Contacts of the helix formed by residues 459 - 472 (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 GLY 459 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415B PRO 3.3 14.8 - - - -
416B PHE 3.6 2.2 - - - -
418B ILE* 4.6 1.3 - - - -
458B LYS* 1.3 79.9 - - - +
460B PHE* 1.3 64.2 + - - -
461B CYS 3.7 0.2 - - - -
462B ILE* 3.9 1.7 - - - +
463B ASP* 2.9 26.1 + - - +
796B TRP* 3.2 31.4 + - - -
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Residues in contact with PHE 460 (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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415B PRO 3.4 4.4 + - - +
416B PHE* 3.2 25.7 + + + -
459B GLY* 1.3 68.0 - - - +
461B CYS* 1.3 60.6 + - - +
462B ILE 3.1 3.8 - - - -
463B ASP* 3.0 8.0 + - - +
464B ILE* 2.9 39.6 + - + +
529B PHE* 3.5 22.7 - + - -
530B ILE* 3.5 31.9 - - + -
789B MET* 3.5 25.4 - - - -
792B LEU* 3.2 45.8 - - + -
793B GLU* 3.6 9.4 - - - -
796B TRP* 3.7 19.6 - + + -
797B LEU* 4.3 12.3 - - + -
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Residues in contact with CYS 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B PHE* 3.1 33.4 + - - +
417B VAL* 4.3 2.9 - - + -
460B PHE* 1.3 79.2 - - - +
462B ILE* 1.3 58.5 + - - +
464B ILE* 3.7 11.1 - - - +
465B LEU* 2.9 28.9 + - - +
510B VAL* 4.7 6.3 - - + +
511B GLY* 3.6 42.8 - - - +
512B SER* 5.0 0.2 - - - -
529B PHE* 3.7 28.5 - - + -
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Residues in contact with ILE 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B THR* 5.4 2.0 - - + +
416B PHE 3.9 3.8 + - - +
417B VAL* 4.9 11.2 - - + -
432B ASN 5.3 4.0 - - - +
433B THR* 5.5 0.2 - - - -
434B VAL* 3.7 26.5 - - + +
457B CYS* 3.7 19.3 - - + +
458B LYS* 3.2 41.3 - - - +
459B GLY 3.8 1.1 + - - +
460B PHE 3.1 0.6 - - - -
461B CYS* 1.3 78.0 - - - +
463B ASP* 1.3 65.0 + - - +
465B LEU* 3.3 8.9 + - + +
466B LYS* 2.9 28.8 + - + +
476B TYR* 5.4 0.9 + - - -
478B LEU* 3.7 29.8 - - + -
510B VAL* 5.5 2.2 - - + -
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Residues in contact with ASP 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B ASN* 5.1 9.4 + - - -
459B GLY 2.9 16.4 + - - +
460B PHE* 3.0 8.8 + - - +
462B ILE* 1.3 80.9 - - - +
464B ILE* 1.3 61.4 + - - +
466B LYS* 3.4 6.8 + - - +
467B LYS* 2.9 30.0 + - - +
792B LEU* 3.6 31.1 - - + +
795B LEU* 4.2 6.2 - - - +
796B TRP* 3.2 25.5 + - - +
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Residues in contact with ILE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B PHE* 2.9 37.9 + - + +
461B CYS* 3.7 10.5 - - + +
463B ASP* 1.3 77.2 - - - +
465B LEU* 1.3 59.0 + - - +
467B LYS* 3.2 4.2 + - - +
468B ILE* 2.9 42.3 + - + +
529B PHE* 4.4 19.1 - - + -
764B ILE* 4.8 14.6 - - + -
780B ILE* 5.2 4.0 - - + -
783B LEU* 4.0 8.1 - - + -
789B MET* 3.8 32.5 - - + -
792B LEU* 3.7 22.4 - - + -
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Residues in contact with LEU 465 (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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408B ILE* 3.6 24.7 - - + -
434B VAL* 5.8 0.7 - - + -
461B CYS 2.9 18.7 + - - +
462B ILE* 3.6 7.6 - - + +
464B ILE* 1.3 76.2 - - - +
466B LYS* 1.3 58.6 + - - +
468B ILE* 3.2 21.1 - - + +
469B SER* 2.9 30.1 + - - -
474B PHE* 4.7 4.9 - - + -
476B TYR* 3.7 31.2 - - + +
478B LEU* 3.8 20.2 - - + -
508B MET* 5.6 0.9 - - + -
510B VAL* 3.7 37.0 - - + -
764B ILE* 6.0 0.2 - - - -
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Residues in contact with LYS 466 (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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434B VAL* 5.2 7.4 - - + -
462B ILE* 2.9 18.1 + - + +
463B ASP* 3.7 7.4 - - - +
465B LEU* 1.3 76.5 - - - +
467B LYS* 1.3 58.4 + - - +
469B SER* 2.6 22.0 + - - -
470B LYS* 2.9 18.4 + - - +
476B TYR* 4.3 11.8 + - - +
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Residues in contact with LYS 467 (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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463B ASP 2.9 18.3 + - - +
464B ILE 3.6 4.3 - - - +
466B LYS* 1.3 78.3 - - - +
468B ILE* 1.3 57.5 + - - +
470B LYS* 3.2 7.9 + - - +
471B SER* 2.9 27.1 + - - -
783B LEU* 4.0 29.0 - - + +
792B LEU* 5.5 4.0 - - + -
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Residues in contact with ILE 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ILE* 2.9 25.1 + - + +
465B LEU* 3.2 32.5 - - + +
467B LYS* 1.3 74.2 - - - +
469B SER* 1.3 60.5 + - - +
471B SER* 3.6 7.2 - - - -
472B VAL* 2.8 36.4 + - + +
474B PHE* 3.5 6.8 - - + -
508B MET* 4.7 11.7 - - + -
764B ILE* 3.7 28.9 - - + -
776B VAL* 4.9 8.1 - - + +
779B ALA* 4.1 21.3 - - + -
780B ILE* 4.3 17.0 - - + -
783B LEU* 4.6 9.6 - - + -
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Residues in contact with SER 469 (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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465B LEU 2.9 17.1 + - - -
466B LYS* 2.6 26.5 + - - -
468B ILE* 1.3 78.4 - - - +
470B LYS* 1.3 58.3 + - - +
473B LYS* 3.2 24.1 + - - -
474B PHE* 3.4 25.5 + - - +
476B TYR* 3.5 32.2 - - - -
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Residues in contact with LYS 470 (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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466B LYS 2.9 18.6 + - - +
467B LYS* 3.2 7.2 + - - +
469B SER* 1.3 76.3 + - - +
471B SER* 1.3 60.4 + - - +
473B LYS* 4.3 4.5 + - - +
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Residues in contact with SER 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B LYS 2.9 16.0 + - - -
468B ILE* 3.9 7.4 - - - -
470B LYS* 1.3 79.8 - - - +
472B VAL* 1.3 64.7 + - - +
473B LYS* 3.1 4.2 + - - +
775B GLN* 5.4 4.6 + - - -
779B ALA* 3.9 19.9 - - - +
782B GLN* 5.7 2.4 - - - +
783B LEU* 5.6 6.0 - - - +
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Residues in contact with VAL 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ILE* 2.8 24.4 + - + +
471B SER* 1.3 71.6 - - - +
473B LYS* 1.3 70.6 + - - +
474B PHE* 3.6 11.9 - - + -
772B TRP* 3.6 34.8 - - + -
775B GLN* 3.6 51.4 - - + +
776B VAL* 4.4 8.5 - - + +
779B ALA* 4.0 13.7 - - + -
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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