Contacts of the helix formed by residues 423 - 436 (chain A) in PDB entry 1PD0
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 ALA 423 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A VAL* 3.8 11.1 - - + +
351A ASP 3.0 15.1 + - - +
352A ASN 4.6 2.0 - - - +
354A ILE* 5.6 1.1 - - + -
381A LEU* 3.9 24.2 - - + -
422A PHE* 1.3 69.0 - - - +
424A LEU* 1.3 64.3 + - - +
425A GLY 3.3 3.3 + - - -
426A PRO* 3.4 12.6 - - + +
427A ALA* 3.1 21.7 + - - +
452A LEU* 3.4 25.8 - - + +
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Residues in contact with LEU 424 (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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309A LEU* 3.9 20.4 - - + -
422A PHE* 3.2 26.4 + - + -
423A ALA* 1.3 73.8 - - - +
425A GLY* 1.3 65.7 + - - +
427A ALA* 4.5 1.8 - - - -
428A LEU* 2.7 63.9 + - + +
444A VAL* 4.2 11.7 - - + -
450A PRO* 3.7 36.0 - - + +
452A LEU 4.5 0.6 + - - -
483A TYR* 4.1 9.2 - - + +
499A LEU* 5.3 1.8 - - + -
512A LEU* 3.8 24.2 - - + -
515A LEU* 4.6 4.3 - - + -
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Residues in contact with GLY 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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424A LEU* 1.3 82.1 - - - +
426A PRO* 1.3 68.9 - - - +
428A LEU* 3.0 3.9 + - - +
429A LYS* 3.0 21.5 + - - +
450A PRO* 5.4 0.4 - - - +
452A LEU 4.9 0.6 + - - -
454A ILE* 3.2 24.6 + - - -
455A GLY* 4.9 0.8 + - - -
482A PHE* 3.8 23.0 - - - -
483A TYR* 5.0 2.0 + - - -
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Residues in contact with PRO 426 (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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354A ILE* 3.4 14.8 - - + +
381A LEU* 3.8 45.8 - - + +
383A GLU 6.0 0.7 - - - +
423A ALA* 3.4 18.6 - - + +
425A GLY* 1.3 86.1 - - - +
427A ALA* 1.3 56.6 + - - +
429A LYS* 2.9 11.7 + - + +
430A SER* 2.8 28.1 + - - -
452A LEU 4.0 2.9 - - - +
453A GLY* 4.0 12.1 - - - -
454A ILE* 3.7 19.0 - - + +
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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
----------------------------------------------------------
309A LEU* 3.7 16.0 - - + +
348A LEU* 4.1 2.3 - - + +
350A VAL* 3.4 35.2 - - + -
354A ILE* 3.3 17.1 - - + +
423A ALA 3.1 14.7 + - - +
424A LEU 3.7 3.4 - - - +
426A PRO* 1.3 76.7 - - - +
428A LEU* 1.3 53.5 + - - +
430A SER* 2.8 5.5 + - - -
431A ALA* 2.7 35.2 + - - +
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Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 3.4 15.9 - - + -
424A LEU* 2.7 55.4 + - + +
425A GLY* 3.2 4.7 - - - +
427A ALA* 1.3 72.9 - - - +
429A LYS* 1.3 56.2 + - - +
431A ALA* 3.3 3.4 + - - +
432A TYR* 2.8 28.2 + - - +
442A ILE* 4.2 8.2 - - + +
444A VAL* 3.9 13.5 - - + -
482A PHE* 4.3 9.2 - - + -
483A TYR* 4.2 9.0 - - + -
486A PHE* 3.4 37.1 - - + -
497A VAL* 5.2 2.5 - - + -
515A LEU* 3.9 23.6 - - + -
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Residues in contact with LYS 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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425A GLY 3.0 14.7 + - - +
426A PRO* 2.9 10.8 + - + +
428A LEU* 1.3 73.9 - - - +
430A SER* 1.3 64.7 + - - +
432A TYR* 3.3 7.6 - - - +
433A HIS* 2.9 42.6 + - + +
454A ILE* 3.9 24.2 - - + +
482A PHE* 3.5 29.8 - - + -
486A PHE* 4.3 9.9 - - + -
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Residues in contact with SER 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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348A LEU* 4.4 2.7 - - - -
354A ILE* 3.1 27.9 - - - +
356A TYR* 2.8 30.2 + - - -
383A GLU 5.1 5.7 + - - -
426A PRO 2.8 8.1 + - - -
427A ALA* 3.0 14.6 - - - -
429A LYS* 1.3 75.3 - - - +
431A ALA* 1.3 57.7 + - - +
433A HIS* 3.2 7.0 + - - +
434A LEU* 2.8 28.8 + - - +
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Residues in contact with ALA 431 (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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307A CYS* 3.7 23.6 - - - -
309A LEU* 4.6 1.8 - - + -
348A LEU* 3.8 9.6 - - + +
427A ALA 2.7 16.6 + - - +
428A LEU* 3.7 2.9 - - - +
430A SER* 1.3 73.0 - - - +
432A TYR* 1.3 64.8 + - - +
434A LEU* 2.8 19.9 + - - +
435A ILE* 3.0 17.7 + - - +
442A ILE* 3.5 29.8 - - + -
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Residues in contact with TYR 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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428A LEU 2.8 16.0 + - - +
429A LYS* 3.3 14.6 - - - +
430A SER 3.1 0.2 - - - -
431A ALA* 1.3 75.7 - - - +
433A HIS* 1.3 77.4 + + - +
436A GLY* 2.7 39.8 + - - -
442A ILE* 4.0 2.7 - - - +
486A PHE* 3.8 23.6 - + + -
489A ASP* 3.4 44.5 + - + +
490A CYS* 4.0 4.0 - - - -
492A LYS* 4.7 3.1 - - - +
493A VAL* 3.5 36.5 - - + +
495A ILE* 3.8 16.6 - - + +
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Residues in contact with HIS 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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389A PRO* 5.3 6.2 - - - +
429A LYS* 2.9 34.3 + - + +
430A SER* 3.2 7.5 + - - +
432A TYR* 1.3 99.0 - + - +
434A LEU* 1.3 63.3 + - - +
435A ILE 3.3 0.2 - - - -
436A GLY* 4.1 4.5 + - - +
437A GLY 5.1 1.9 + - - -
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Residues in contact with LEU 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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307A CYS* 4.3 4.5 - - - -
346A SER* 3.3 28.0 - - - +
348A LEU* 4.2 18.6 - - + -
356A TYR* 3.6 35.7 - - + +
389A PRO* 4.8 18.8 - - + +
392A MET* 4.2 18.4 - - + -
393A VAL* 3.6 27.4 - - + +
430A SER 2.8 11.1 + - - +
431A ALA* 2.8 12.5 + - - +
433A HIS* 1.3 80.0 - - - +
435A ILE* 1.3 59.6 - - + +
437A GLY 5.5 0.4 - - - -
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Residues in contact with ILE 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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305A THR* 3.6 28.3 - - + -
306A TYR 5.2 0.2 - - - +
307A CYS* 4.3 14.6 - - + -
393A VAL* 4.3 12.1 - - + -
431A ALA 3.0 15.5 + - - +
434A LEU* 1.3 84.5 - - + +
436A GLY* 1.3 63.3 + - - +
437A GLY 3.2 3.4 - - - -
438A VAL* 3.1 6.0 + - - +
439A GLY 2.8 27.6 + - - +
440A GLY* 4.0 19.7 - - - -
441A LYS 4.0 13.2 - - - +
442A ILE* 3.8 27.4 - - + -
495A ILE* 3.6 16.8 - - + -
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Residues in contact with GLY 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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432A TYR* 2.7 27.8 + - - -
433A HIS* 4.1 3.1 - - - -
434A LEU 3.8 0.8 - - - -
435A ILE* 1.3 72.8 - - - +
437A GLY* 1.3 60.7 + - - +
438A VAL* 3.1 1.8 + - - -
439A GLY 4.0 0.4 + - - -
493A VAL* 3.3 35.5 - - - +
495A ILE* 3.8 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