Contacts of the helix formed by residues 810 - 830 (chain A) 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 CYS 810 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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809A THR* 1.3 70.5 - - - +
811A GLU* 1.3 59.7 + - - +
812A ASN 3.2 1.1 - - - -
813A MET* 3.4 10.5 + - - +
814A ALA* 2.9 29.2 + - - +
555D SER* 4.2 13.0 - - - -
557D CYS* 2.0 46.7 - - - -
558D VAL* 4.7 2.0 - - - -
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Residues in contact with GLU 811 (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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552A ASP* 4.4 10.1 - - + +
809A THR* 3.2 7.6 - - - -
810A CYS* 1.3 80.0 - - - +
812A ASN* 1.3 58.1 + - - +
814A ALA* 3.3 9.0 + - - +
815A GLY* 2.9 25.6 + - - -
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Residues in contact with ASN 812 (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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550A THR 5.6 1.8 - - - +
551A LEU 4.4 4.9 - - - +
552A ASP* 3.7 14.0 - - - +
553A SER* 3.3 30.8 + - - +
809A THR* 3.6 17.4 + - - +
810A CYS 3.2 0.6 - - - -
811A GLU* 1.3 79.6 - - - +
813A MET* 1.3 57.6 + - - +
815A GLY 3.3 0.7 + - - -
816A VAL* 2.9 25.9 + - - +
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Residues in contact with MET 813 (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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809A THR 3.9 5.2 + - - +
810A CYS* 3.4 15.5 + - - +
812A ASN* 1.3 77.9 - - - +
814A ALA* 1.3 59.2 + - - +
816A VAL* 3.8 7.1 - - - +
817A PHE* 2.9 29.8 + - - +
558D VAL* 5.0 16.8 - - + -
561D MET* 6.0 5.0 - - + +
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Residues in contact with ALA 814 (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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810A CYS* 2.9 20.4 + - - +
811A GLU* 3.4 10.5 - - - +
812A ASN 3.2 0.2 - - - -
813A MET* 1.3 75.6 - - - +
815A GLY* 1.3 58.6 + - - +
817A PHE* 3.4 6.1 + - - +
818A MET* 2.9 28.1 + - - +
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Residues in contact with GLY 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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552A ASP* 5.9 1.1 - - - -
553A SER* 3.6 14.6 - - - -
811A GLU 2.9 14.1 + - - -
812A ASN 3.8 2.2 - - - -
814A ALA* 1.3 73.2 - - - +
816A VAL* 1.3 59.7 + - - +
818A MET* 3.2 7.6 + - - +
819A LEU* 2.9 29.6 + - - +
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Residues in contact with VAL 816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A SER* 3.4 17.1 - - - -
554A PHE* 5.2 1.1 - - + +
812A ASN 2.9 18.1 + - - +
813A MET* 3.8 8.5 - - - +
815A GLY* 1.3 75.2 - - - +
817A PHE* 1.3 58.0 + - - +
819A LEU* 3.9 4.9 - - - +
820A VAL* 2.9 30.9 + - - +
638D PHE* 5.3 4.8 - - + +
641D ILE* 6.0 6.5 - - + -
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Residues in contact with PHE 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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813A MET 2.9 19.7 + - - +
814A ALA* 3.7 7.0 - - - +
816A VAL* 1.3 75.4 - - - +
818A MET* 1.3 59.7 + - - +
820A VAL* 3.9 4.7 - - - +
821A ALA* 2.9 33.8 + - - +
561D MET* 5.6 12.1 - - + +
565D MET* 6.0 5.6 - - + -
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Residues in contact with MET 818 (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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814A ALA 2.9 18.1 + - - +
815A GLY* 3.2 8.9 + - - +
817A PHE* 1.3 77.2 - - - +
819A LEU* 1.3 56.7 + - - +
821A ALA* 4.3 2.8 - - - +
822A GLY* 2.9 26.7 + - - -
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Residues in contact with LEU 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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553A SER* 5.7 2.7 - - - -
554A PHE* 6.0 5.8 - - + -
815A GLY 2.9 15.5 + - - +
816A VAL* 3.9 6.3 - - - +
818A MET* 1.3 75.1 - - - +
820A VAL* 1.3 59.9 + - - +
822A GLY* 3.4 1.2 + - - -
823A GLY* 2.9 26.3 + - - -
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Residues in contact with VAL 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 VAL 2.9 19.0 + - - +
817A PHE* 3.9 6.1 - - - +
819A LEU* 1.3 77.0 - - - +
821A ALA* 1.3 56.7 + - - +
823A GLY* 3.4 1.4 + - - -
824A ILE* 2.9 29.9 + - - +
634D VAL* 5.4 7.9 - - - +
635D TRP* 6.1 1.1 - - - -
638D PHE* 3.9 26.7 - - + -
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Residues in contact with ALA 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 PHE 2.9 19.1 + - - +
818A MET* 4.3 3.1 - - - +
820A VAL* 1.3 74.7 - - - +
822A GLY* 1.3 58.6 + - - +
824A ILE* 3.7 7.2 - - - +
825A VAL* 2.9 29.8 + - - +
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Residues in contact with GLY 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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818A MET 2.9 20.8 + - - -
819A LEU* 3.7 1.3 - - - -
821A ALA* 1.3 75.7 - - - +
823A GLY* 1.3 58.2 + - - +
825A VAL* 3.2 5.7 + - - +
826A ALA* 2.9 30.3 + - - +
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Residues in contact with GLY 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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819A LEU 2.9 15.8 + - - -
820A VAL 3.8 1.3 - - - -
822A GLY* 1.3 75.5 - - - +
824A ILE* 1.3 57.0 + - - +
826A ALA* 3.8 6.4 - - - +
827A GLY* 2.9 25.1 + - - -
634D VAL* 5.8 5.6 - - - -
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Residues in contact with ILE 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 VAL 2.9 17.7 + - - +
821A ALA* 3.7 9.4 - - - +
823A GLY* 1.3 76.8 - - - +
825A VAL* 1.3 58.4 + - - +
827A GLY* 3.8 1.4 - - - -
828A ILE* 2.9 28.1 + - - +
631D MET* 5.2 17.3 - - + +
634D VAL* 5.8 5.5 - - + +
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Residues in contact with VAL 825 (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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821A ALA 2.9 18.8 + - - +
822A GLY* 3.6 6.1 - - - +
824A ILE* 1.3 75.0 - - - +
826A ALA* 1.3 59.9 - - - +
828A ILE* 3.1 6.9 + - - +
829A PHE* 2.9 29.6 + - - +
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Residues in contact with ALA 826 (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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822A GLY 2.9 17.4 + - - +
823A GLY* 4.0 7.0 - - - +
825A VAL* 1.3 76.7 - - - +
827A GLY* 1.3 56.9 + - - +
829A PHE* 3.6 6.3 + - - +
830A LEU* 3.2 27.4 + - - +
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Residues in contact with GLY 827 (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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823A GLY 2.9 17.4 + - - -
824A ILE* 3.8 1.6 - - - -
826A ALA* 1.3 77.5 - - - +
828A ILE* 1.3 63.0 + - - +
830A LEU* 3.4 20.7 - - - -
631D MET* 5.5 11.2 - - - +
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Residues in contact with ILE 828 (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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824A ILE 2.9 18.8 + - - +
825A VAL* 3.1 8.3 + - - +
827A GLY* 1.3 74.8 - - - +
829A PHE* 1.3 64.9 + - - +
830A LEU 4.6 1.6 - - - -
631D MET* 5.7 1.3 - - - +
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Residues in contact with PHE 829 (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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825A VAL 2.9 15.5 + - - +
826A ALA* 3.8 8.3 - - - +
827A GLY 3.3 0.2 - - - -
828A ILE* 1.3 79.5 - - - +
830A LEU* 1.3 59.1 + - + +
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Residues in contact with LEU 830 (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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826A ALA 3.2 14.4 + - - +
827A GLY* 3.4 17.5 - - - +
828A ILE 3.5 2.2 - - - -
829A PHE* 1.3 82.6 - - + +
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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