Contacts of the helix formed by residues 459 - 473 (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 GLY 459 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415D PRO 3.3 15.5 - - - -
416D PHE 3.5 2.5 - - - -
418D ILE* 4.7 1.3 - - - -
458D LYS* 1.3 80.5 - - - +
460D PHE* 1.3 62.9 + - - -
462D ILE* 3.9 1.5 - - - +
463D ASP* 2.9 24.8 + - - +
796D TRP* 3.3 30.7 - - - -
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Residues in contact with PHE 460 (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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415D PRO 3.3 4.2 + - - -
416D PHE* 3.0 35.3 + + + +
459D GLY* 1.3 67.9 - - - -
461D CYS* 1.3 66.3 + - - +
462D ILE 3.1 1.1 - - - -
463D ASP* 3.0 7.7 + - - +
464D ILE* 2.9 46.6 + - + +
529D PHE* 3.6 9.4 - + - -
530D ILE* 3.5 29.4 - - + -
789D MET* 3.6 24.2 - - - -
792D LEU* 3.4 44.6 - - + +
793D GLU* 3.6 9.4 - - - -
796D TRP* 3.9 16.5 - + + -
797D LEU* 4.2 14.4 - - + -
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Residues in contact with CYS 461 (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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416D PHE* 3.1 32.0 + - - +
417D VAL* 4.0 2.7 - - + -
460D PHE* 1.3 77.8 - - - +
462D ILE* 1.3 58.7 + - - +
464D ILE* 3.5 11.2 - - - +
465D LEU* 2.9 29.3 + - - +
510D VAL* 4.7 5.5 - - + +
511D GLY* 3.6 44.9 - - - +
512D SER* 4.7 0.4 - - - -
529D PHE* 3.7 28.0 - - + -
762D TYR* 5.1 0.2 - - - -
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Residues in contact with ILE 462 (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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410D THR* 5.2 2.0 - - + +
416D PHE 3.8 4.2 + - - +
417D VAL* 4.7 13.7 - - + -
432D ASN 5.3 3.6 - - - +
434D VAL* 3.6 19.9 - - + +
457D CYS* 3.5 27.6 - - + +
458D LYS* 3.2 39.9 - - - +
459D GLY 3.9 0.7 - - - +
460D PHE 3.1 0.2 - - - -
461D CYS* 1.3 75.9 - - - +
463D ASP* 1.3 66.9 + - - +
465D LEU* 3.2 8.0 + - + +
466D LYS* 2.9 29.0 + - + +
476D TYR* 5.1 1.0 + - - -
478D LEU* 3.7 29.4 - - + -
510D VAL* 5.4 4.7 - - + -
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Residues in contact with ASP 463 (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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432D ASN 5.4 1.2 - - - +
458D LYS* 5.2 0.9 - - - +
459D GLY 2.9 17.0 + - - +
460D PHE* 3.0 8.6 + - - +
462D ILE* 1.3 79.9 - - - +
464D ILE* 1.3 61.0 + - - +
466D LYS* 3.3 27.1 + - - +
467D LYS* 2.9 39.0 + - + +
792D LEU* 4.0 25.9 - - + +
795D LEU* 4.4 4.7 - - - +
796D TRP* 3.5 23.4 + - - +
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Residues in contact with ILE 464 (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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460D PHE* 2.9 38.2 + - + +
461D CYS* 3.5 10.8 - - + +
463D ASP* 1.3 76.1 - - - +
465D LEU* 1.3 58.1 + - - +
467D LYS* 3.2 5.0 + - - +
468D ILE* 2.9 46.1 + - + +
529D PHE* 4.5 22.9 - - + -
764D ILE* 4.8 7.9 - - + -
780D ILE* 5.3 4.0 - - + -
783D LEU* 4.2 6.1 - - + -
789D MET* 3.7 36.6 - - + -
792D LEU* 3.7 19.3 - - + -
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Residues in contact with LEU 465 (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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408D ILE* 3.6 26.0 - - + -
434D VAL* 5.9 0.7 - - + -
461D CYS 2.9 18.1 + - - +
462D ILE* 3.2 7.8 + - + +
464D ILE* 1.3 76.4 - - - +
466D LYS* 1.3 58.3 + - - +
468D ILE* 3.2 21.4 - - + +
469D SER* 2.9 31.6 + - - -
474D PHE* 4.5 6.1 - - + -
476D TYR* 3.7 33.9 - - + -
478D LEU* 3.9 15.3 - - + -
508D MET* 5.3 1.1 - - + -
510D VAL* 3.7 39.7 - - + +
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Residues in contact with LYS 466 (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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432D ASN* 3.7 30.1 + - - +
434D VAL* 4.8 13.9 - - + -
462D ILE* 2.9 16.1 + - - +
463D ASP* 3.6 29.9 + - - +
464D ILE 3.2 0.2 - - - -
465D LEU* 1.3 77.9 - - - +
467D LYS* 1.3 68.2 + - + +
469D SER* 2.5 22.9 + - - +
470D LYS* 2.9 18.0 + - + +
476D TYR* 4.1 12.9 + - - +
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Residues in contact with LYS 467 (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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463D ASP* 2.9 24.0 + - - +
464D ILE 3.2 4.0 + - - +
466D LYS* 1.3 88.9 - - + +
468D ILE* 1.3 57.4 + - - +
470D LYS* 3.1 8.3 + - + +
471D SER* 2.9 28.7 + - - -
783D LEU* 4.0 29.5 - - + +
788D GLU* 4.9 12.7 - - + +
792D LEU* 4.2 27.9 - - + +
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Residues in contact with ILE 468 (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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464D ILE* 2.9 23.4 + - + +
465D LEU* 3.2 34.3 - - + +
467D LYS* 1.3 75.2 - - - +
469D SER* 1.3 57.3 + - - +
471D SER* 3.7 8.7 - - - -
472D VAL* 2.9 32.0 + - + +
474D PHE* 3.4 6.6 - - + -
508D MET* 4.7 7.6 - - + -
764D ILE* 3.7 29.6 - - + -
776D VAL* 4.3 15.0 - - + +
779D ALA* 4.3 15.0 - - + +
780D ILE* 4.1 22.9 - - + -
783D LEU* 4.5 11.2 - - + -
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Residues in contact with SER 469 (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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465D LEU 2.9 17.1 + - - -
466D LYS* 2.5 27.9 + - - +
468D ILE* 1.3 76.4 - - - +
470D LYS* 1.3 56.0 + - - +
471D SER 3.1 5.2 - - - -
473D LYS* 3.2 25.8 + - - -
474D PHE* 3.5 27.3 + - - +
476D TYR* 3.5 30.3 - - - -
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Residues in contact with LYS 470 (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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466D LYS* 2.9 19.7 + - + +
467D LYS* 3.1 9.6 + - + +
469D SER* 1.3 75.8 + - - +
471D SER* 1.3 56.6 + - - +
473D LYS* 4.5 2.9 - - - +
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Residues in contact with SER 471 (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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467D LYS 2.9 15.4 + - - -
468D ILE* 4.0 7.9 - - - -
469D SER 3.1 0.2 - - - -
470D LYS* 1.3 80.3 - - - +
472D VAL* 1.3 60.6 + - - +
473D LYS* 3.2 6.6 + - - +
775D GLN* 4.4 8.0 + - - -
779D ALA* 3.8 20.2 + - - +
782D GLN* 5.6 2.9 - - - +
783D LEU* 5.4 6.9 - - - +
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Residues in contact with VAL 472 (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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468D ILE 2.9 18.2 + - - +
471D SER* 1.3 75.4 - - - +
473D LYS* 1.3 72.9 + - - +
474D PHE* 3.8 15.3 - - + -
772D TRP* 4.0 15.2 - - + -
775D GLN* 3.7 36.8 + - + +
776D VAL* 5.0 7.2 - - + -
779D ALA* 5.1 3.8 - - + +
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Residues in contact with LYS 473 (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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404D ASP* 4.9 5.5 - - - +
469D SER 3.2 11.2 + - - -
470D LYS 5.2 1.8 - - - -
471D SER 3.2 4.0 - - - +
472D VAL* 1.3 85.2 - - - +
474D PHE* 1.3 60.4 + - - +
772D TRP* 4.5 5.0 - - - -
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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