Contacts of the helix formed by residues 809 - 831 (chain C) in PDB entry 4PE5
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 809 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807C THR 3.6 3.2 + - - -
808C LEU* 1.3 74.8 - - - +
810C CYS* 1.3 63.0 + - - +
811C GLU* 3.4 10.7 + - - -
812C ASN* 3.6 20.6 + - - +
813C MET* 3.8 8.5 + - - +
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Residues in contact with CYS 810 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B SER* 4.6 6.1 - - - -
557B CYS* 2.0 47.6 - - - -
558B VAL* 5.6 0.7 - - - -
808C LEU 3.5 3.2 + - - -
809C THR* 1.3 70.9 - - - +
811C GLU* 1.3 58.8 + - - +
812C ASN 3.3 0.2 - - - -
813C MET* 3.4 11.4 + - - -
814C ALA* 2.9 29.7 + - - +
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Residues in contact with GLU 811 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809C THR* 3.1 8.2 - - - -
810C CYS* 1.3 77.6 - - - +
812C ASN* 1.3 59.4 + - - +
814C ALA* 3.2 8.5 + - - +
815C GLY* 2.9 24.9 + - - -
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Residues in contact with ASN 812 (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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554C PHE 3.5 13.6 + - - +
809C THR* 3.6 15.6 + - - +
810C CYS 3.3 0.2 - - - -
811C GLU* 1.3 78.4 - - - +
813C MET* 1.3 58.9 + - - +
815C GLY* 3.3 1.4 + - - +
816C VAL* 2.9 28.8 + - - +
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Residues in contact with MET 813 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B VAL* 5.5 12.3 - - + -
809C THR 3.8 6.5 + - - +
810C CYS* 3.4 17.4 + - - +
811C GLU 3.3 0.2 - - - -
812C ASN* 1.3 78.4 - - - +
814C ALA* 1.3 58.4 + - - +
816C VAL* 3.8 7.0 - - - +
817C PHE* 2.9 29.6 + - - +
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Residues in contact with ALA 814 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810C CYS* 2.9 21.9 + - - +
811C GLU* 3.2 9.8 + - - +
813C MET* 1.3 76.3 - - - +
815C GLY* 1.3 60.7 + - - +
817C PHE* 3.4 6.1 + - - +
818C MET* 2.9 28.8 + - - +
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Residues in contact with GLY 815 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554C PHE* 4.5 4.9 - - - -
811C GLU 2.9 13.8 + - - -
812C ASN* 3.7 3.4 - - - -
814C ALA* 1.3 74.2 - - - +
816C VAL* 1.3 60.1 + - - +
818C MET* 3.3 6.4 + - - +
819C LEU* 2.9 30.7 + - - +
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Residues in contact with VAL 816 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B PHE* 5.5 4.3 - - + +
641B ILE* 6.3 2.9 - - + -
554C PHE* 3.7 30.5 - - + +
812C ASN 2.9 17.0 + - - +
813C MET* 3.8 8.5 - - - +
815C GLY* 1.3 77.2 - - - +
817C PHE* 1.3 56.3 + - - +
819C LEU* 3.5 2.0 + - - +
820C VAL* 2.9 30.5 + - - +
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Residues in contact with PHE 817 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B MET* 5.8 8.1 - - + -
813C MET 2.9 19.0 + - - +
814C ALA* 3.7 8.1 - - - +
816C VAL* 1.3 73.8 - - - +
818C MET* 1.3 61.2 + - - +
820C VAL* 3.9 4.8 - - - +
821C ALA* 2.9 33.1 + - - +
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Residues in contact with MET 818 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814C ALA 2.9 18.4 + - - +
815C GLY* 3.6 8.7 - - - +
816C VAL 3.3 0.2 - - - -
817C PHE* 1.3 77.8 - - - +
819C LEU* 1.3 58.2 + - - +
821C ALA* 3.9 3.3 - - - +
822C GLY* 2.9 25.8 + - - -
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Residues in contact with LEU 819 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554C PHE* 4.9 9.2 - - + -
815C GLY 2.9 17.4 + - - +
816C VAL* 3.9 6.1 - - - +
818C MET* 1.3 76.0 - - - +
820C VAL* 1.3 58.6 + - - +
822C GLY* 3.3 1.6 + - - -
823C GLY* 2.9 26.3 + - - -
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Residues in contact with VAL 820 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B VAL* 5.7 7.2 - - + +
635B TRP* 6.1 2.9 - - - -
638B PHE* 4.3 22.7 - - + -
816C VAL 2.9 19.7 + - - +
817C PHE* 3.9 5.6 - - - +
819C LEU* 1.3 77.2 - - - +
821C ALA* 1.3 57.0 + - - +
823C GLY* 3.4 1.4 + - - -
824C ILE* 2.9 30.4 + - - +
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Residues in contact with ALA 821 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817C PHE 2.9 18.8 + - - +
818C MET* 4.1 4.0 - - - +
820C VAL* 1.3 74.5 - - - +
822C GLY* 1.3 60.8 + - - +
824C ILE* 3.8 6.6 - - - +
825C VAL* 2.9 29.6 + - - +
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Residues in contact with GLY 822 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818C MET 2.9 19.0 + - - -
819C LEU 3.7 1.3 - - - -
820C VAL 3.2 0.2 - - - -
821C ALA* 1.3 75.1 - - - +
823C GLY* 1.3 58.6 + - - +
825C VAL* 3.2 5.9 + - - +
826C ALA* 2.9 30.3 + - - +
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Residues in contact with GLY 823 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B VAL* 6.0 4.0 - - - -
819C LEU 2.9 15.8 + - - -
820C VAL 3.8 1.1 - - - -
822C GLY* 1.3 75.1 - - - +
824C ILE* 1.3 57.0 + - - +
826C ALA* 3.9 5.8 - - - +
827C GLY* 2.9 25.6 + - - -
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Residues in contact with ILE 824 (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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631B MET* 5.9 4.9 - - - +
634B VAL* 5.9 6.2 - - + +
820C VAL 2.9 19.3 + - - +
821C ALA* 3.8 7.9 - - - +
823C GLY* 1.3 74.7 - - - +
825C VAL* 1.3 60.4 + - - +
827C GLY* 3.8 1.0 - - - -
828C ILE* 2.9 30.1 + - - +
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Residues in contact with VAL 825 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821C ALA 2.9 18.8 + - - +
822C GLY* 3.6 6.7 - - - +
824C ILE* 1.3 74.3 - - - +
826C ALA* 1.3 59.8 + - - +
828C ILE* 3.1 6.9 + - - +
829C PHE* 2.9 30.4 + - - +
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Residues in contact with ALA 826 (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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822C GLY 2.9 16.2 + - - +
823C GLY* 4.0 6.7 - - - +
825C VAL* 1.3 76.2 - - - +
827C GLY* 1.3 56.1 + - - +
829C PHE* 3.7 5.5 - - - +
830C LEU* 2.9 34.0 + - - +
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Residues in contact with GLY 827 (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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631B MET* 5.9 7.5 - - - +
823C GLY 2.9 19.6 + - - -
824C ILE* 3.8 1.8 - - - -
826C ALA* 1.3 79.2 - - - +
828C ILE* 1.3 55.2 + - - +
829C PHE 3.1 0.4 - - - -
830C LEU* 5.1 0.4 - - - -
831C ILE* 2.9 37.7 + - - +
832C PHE* 3.1 9.2 + - - -
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Residues in contact with ILE 828 (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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824C ILE 2.9 19.3 + - - +
825C VAL* 3.1 6.7 + - - +
827C GLY* 1.3 76.5 - - - +
829C PHE* 1.3 56.8 + - - +
832C PHE* 3.3 23.5 - - + +
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Residues in contact with PHE 829 (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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825C VAL 2.9 15.0 + - - +
826C ALA* 3.3 7.8 + - - +
828C ILE* 1.3 81.0 - - - +
830C LEU* 1.3 57.8 + - + +
832C PHE* 4.9 2.0 - - - -
833C ILE 5.7 0.8 + - - -
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Residues in contact with LEU 830 (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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826C ALA 2.9 14.8 + - - +
827C GLY* 5.1 0.4 - - - -
828C ILE 3.6 0.2 - - - -
829C PHE* 1.3 81.8 - - + +
831C ILE* 1.3 60.9 + - - +
832C PHE 3.1 5.1 + - - -
833C ILE 3.7 19.1 + - - +
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Residues in contact with ILE 831 (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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631B MET* 6.3 2.9 - - + -
827C GLY* 2.9 24.1 + - - +
830C LEU* 1.3 73.0 - - + +
832C PHE* 1.3 63.9 + - - +
833C ILE 3.5 3.4 - - - +
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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
------------------------------------------------------------
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