Contacts of the helix formed by residues 733 - 740 (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 SER 733 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536C GLN* 4.9 2.5 - - - -
537C GLY 2.9 20.0 + - - +
539C THR* 3.4 20.0 - - - +
731C TRP 3.6 0.8 + - - -
732C ASP* 1.3 67.9 - - - +
734C ALA* 1.3 58.6 + - - +
735C VAL 3.0 5.4 - - - -
736C LEU 4.4 0.2 - - - +
737C GLU* 2.9 51.4 + - - +
752C LEU* 3.2 33.8 - - - +
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Residues in contact with ALA 734 (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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407C PRO* 3.3 15.8 - - - +
408C PHE* 3.6 15.9 - - + -
534C LYS* 3.4 30.2 + - - +
536C GLN* 4.0 10.5 - - + +
732C ASP* 3.2 0.8 - - - +
733C SER* 1.3 77.9 - - - +
735C VAL* 1.3 58.5 + - + +
737C GLU* 5.4 0.4 - - - -
738C PHE* 3.5 12.4 - - - +
758C PHE* 3.9 20.0 - - + -
793C VAL* 5.4 5.7 - - - +
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Residues in contact with VAL 735 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C GLN* 3.5 27.8 - - + +
406C GLU* 4.0 12.6 - - + -
407C PRO* 3.7 28.0 - - + -
408C PHE* 5.2 4.0 - - + -
516C PRO* 5.8 0.7 - - + -
714C ALA* 5.6 0.7 - - + -
718C ILE* 4.6 7.2 - - + -
731C TRP* 3.6 28.7 - - + +
732C ASP* 3.2 12.3 + - + +
733C SER 3.0 0.4 - - - -
734C ALA* 1.3 82.0 - - + +
736C LEU* 1.3 61.5 + - + +
737C GLU 3.3 1.3 - - - -
738C PHE* 3.1 5.5 + - - +
739C GLU* 2.9 36.9 + - + +
758C PHE* 5.4 0.9 - - + -
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Residues in contact with LEU 736 (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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539C THR* 3.3 35.9 - - + +
541C LEU* 3.5 42.7 - - + +
718C ILE* 5.1 2.2 - - + -
729C PHE* 3.4 24.9 - - + +
731C TRP* 3.6 28.3 - - + +
732C ASP 2.9 16.9 + - - +
735C VAL* 1.3 80.3 - - + +
737C GLU* 1.3 58.1 + - - +
739C GLU* 3.3 6.9 + - + +
740C ALA* 3.2 20.3 + - - +
748C THR* 3.4 21.5 - - + +
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Residues in contact with GLU 737 (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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539C THR* 5.1 2.7 - - + +
733C SER* 2.9 34.9 + - - +
734C ALA* 5.4 0.2 - - - -
736C LEU* 1.3 75.6 - - - +
738C PHE* 1.3 59.2 + - - +
740C ALA* 3.6 6.8 + - - +
741C SER* 2.8 25.6 + - - -
748C THR* 3.8 25.3 + - + +
752C LEU* 5.9 2.1 - - - +
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Residues in contact with PHE 738 (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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406C GLU 4.0 2.2 - - - -
407C PRO* 3.4 29.4 - - + -
410C TYR* 3.2 28.9 - + - -
733C SER 4.3 0.8 + - - -
734C ALA 3.5 16.3 + - - +
735C VAL 3.1 10.3 + - - +
737C GLU* 1.3 76.4 - - - +
739C GLU* 1.3 74.9 + - - +
740C ALA 3.1 2.0 - - - -
741C SER* 3.1 21.5 + - - -
742C GLN* 3.2 23.8 + - + +
792C TRP 3.2 28.3 - - - -
793C VAL* 4.3 19.7 - - + -
795C TYR 5.0 6.7 - - - -
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Residues in contact with GLU 739 (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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406C GLU* 3.2 24.2 - - - +
541C LEU* 4.5 13.2 - - + -
718C ILE* 3.7 39.6 - - + +
735C VAL* 2.9 18.7 + - + +
736C LEU* 3.3 10.3 + - - +
738C PHE* 1.3 92.7 - - - +
740C ALA* 1.3 56.7 + - - +
741C SER 3.2 3.1 - - - -
742C GLN* 4.0 7.3 - - - +
743C LYS* 3.2 33.3 + - - +
746C LEU* 4.0 12.5 - - + +
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Residues in contact with ALA 740 (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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736C LEU 3.2 14.6 + - - +
737C GLU* 3.8 10.5 - - - +
738C PHE 3.1 0.8 - - - -
739C GLU* 1.3 75.8 - - - +
741C SER* 1.3 60.7 + - - +
743C LYS 3.7 8.4 - - - +
744C CYS* 5.3 0.3 - - - -
746C LEU 3.3 23.7 - - - +
747C VAL* 4.5 5.6 - - + -
748C THR* 4.5 10.1 - - + +
798C CYS* 4.4 2.6 - - - +
799C ASP 4.1 15.8 - - - +
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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