Contacts of the helix formed by residues 822 - 840 (chain B) 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 PHE 822 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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821B VAL* 1.3 77.7 - - + +
823B TYR* 1.3 60.3 + - - +
824B MET 3.2 0.2 - - - -
825B LEU* 3.1 11.4 + - + +
826B GLY* 2.9 24.1 + - - -
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Residues in contact with TYR 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821B VAL 3.2 7.5 - - - +
822B PHE* 1.3 80.1 - - - +
824B MET* 1.3 56.3 + - - +
826B GLY* 3.3 3.0 + - - +
827B ALA* 3.1 24.6 + - - +
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Residues in contact with MET 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821B VAL* 3.2 15.9 + - - +
822B PHE 3.2 0.4 - - - -
823B TYR* 1.3 78.0 - - - +
825B LEU* 1.3 59.3 + - - +
827B ALA* 3.3 9.8 + - - +
828B ALA* 3.1 23.9 + - - +
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Residues in contact with LEU 825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A SER* 6.6 0.2 - - - -
635A VAL* 5.8 3.1 - - - +
639A PHE* 4.9 17.5 - - + -
821B VAL 3.4 5.8 + - - +
822B PHE* 3.1 16.5 + - + +
824B MET* 1.3 76.9 - - - +
826B GLY* 1.3 64.1 + - - +
828B ALA* 3.2 11.4 + - - +
829B MET* 3.2 18.7 + - - +
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Residues in contact with GLY 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822B PHE 2.9 13.7 + - - -
823B TYR* 3.3 6.4 + - - -
824B MET 3.2 0.4 - - - -
825B LEU* 1.3 77.0 - - - +
827B ALA* 1.3 59.0 + - - +
829B MET* 3.3 17.4 + - - +
830B ALA* 3.3 11.3 + - - +
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Residues in contact with ALA 827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823B TYR 3.1 12.8 + - - +
824B MET* 3.5 12.6 - - - +
825B LEU 3.2 0.2 - - - -
826B GLY* 1.3 75.1 - - - +
828B ALA* 1.3 60.6 + - - +
830B ALA* 3.2 11.1 + - + +
831B LEU* 2.9 25.6 + - - +
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Residues in contact with ALA 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632A LEU* 5.7 5.2 - - - +
635A VAL* 3.7 30.1 - - + -
824B MET 3.1 12.2 + - - +
825B LEU* 3.3 13.5 - - - +
826B GLY 3.2 0.4 - - - -
827B ALA* 1.3 77.0 - - - +
829B MET* 1.3 54.5 + - - +
831B LEU* 3.2 9.6 + - - +
832B SER* 2.7 33.0 + - - -
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Residues in contact with MET 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825B LEU 3.2 11.0 + - - +
826B GLY* 3.4 13.2 - - - +
827B ALA 3.2 0.4 - - - -
828B ALA* 1.3 77.6 - - - +
830B ALA* 1.3 57.1 + - - +
832B SER* 3.3 9.4 + - - -
833B LEU* 3.0 25.8 + - - +
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Residues in contact with ALA 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826B GLY 3.3 8.7 + - - +
827B ALA* 3.2 14.0 + - - +
829B MET* 1.3 77.8 - - - +
831B LEU* 1.3 58.8 + - - +
833B LEU* 3.4 8.1 + - - +
834B ILE* 3.1 24.3 + - - +
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Residues in contact with LEU 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827B ALA 2.9 13.7 + - - +
828B ALA* 3.2 12.1 + - - +
830B ALA* 1.3 74.5 - - - +
832B SER* 1.3 59.3 + - - +
834B ILE* 3.4 8.6 + - - +
835B THR* 2.9 27.0 + - - -
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Residues in contact with SER 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632A LEU* 4.9 16.6 - - - -
828B ALA 2.7 16.8 + - - -
829B MET* 3.4 11.9 - - - -
831B LEU* 1.3 78.0 - - - +
833B LEU* 1.3 57.3 + - - +
835B THR* 3.4 6.8 + - - -
836B PHE* 2.9 27.9 + - - +
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Residues in contact with LEU 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829B MET 3.0 13.2 + - - +
830B ALA* 3.6 11.4 - - - +
831B LEU 3.3 0.4 - - - -
832B SER* 1.3 76.1 - - - +
834B ILE* 1.3 61.1 + - - +
836B PHE* 3.4 9.0 + - - +
837B ILE* 3.3 21.0 + - - +
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Residues in contact with ILE 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830B ALA 3.1 13.5 + - - +
831B LEU* 3.6 12.3 - - - +
832B SER 3.3 0.4 - - - -
833B LEU* 1.3 76.6 - - - +
835B THR* 1.3 61.1 + - - +
837B ILE* 3.6 14.1 + - - +
838B SER* 3.7 11.4 + - - -
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Residues in contact with THR 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A SER 5.7 4.5 - - - -
631A ILE* 6.0 6.1 - - - -
831B LEU 2.9 16.9 + - - -
832B SER* 3.8 7.9 - - - -
833B LEU 3.2 0.2 - - - -
834B ILE* 1.3 75.4 - - - +
836B PHE* 1.3 62.5 + - - +
837B ILE 3.2 0.7 - - - -
838B SER* 3.5 8.6 + - - +
839B GLU* 3.4 20.3 + - - +
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Residues in contact with PHE 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832B SER 2.9 17.4 + - - +
833B LEU* 3.7 10.8 - - - +
834B ILE 3.3 0.4 - - - -
835B THR* 1.3 76.4 - - - +
837B ILE* 1.3 60.4 + - - +
838B SER 3.3 0.2 - - - -
839B GLU* 3.7 14.2 + - - +
840B HIS* 3.8 12.8 + - - +
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Residues in contact with ILE 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833B LEU 3.3 11.9 + - - +
834B ILE* 3.8 11.7 - - - +
835B THR 3.2 0.8 - - - -
836B PHE* 1.3 78.3 - - - +
838B SER* 1.3 59.2 + - - +
839B GLU 3.4 0.2 - - - -
840B HIS* 3.9 5.8 + - - +
841B LEU* 3.9 16.6 + - - +
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Residues in contact with SER 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834B ILE 3.7 9.4 + - - -
835B THR* 3.5 12.0 + - - -
836B PHE 3.3 0.2 - - - -
837B ILE* 1.3 78.5 - - - +
839B GLU* 1.3 61.5 + - - +
840B HIS 3.3 1.1 - - - -
841B LEU* 3.5 19.4 + - - +
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Residues in contact with GLU 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A SER* 5.4 12.8 - - - -
835B THR 3.4 14.0 + - - +
836B PHE* 3.9 9.9 - - - +
837B ILE 3.4 0.6 - - - -
838B SER* 1.3 79.9 - - - +
840B HIS* 1.3 56.9 + - + +
841B LEU 3.3 5.3 + - - +
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Residues in contact with HIS 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836B PHE 3.8 11.8 + - - +
837B ILE* 3.9 7.1 + - - +
838B SER 3.3 0.4 - - - -
839B GLU* 1.3 77.8 - - + +
841B LEU* 1.3 59.5 + - - +
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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