Contacts of the helix formed by residues 457 - 471 (chain A) in PDB entry 4PK7
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 ASN 457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A GLY 3.7 0.2 - - - -
456A PRO* 1.3 87.5 - - + +
458A ALA* 1.3 65.3 + - - +
459A ASN 3.1 1.1 - - - -
460A LEU* 2.9 30.8 + - - +
461A VAL* 3.2 9.2 + - - +
490A GLU* 4.4 7.4 + - - +
491A LEU* 3.9 36.2 - - + +
494A ASP* 3.2 30.1 + - - +
497A CYS* 4.2 6.9 - - - -
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Residues in contact with ALA 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A GLY 3.6 21.2 + - - +
456A PRO 3.1 3.0 + - - -
457A ASN* 1.3 77.4 - - - +
459A ASN* 1.3 62.2 + - - +
461A VAL* 3.2 5.6 + - - +
462A LYS* 3.0 27.6 + - + +
497A CYS* 3.8 22.3 - - - -
501A LEU* 4.3 17.7 - - + +
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Residues in contact with ASN 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A PRO 3.9 7.8 + - - +
457A ASN 3.0 1.0 + - - -
458A ALA* 1.3 79.8 - - - +
460A LEU* 1.3 63.5 + - + +
462A LYS* 3.6 13.9 + - - +
463A THR* 3.0 30.0 + - - -
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Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A TYR* 5.3 8.7 - - + +
436A LEU 5.2 1.1 - - - +
437A PHE* 3.5 48.9 - - + -
438A SER 4.2 14.8 - - - +
456A PRO 5.6 0.9 - - - +
457A ASN* 2.9 28.1 + - - +
459A ASN* 1.3 80.4 - - + +
461A VAL* 1.3 61.2 + - - +
463A THR* 3.3 8.1 - - - +
464A LEU* 3.2 18.4 + - - +
491A LEU* 3.7 27.5 - - + +
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Residues in contact with VAL 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ASN* 3.2 7.3 + - + +
458A ALA* 3.2 9.4 + - - +
460A LEU* 1.3 72.1 - - - +
462A LYS* 1.3 66.8 + - - +
463A THR 3.0 2.3 + - - -
464A LEU* 3.3 9.1 + - + +
465A VAL* 3.2 22.9 + - + +
491A LEU* 3.6 29.4 - - + +
494A ASP* 5.6 0.7 - - + +
497A CYS* 4.5 11.9 - - + -
498A MET* 4.0 22.7 - - + -
501A LEU* 4.6 12.6 - - + -
521A LEU* 3.8 29.8 - - + -
524A ILE* 6.3 1.1 - - + -
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Residues in contact with LYS 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 ALA* 3.0 22.0 + - + +
459A ASN* 3.6 15.5 + - - +
461A VAL* 1.3 76.8 - - - +
463A THR* 1.3 56.7 + - - +
465A VAL* 3.5 7.8 + - - +
466A PHE* 3.0 61.6 + - + -
501A LEU* 3.9 19.3 - - + -
512A ALA 3.3 26.9 + - - +
513A LEU* 3.9 22.4 - - + +
517A GLN* 5.0 0.4 + - - -
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Residues in contact with THR 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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436A LEU* 3.8 22.4 + - + +
437A PHE* 3.5 25.8 - - + -
459A ASN* 3.0 20.2 + - - -
460A LEU* 3.3 13.3 - - + +
462A LYS* 1.3 78.0 - - - +
464A LEU* 1.3 61.3 + - - +
466A PHE* 3.2 11.2 + - - +
467A PHE* 2.9 27.3 + - + +
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Residues in contact with LEU 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 LEU* 5.6 0.9 - - + -
437A PHE* 4.1 19.7 - - + -
460A LEU 3.2 9.3 + - - +
461A VAL* 3.3 11.9 + - + +
463A THR* 1.3 78.6 - - - +
465A VAL* 1.3 58.2 + - + +
467A PHE* 3.1 9.1 + - + +
468A PHE* 2.8 28.6 + - - +
480A LEU* 4.0 32.5 - - + -
481A VAL* 5.5 4.0 - - + -
484A MET* 4.9 11.9 - - + -
491A LEU* 5.6 5.4 - - + -
492A LEU* 4.0 27.6 - - + -
524A ILE* 3.8 29.2 - - + -
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Residues in contact with VAL 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 VAL* 3.2 17.4 + - + +
462A LYS* 3.7 10.5 - - - +
464A LEU* 1.3 76.4 - - - +
466A PHE* 1.3 61.0 + - + +
468A PHE* 3.6 2.5 + - - +
469A LEU* 3.1 35.8 + - + +
513A LEU* 6.0 1.6 - - + -
517A GLN* 3.8 28.0 - - + +
520A ALA* 3.9 14.8 - - + -
521A LEU* 3.9 29.8 - - + -
524A ILE* 3.9 20.9 - - + -
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Residues in contact with PHE 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 LYS* 3.0 56.1 + - + +
463A THR* 3.5 8.5 - - - +
464A LEU 3.2 0.2 - - - -
465A VAL* 1.3 79.1 - - + +
467A PHE* 1.3 68.0 + - - +
469A LEU* 3.2 7.6 + - + +
470A GLU* 2.9 38.5 + - + +
513A LEU* 5.8 0.2 - - + -
517A GLN* 3.2 42.0 - - + -
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Residues in contact with PHE 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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411A GLU* 6.0 0.9 - - - -
414A TYR* 3.7 44.4 - + + -
417A VAL* 4.9 2.0 - - + -
418A TYR* 4.0 14.8 - + - -
432A LEU* 3.5 44.2 - - + -
436A LEU* 4.8 9.9 - - + -
437A PHE* 5.4 4.0 - - + -
463A THR* 2.9 14.3 + - + +
464A LEU* 3.1 13.2 + - + +
466A PHE* 1.3 78.9 - - - +
468A PHE* 1.3 62.8 + - - +
470A GLU* 3.4 6.4 + - + +
471A SER* 3.1 33.3 + - - -
480A LEU* 3.9 24.9 - - + -
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Residues in contact with PHE 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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418A TYR* 4.0 5.8 - - - -
464A LEU 2.8 16.2 + - - +
465A VAL 3.8 3.1 - - - +
467A PHE* 1.3 77.6 - - - +
469A LEU* 1.3 61.9 + - + +
471A SER* 3.1 20.3 + - - +
474A HIS* 3.7 20.2 - - + +
475A GLU* 3.9 6.3 - - - -
476A HIS* 3.3 47.1 - - - -
477A ALA* 3.7 2.5 - - + -
480A LEU* 3.4 28.9 - - + -
520A ALA* 3.9 27.8 - - + -
523A GLU* 4.1 17.7 - - + -
524A ILE* 4.2 15.9 - - + -
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Residues in contact with LEU 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 VAL* 3.1 31.2 + - + +
466A PHE* 3.2 10.1 + - + +
468A PHE* 1.3 79.5 - - + +
470A GLU* 1.3 70.3 + - - +
471A SER 4.0 0.2 - - - +
472A GLU* 3.9 10.7 - - - +
516A ARG* 3.2 58.4 + - + +
517A GLN* 3.7 36.1 - - + +
520A ALA* 4.1 17.5 - - + -
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Residues in contact with GLU 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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411A GLU* 5.9 2.0 - - - +
466A PHE* 2.9 30.4 + - + +
467A PHE* 3.9 6.7 - - + +
469A LEU* 1.3 82.5 - - - +
471A SER* 1.3 62.7 + - - +
472A GLU* 3.3 13.9 + - - +
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Residues in contact with SER 471 (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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411A GLU* 5.6 5.4 - - - -
415A HIS* 5.2 13.7 - - - -
418A TYR* 2.5 43.6 + - - -
467A PHE* 3.1 25.7 + - - -
468A PHE 3.1 14.4 + - - +
469A LEU 4.0 1.9 - - - +
470A GLU* 1.3 73.4 - - - +
472A GLU* 1.3 59.5 + - - +
473A LEU* 3.3 7.4 + - - -
474A HIS 4.1 8.8 + - - +
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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