Contacts of the helix formed by residues 421 - 437 (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 HIS 421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384A TYR* 3.7 59.8 - + + +
385A ASP* 5.0 8.1 - - - -
388A VAL* 5.6 0.7 - - + -
419A SER* 3.1 7.4 + - - +
420A ALA* 1.3 77.7 - - + +
422A ARG* 1.3 67.0 + - - +
423A PRO* 3.5 32.9 - - + +
424A VAL* 3.3 17.1 + - + +
425A ALA* 3.2 18.4 + - - +
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Residues in contact with ARG 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ALA 3.7 3.4 + - - -
421A HIS* 1.3 69.8 - - - +
423A PRO* 1.3 77.8 - - + +
425A ALA* 2.9 2.4 + - - -
426A VAL* 2.8 37.5 + - + +
482A ASP* 2.9 49.0 + - - +
485A TRP* 4.3 9.7 - - - +
486A ASP* 3.8 30.9 + - - -
531A GLN* 5.1 0.2 - - - +
537A PRO* 4.4 9.9 - - - +
540A GLY 5.3 0.8 + - - -
541A ARG* 3.4 49.8 - - - +
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Residues in contact with PRO 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A VAL* 3.6 20.4 - - + +
421A HIS* 3.5 28.3 - - + +
422A ARG* 1.3 94.5 - - + +
424A VAL* 1.3 60.7 + - - +
426A VAL* 3.8 5.8 + - + +
427A ALA* 3.3 22.0 + - - +
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Residues in contact with VAL 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A THR 5.6 2.0 - - - +
384A TYR* 3.9 24.5 - - + +
387A ALA* 4.6 8.1 - - + -
388A VAL* 3.8 18.4 - - + -
391A ILE* 3.8 12.2 - - + +
416A LEU* 3.9 15.0 - - + +
419A SER* 3.2 32.5 - - - +
421A HIS* 3.3 21.7 + - + +
422A ARG 3.2 0.8 - - - -
423A PRO* 1.3 74.2 - - - +
425A ALA* 1.3 63.4 + - - +
427A ALA* 3.2 4.7 + - - +
428A ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 425 (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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416A LEU 3.5 15.3 - - - +
417A VAL* 3.6 6.5 - - - +
419A SER 4.3 1.1 - - - +
421A HIS 3.2 8.0 + - - +
422A ARG* 2.9 7.0 + - + +
424A VAL* 1.3 80.3 - - - +
426A VAL* 1.3 53.6 + - - +
428A ALA* 3.3 2.8 + - - +
429A GLY* 2.8 30.8 + - - -
483A SER* 3.6 19.1 - - - +
541A ARG* 3.5 34.8 - - - +
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Residues in contact with VAL 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ARG* 2.8 57.1 + - + +
423A PRO* 4.1 5.4 - - + +
425A ALA* 1.3 78.5 - - - +
427A ALA* 1.3 57.5 + - + +
429A GLY* 3.8 0.7 - - - -
430A GLU* 3.0 46.8 + - + +
482A ASP 4.4 2.2 - - - +
483A SER* 3.7 19.7 - - - +
486A ASP* 3.7 19.1 - - + +
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Residues in contact with ALA 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A VAL* 4.2 18.8 - - + +
391A ILE* 3.5 26.3 - - + +
392A LYS* 4.2 16.3 - - + +
395A THR* 4.3 2.6 + - - -
423A PRO 3.3 16.1 + - - +
424A VAL* 3.2 6.3 + - - +
426A VAL* 1.3 78.6 - - - +
428A ALA* 1.3 59.0 + - - +
430A GLU* 3.4 13.0 + - - +
431A PHE* 3.1 20.1 + - - +
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Residues in contact with ALA 428 (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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391A ILE* 3.9 11.6 - - + +
413A VAL* 3.4 28.7 - - + +
414A TYR* 5.4 0.3 - - - -
416A LEU* 3.9 14.8 - - + -
417A VAL* 4.0 9.9 - - + +
424A VAL 2.9 17.2 + - - +
425A ALA 3.7 4.3 - - - +
427A ALA* 1.3 76.5 - - - +
429A GLY* 1.3 58.8 + - - +
431A PHE* 3.3 6.0 + - - +
432A LEU* 2.8 29.5 + - - +
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Residues in contact with GLY 429 (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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417A VAL* 4.1 5.8 - - - +
425A ALA 2.8 17.2 + - - -
426A VAL 3.8 2.2 - - - -
427A ALA 3.3 0.2 - - - -
428A ALA* 1.3 77.4 - - - +
430A GLU* 1.3 56.6 + - - +
432A LEU* 3.3 5.0 + - - +
433A TYR* 2.9 29.6 + - - +
483A SER* 4.2 7.6 - - - -
484A MET* 3.7 22.5 - - - +
487A CYS* 3.9 7.1 - - - -
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Residues in contact with GLU 430 (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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392A LYS* 4.4 15.5 + - - +
395A THR* 5.0 5.8 - - + +
426A VAL* 3.0 39.4 + - + +
427A ALA* 3.7 10.7 - - - +
428A ALA 3.2 0.2 - - - -
429A GLY* 1.3 75.8 - - - +
431A PHE* 1.3 62.8 + - - +
433A TYR* 3.3 3.7 + - - +
434A LYS* 3.1 31.8 + - + +
486A ASP* 4.7 7.3 - - - +
487A CYS* 4.0 26.0 - - + +
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Residues in contact with PHE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ILE* 4.3 2.0 - - + -
394A LEU* 3.7 24.2 - - + -
395A THR* 3.7 27.2 + - - +
398A LEU* 3.6 31.6 - - + +
405A LEU* 4.1 7.9 - - + -
410A CYS* 3.9 29.6 - - + -
413A VAL* 3.2 38.8 - - + -
414A TYR* 3.8 22.4 - + - -
427A ALA 3.1 14.3 + - - +
428A ALA 3.4 7.2 - - - +
430A GLU* 1.3 76.4 - - - +
432A LEU* 1.3 58.2 + - - +
434A LYS* 3.4 2.6 + - - +
435A LYS* 2.9 31.3 + - + +
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Residues in contact with LEU 432 (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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414A TYR* 3.7 33.9 - - + -
417A VAL* 4.2 11.2 - - + -
428A ALA 2.8 21.0 + - - +
429A GLY* 3.3 5.8 + - - +
431A PHE* 1.3 70.7 - - - +
433A TYR* 1.3 65.9 + - - +
435A LYS* 3.9 0.2 - - - +
436A LEU* 3.1 31.3 + - + -
437A PHE* 3.6 18.0 - - + -
464A LEU* 5.6 0.7 - - + -
467A PHE* 3.5 45.5 - - + -
480A LEU* 4.7 3.4 - - + -
484A MET* 3.9 20.9 - - + -
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Residues in contact with TYR 433 (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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429A GLY 2.9 13.8 + - - +
430A GLU 3.4 9.9 - - - +
432A LEU* 1.3 74.1 - - - +
434A LYS* 1.3 69.9 + - + +
437A PHE* 2.7 75.7 + + + +
460A LEU* 5.3 7.8 - - + +
484A MET* 4.0 15.5 - - + -
487A CYS* 3.7 29.1 + - + -
488A ALA* 3.8 18.2 - - + -
490A GLU* 3.3 19.1 + - - -
491A LEU* 5.1 4.8 - - + +
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Residues in contact with LYS 434 (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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395A THR* 3.2 28.3 - - + +
398A LEU* 4.4 11.7 - - + -
399A GLN* 2.4 44.8 + - - -
430A GLU* 3.1 20.5 + - + +
431A PHE 4.0 2.9 - - - +
433A TYR* 1.3 84.8 - - + +
435A LYS* 1.3 63.7 + - - +
437A PHE 4.5 5.5 + - - +
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Residues in contact with LYS 435 (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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398A LEU* 3.9 30.9 - - + +
402A GLU* 4.9 17.5 - - + +
405A LEU* 5.5 3.6 + - - -
410A CYS* 3.4 28.7 - - - -
414A TYR* 2.9 29.4 + - + +
431A PHE* 2.9 22.3 + - + +
432A LEU 3.9 2.9 - - - +
434A LYS* 1.3 79.9 - - - +
436A LEU* 1.3 69.7 + - + +
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Residues in contact with LEU 436 (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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414A TYR* 3.6 38.8 - - + +
432A LEU* 3.1 21.8 + - + +
435A LYS* 1.3 92.2 - - + +
437A PHE* 1.3 74.4 + - + +
438A SER 4.0 2.6 + - - -
460A LEU* 5.2 0.5 - - - +
463A THR* 3.8 17.8 + - + +
467A PHE* 4.8 10.1 - - + -
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Residues in contact with PHE 437 (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* 3.6 33.7 - - + -
433A TYR* 2.7 57.7 + + + +
434A LYS* 5.1 4.1 - - - +
435A LYS 3.8 1.2 - - - -
436A LEU* 1.3 79.0 - - + +
438A SER* 1.3 64.4 + - - +
460A LEU* 3.5 45.8 - - + -
463A THR* 3.5 22.7 - - + -
464A LEU* 4.0 26.0 - - + -
467A PHE* 5.4 3.6 - - + -
484A MET* 4.6 7.6 - - + -
491A LEU* 4.2 17.7 - - + -
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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
------------------------------------------------------------
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