 7.0 - - + +
825q LEU* 3.0 12.6 + - + +
826q SER* 2.9 19.4 + - - -
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Residues in contact with PRO 823 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762q GLY* 5.3 13.5 - - - +
763q ASN* 5.6 5.1 - - - +
766q LEU* 5.6 8.3 - - + -
797q LEU* 6.4 2.5 - - + -
800q LEU* 5.7 10.7 - - + +
802q ALA* 5.8 6.7 - - + -
816q MET* 5.3 6.3 - - + +
821q VAL 3.5 2.3 - - - +
822q ASP* 1.3 72.3 - - - +
824q MET* 1.3 57.5 + - - +
826q SER* 3.7 6.8 - - - -
827q LYS* 2.9 32.4 + - - +
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Residues in contact with MET 824 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822q ASP* 3.2 5.8 - - + +
823q PRO* 1.3 77.7 - - - +
825q LEU* 1.3 58.2 + - - +
827q LYS* 3.8 1.7 - - - +
828q MET* 3.0 28.9 + - - +
947q GLY* 3.6 29.9 - - - +
948q TYR* 5.2 2.9 - - + -
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Residues in contact with LEU 825 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821q VAL* 4.0 17.0 - - + -
822q ASP* 3.0 15.9 + - + +
824q MET* 1.3 77.1 - - - +
826q SER* 1.3 59.7 + - - +
828q MET* 3.3 6.8 + - - +
829q ILE* 2.9 29.9 + - - +
845q ALA* 5.2 16.2 - - + +
848q LEU* 6.3 3.1 - - + -
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Residues in contact with SER 826 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816q MET* 3.7 37.5 - - - -
819q LEU* 4.3 16.4 - - - -
821q VAL* 4.6 6.7 - - - +
822q ASP 2.9 12.8 + - - -
823q PRO* 3.2 8.9 + - - -
825q LEU* 1.3 76.0 - - - +
827q LYS* 1.3 59.2 + - - +
829q ILE* 3.2 6.4 + - - +
830q LEU* 2.9 31.2 + - - +
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Residues in contact with LYS 827 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800q LEU* 5.1 16.6 - - + +
816q MET* 5.1 3.8 - - + +
823q PRO 2.9 17.2 + - - +
824q MET* 3.8 5.4 - - - +
826q SER* 1.3 76.7 - - - +
828q MET* 1.3 62.3 + - - +
830q LEU* 3.1 7.3 + - - +
831q ALA* 3.0 26.4 + - - +
946q ALA* 5.1 3.8 - - - +
947q GLY* 4.5 10.5 - - - +
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Residues in contact with MET 828 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824q MET 3.0 15.8 + - - +
825q LEU* 3.5 7.6 - - - +
827q LYS* 1.3 81.6 - - - +
829q ILE* 1.3 61.5 + - - +
831q ALA* 3.5 4.2 + - - +
832q SER* 3.3 21.0 + - - -
841q ILE* 4.8 4.1 - - + +
845q ALA* 6.5 0.2 - - + -
943q ALA* 4.1 26.0 - - - +
944q ILE* 4.9 5.6 - - - +
947q GLY* 4.1 11.1 - - - +
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Residues in contact with ILE 829 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825q LEU 2.9 16.6 + - - +
826q SER* 3.8 6.3 - - - +
828q MET* 1.3 79.3 - - - +
830q LEU* 1.3 61.9 + - - +
832q SER* 3.2 19.7 + - - -
833q GLU 4.7 0.7 + - - -
838q SER* 5.5 1.9 - - - -
841q ILE* 5.0 8.5 - - + +
842q LEU* 5.8 4.7 - - - -
845q ALA* 4.9 14.4 - - + -
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Residues in contact with LEU 830 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812q SER* 6.1 3.8 - - - +
815q LYS* 5.7 9.2 - - + -
816q MET* 6.2 3.4 - - + +
826q SER 2.9 17.4 + - - +
827q LYS* 3.1 6.9 + - - +
829q ILE* 1.3 78.4 - - - +
831q ALA* 1.3 62.4 + - - +
832q SER 3.5 0.2 + - - -
833q GLU* 4.3 7.6 + - - +
928q VAL* 5.2 12.2 - - - +
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Residues in contact with ALA 831 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827q LYS 3.0 15.8 + - - +
828q MET 4.0 3.6 - - - +
830q LEU* 1.3 78.2 - - - +
832q SER* 1.3 53.8 + - - +
833q GLU 3.2 0.2 - - - -
834q LYS* 2.8 40.3 + - + +
835q TYR* 3.6 2.2 + - - +
943q ALA* 5.6 2.5 - - - +
946q ALA* 4.3 21.1 - - + -
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Residues in contact with SER 832 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828q MET 3.3 8.0 + - - -
829q ILE 3.2 15.8 + - - -
831q ALA* 1.3 76.4 - - - +
833q GLU* 1.3 57.0 + - - +
835q TYR* 2.8 28.8 + - - +
836q SER 2.9 8.8 + - - -
837q CYS 3.2 5.1 + - - -
838q SER* 3.5 16.4 - - - -
841q ILE* 3.5 31.0 - - - -
943q ALA* 4.5 7.4 - - - -
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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