Contacts of the helix formed by residues 821 - 837 (chain D) 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 VAL 821 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639C PHE* 5.7 11.8 - - + +
642C ILE* 6.5 0.4 - - + -
550D PHE* 4.8 5.9 - - - +
820D GLY* 1.3 67.6 - - - +
822D PHE* 1.3 54.2 + - - +
823D TYR 3.1 2.3 - - - +
824D MET* 3.0 17.5 + - - +
825D LEU* 2.8 34.6 + - - +
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Residues in contact with PHE 822 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817D ASN 6.2 0.2 - - - +
818D MET* 5.8 2.2 - - - -
819D ALA* 4.3 9.2 - - + +
820D GLY 2.4 24.7 + - - +
821D VAL* 1.3 69.8 - - - +
823D TYR* 1.3 55.2 + - - +
825D LEU* 3.4 8.6 + - - +
826D GLY* 2.9 23.6 + - - -
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Residues in contact with TYR 823 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818D MET* 5.6 6.1 - - + +
819D ALA 3.5 18.3 + - - +
820D GLY* 4.9 4.0 - - - -
821D VAL 3.1 0.6 - - - +
822D PHE* 1.3 77.0 - - - +
824D MET* 1.3 61.2 + - - +
826D GLY* 3.3 2.5 + - - +
827D ALA* 2.9 27.5 + - - +
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Residues in contact with MET 824 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635C VAL* 5.3 2.4 - - - +
639C PHE* 5.8 8.5 - - + -
821D VAL* 3.0 18.8 + - - +
823D TYR* 1.3 78.4 - - - +
825D LEU* 1.3 58.8 + - - +
827D ALA* 3.4 6.7 + - - +
828D ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 825 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569C SER* 6.4 2.0 - - - -
821D VAL 2.8 15.3 + - - +
822D PHE* 3.6 10.1 - - - +
823D TYR 3.3 0.2 - - - -
824D MET* 1.3 76.3 - - - +
826D GLY* 1.3 58.7 + - - +
828D ALA* 3.5 8.3 + - - +
829D MET* 2.9 27.4 + - - +
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Residues in contact with GLY 826 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822D PHE 2.9 15.2 + - - -
823D TYR* 3.3 4.7 + - - -
824D MET 3.2 0.2 - - - -
825D LEU* 1.3 75.9 - - - +
827D ALA* 1.3 58.3 + - - +
829D MET* 3.1 8.0 + - - +
830D ALA* 2.9 27.5 + - - +
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Residues in contact with ALA 827 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823D TYR 2.9 15.9 + - - +
824D MET* 3.8 7.9 - - - +
826D GLY* 1.3 75.1 - - - +
828D ALA* 1.3 58.1 + - - +
830D ALA* 3.3 7.4 + - - +
831D LEU* 2.9 28.4 + - - +
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Residues in contact with ALA 828 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635C VAL* 3.8 28.0 - - + -
824D MET 2.9 18.0 + - - +
825D LEU* 3.7 9.0 - - - +
827D ALA* 1.3 76.4 - - - +
829D MET* 1.3 57.9 + - - +
831D LEU* 3.8 7.0 - - - +
832D SER* 2.9 29.1 + - - -
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Residues in contact with MET 829 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825D LEU 2.9 18.8 + - - +
826D GLY* 3.3 10.3 - - - +
828D ALA* 1.3 76.4 - - - +
830D ALA* 1.3 59.1 - - - +
832D SER* 3.5 6.5 + - - -
833D LEU* 2.9 27.0 + - - +
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Residues in contact with ALA 830 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826D GLY 2.9 12.3 + - - +
827D ALA* 3.7 11.2 - - - +
829D MET* 1.3 75.8 - - - +
831D LEU* 1.3 58.8 + - - +
833D LEU* 3.1 9.8 + - - +
834D ILE* 2.9 27.4 + - - +
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Residues in contact with LEU 831 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827D ALA 2.9 17.0 + - - +
828D ALA* 3.8 8.5 - - - +
830D ALA* 1.3 76.5 - - - +
832D SER* 1.3 57.3 + - - +
834D ILE* 3.2 8.8 + - - +
835D THR* 2.9 28.5 + - - -
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Residues in contact with SER 832 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828D ALA 2.9 18.8 + - - -
829D MET* 3.7 8.5 - - - -
831D LEU* 1.3 75.0 - - - +
833D LEU* 1.3 58.8 + - - +
835D THR* 3.7 7.6 - - - -
836D PHE* 2.9 32.9 + - - +
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Residues in contact with LEU 833 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829D MET 2.9 15.0 + - - +
830D ALA* 3.1 13.0 + - - +
832D SER* 1.3 76.9 - - - +
834D ILE* 1.3 58.2 + - - +
836D PHE* 4.1 3.9 - - - +
837D ILE* 3.4 26.5 + - - +
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Residues in contact with ILE 834 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830D ALA 2.9 14.3 + - - +
831D LEU* 3.2 9.2 + - - +
832D SER 3.2 0.2 - - - -
833D LEU* 1.3 76.3 - - - +
835D THR* 1.3 59.0 + - - +
836D PHE 3.5 0.2 - - - -
837D ILE* 4.3 4.2 - - - -
838D SER* 3.6 18.1 + - - -
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Residues in contact with THR 835 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831D LEU 2.9 15.6 + - - -
832D SER* 3.2 9.3 + - - -
834D ILE* 1.3 79.9 - - - +
836D PHE* 1.3 59.2 + - - +
837D ILE 3.5 0.4 - - - -
838D SER* 4.1 14.1 + - - +
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Residues in contact with PHE 836 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832D SER 2.9 16.6 + - - +
833D LEU* 4.6 3.6 - - - +
835D THR* 1.3 77.3 - - - +
837D ILE* 1.3 59.4 - - - +
838D SER 3.3 7.3 - - - +
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Residues in contact with ILE 837 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833D LEU 3.4 19.0 + - - +
834D ILE* 5.0 2.9 - - - +
836D PHE* 1.3 76.8 - - - +
838D SER* 1.3 62.3 + - - +
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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