Contacts of the helix formed by residues 458 - 470 (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 PHE 458 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A PRO 4.5 2.2 - - - +
408A PHE* 2.7 47.7 + + + +
457A GLY* 1.3 69.5 - - - +
459A CYS* 1.3 63.5 + - - +
460A ILE 3.2 0.3 + - - -
461A ASP* 3.3 5.2 + - - +
462A LEU* 2.9 33.7 + - + +
533A PHE* 3.5 48.9 - + - -
534A LYS* 5.1 3.6 - - + -
785A MET* 4.3 5.8 - - + -
788A LEU* 3.5 44.1 - - + +
789A ASP* 3.4 25.6 - - - -
792A TRP* 4.3 17.7 - + + +
793A VAL* 4.9 4.3 - - + -
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Residues in contact with CYS 459 (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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408A PHE* 3.6 18.6 + - - -
409A VAL* 3.9 11.0 - - + -
458A PHE* 1.3 80.4 - - - +
460A ILE* 1.3 59.1 + - + +
462A LEU* 3.6 8.1 - - - +
463A LEU* 2.9 22.9 + - - +
514A VAL* 3.3 33.4 - - + +
515A ALA* 3.7 11.9 - - - -
516A PRO* 3.6 31.2 - - - -
533A PHE* 4.3 15.7 - - - -
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Residues in contact with ILE 460 (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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402A THR* 5.1 5.4 - - + -
408A PHE 5.2 0.7 - - - +
409A VAL* 4.9 13.7 - - + -
432A LYS 4.3 7.2 - - - +
434A VAL* 3.7 27.8 - - + +
455A CYS* 3.7 27.4 - - + +
456A TYR* 3.7 25.6 - - - +
457A GLY* 3.6 12.5 + - - +
458A PHE 3.1 0.6 - - - -
459A CYS* 1.3 75.8 - - + +
461A ASP* 1.3 66.5 + - - +
463A LEU* 3.0 13.5 + - + +
464A ILE* 2.9 39.3 + - + +
476A VAL* 4.6 11.9 - - + -
514A VAL* 6.0 0.9 - - + +
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Residues in contact with ASP 461 (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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431A VAL* 5.2 1.2 - - - +
432A LYS* 3.9 24.5 + - - +
457A GLY 2.9 21.8 + - - +
458A PHE* 3.7 3.4 - - - +
460A ILE* 1.3 78.6 - - - +
462A LEU* 1.3 56.7 + - - +
464A ILE* 3.2 16.1 + - - +
465A LYS* 2.9 27.0 + - - +
784A PHE* 5.1 2.1 - - - -
788A LEU* 4.4 19.6 - - + +
792A TRP* 3.7 21.8 + - - -
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Residues in contact with LEU 462 (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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458A PHE* 2.9 19.9 + - + +
459A CYS* 3.6 9.2 - - - +
460A ILE 3.2 0.2 - - - -
461A ASP* 1.3 77.0 - - - +
463A LEU* 1.3 55.9 + - - +
465A LYS* 3.2 12.7 + - + +
466A LEU* 2.9 37.8 + - + +
514A VAL* 5.1 5.8 - - + -
533A PHE* 3.6 44.9 - - + -
760A ILE* 4.5 5.6 - - + -
776A ILE* 3.7 27.1 - - + -
779A SER* 5.3 2.2 - - - +
784A PHE* 4.8 2.2 - - + -
785A MET* 3.8 17.3 - - + -
788A LEU* 4.6 14.7 - - + +
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Residues in contact with LEU 463 (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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400A ILE* 4.1 16.4 - - + -
434A VAL* 5.7 1.3 - - + -
459A CYS 2.9 14.7 + - - +
460A ILE* 3.0 16.4 + - + +
462A LEU* 1.3 74.2 - - - +
464A ILE* 1.3 60.9 + - + +
466A LEU* 3.4 10.8 + - + +
467A ALA* 2.9 27.5 + - - +
472A PHE* 3.8 26.0 - - + -
474A TYR* 4.2 17.0 - - + -
476A VAL* 3.7 31.9 - - + -
512A MET* 5.0 2.5 - - - -
514A VAL* 3.9 28.2 - - + +
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Residues in contact with ILE 464 (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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432A LYS* 3.7 30.3 - - + -
433A LYS 5.9 1.6 - - - +
434A VAL* 6.3 1.3 - - + -
460A ILE* 2.9 28.5 + - + +
461A ASP* 3.2 21.3 + - - +
463A LEU* 1.3 76.8 - - + +
465A LYS* 1.3 57.1 - - - +
467A ALA* 3.3 8.2 + - + +
468A ARG* 2.9 29.4 + - + +
474A TYR* 4.5 17.5 - - + +
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Residues in contact with LYS 465 (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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461A ASP 2.9 10.7 + - - +
462A LEU* 3.2 14.8 + - + +
464A ILE* 1.3 77.2 - - - +
466A LEU* 1.3 56.8 + - + +
468A ARG* 3.1 8.1 + - - +
469A THR* 2.9 32.9 + - - +
775A SER* 5.3 0.7 - - - -
779A SER* 5.5 4.3 - - - +
784A PHE* 3.5 36.1 - - + -
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Residues in contact with LEU 466 (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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462A LEU* 2.9 25.3 + - + +
463A LEU* 3.7 13.9 - - + +
465A LYS* 1.3 76.8 - - + +
467A ALA* 1.3 58.5 + - - +
469A THR* 4.0 2.6 - - - +
470A MET* 2.9 34.5 + - + +
472A PHE* 3.7 12.6 - - + -
512A MET* 4.8 10.8 - - - -
514A VAL* 5.3 2.9 - - + -
760A ILE* 4.4 14.4 - - + -
772A VAL* 4.1 35.0 - - + -
775A SER* 3.3 31.4 - - - +
776A ILE* 4.2 16.2 - - + -
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Residues in contact with ALA 467 (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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463A LEU 2.9 18.1 + - - +
464A ILE* 3.6 6.7 - - + +
465A LYS 3.2 0.2 - - - -
466A LEU* 1.3 76.6 - - - +
468A ARG* 1.3 61.5 + - - +
470A MET 2.9 19.4 - - - +
471A GLN* 3.6 8.7 - - - +
472A PHE* 3.6 18.9 + - + +
474A TYR* 3.9 27.4 - - + -
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Residues in contact with ARG 468 (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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464A ILE* 2.9 15.5 + - + +
465A LYS* 3.1 12.3 + - - +
467A ALA* 1.3 78.5 - - - +
469A THR* 1.3 66.2 + - - +
470A MET 4.7 0.3 - - - -
471A GLN* 4.9 1.7 + - - +
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Residues in contact with THR 469 (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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465A LYS 2.9 15.9 + - - -
466A LEU* 4.0 2.0 - - - -
468A ARG* 1.3 79.2 - - - +
470A MET* 1.3 62.8 + - + +
471A GLN 3.8 1.9 + - - -
775A SER* 3.7 28.5 + - - +
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Residues in contact with MET 470 (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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466A LEU 2.9 27.8 + - - +
467A ALA 2.9 7.8 - - - +
469A THR* 1.3 77.0 - - + +
471A GLN* 1.3 60.4 + - - +
472A PHE* 3.1 15.9 - - + -
768A TRP* 4.3 22.9 - - + -
771A GLN* 5.5 11.2 - - + +
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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