Contacts of the strand formed by residues 429 - 437 (chain A) in PDB entry 3PZ7
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 429 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A ILE* 6.0 0.4 - - - +
425A ARG* 3.9 18.0 + - + +
426A GLU 3.2 46.4 + - - -
427A GLY* 3.8 9.8 + - - -
428A ASN* 1.3 79.9 + - - +
430A ARG* 1.3 65.3 + - - +
431A TYR* 3.2 41.7 + - + +
465A VAL* 3.5 22.2 - - + +
466A GLU 2.9 20.6 - - - +
467A GLU* 4.4 6.9 - - + +
468A ASP* 3.9 4.9 - - - +
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Residues in contact with ARG 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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429A HIS* 1.3 73.8 - - - +
431A TYR* 1.3 64.6 + - - +
432A HIS* 3.7 15.7 + - + -
446A GLU* 2.8 36.9 + - - +
448A PHE* 5.8 0.6 - - + -
464A TRP 3.5 0.7 - - - +
465A VAL* 3.4 8.5 - - - +
466A GLU* 3.0 53.3 + - - +
467A GLU 4.8 3.6 - - - +
468A ASP* 3.0 37.0 - - + +
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Residues in contact with TYR 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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416A LEU* 4.0 13.2 - - + -
419A PHE* 3.7 21.3 - + - -
420A LYS* 3.5 38.5 + - + +
423A ILE* 4.2 14.9 - - + +
425A ARG 5.5 1.2 + - - -
427A GLY 5.0 1.6 + - - -
429A HIS* 3.2 53.1 + + + +
430A ARG* 1.3 77.0 - - - +
432A HIS* 1.3 59.5 - - - +
433A PHE* 3.4 22.1 - - + -
446A GLU* 3.2 8.0 + - - +
447A ILE 2.8 44.9 + - - +
448A PHE* 5.5 2.7 - - - -
464A TRP 3.6 3.4 - - - +
465A VAL* 4.0 12.1 - - + -
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Residues in contact with HIS 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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430A ARG* 3.7 17.5 + - + -
431A TYR* 1.3 74.2 + - - +
433A PHE* 1.3 63.3 + - - +
444A LYS* 3.9 26.9 - - + +
445A GLU 3.8 3.1 - - - -
446A GLU* 3.2 49.6 + - + -
463A ALA* 3.2 3.5 - - - +
464A TRP* 2.7 54.5 + - + +
466A GLU* 3.8 34.5 + - - +
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Residues in contact with PHE 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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416A LEU* 3.8 15.7 - - + -
419A PHE* 3.8 16.8 - + - -
431A TYR* 3.4 37.2 - - + -
432A HIS* 1.3 75.0 - - - +
434A LYS* 1.3 67.2 + - - +
435A ALA* 3.0 6.2 + - - +
443A VAL 3.5 0.3 - - - +
444A LYS* 4.2 0.6 - - - -
445A GLU* 3.0 37.5 + - - +
447A ILE* 3.9 22.7 - - + -
454A ILE* 3.8 32.1 - - + -
455A PRO* 3.9 22.7 - - + +
461A ILE* 4.1 2.7 - - + -
462A VAL 3.3 7.4 - - - +
463A ALA* 3.5 27.8 - - + -
464A TRP* 4.1 3.6 - - - -
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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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433A PHE* 1.3 70.5 - - - +
435A ALA* 1.3 59.7 + - - +
442A THR* 4.4 22.7 - - + +
443A VAL 3.7 5.6 - - - -
455A PRO* 3.9 19.1 - - - +
456A GLY* 4.7 3.3 + - - +
462A VAL* 2.9 49.3 + - + +
464A TRP* 3.5 14.5 - - + -
3318A EDO 4.1 25.9 + - - +
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Residues in contact with ALA 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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433A PHE 3.0 10.2 + - - +
434A LYS* 1.3 76.5 - - - +
436A MET* 1.3 64.8 + - - +
437A ASP* 4.0 0.7 - - + -
441A GLY 3.7 0.3 - - - +
442A THR* 3.4 7.1 - - - +
443A VAL* 3.1 36.0 + - + +
445A GLU* 4.0 22.4 - - + +
455A PRO* 4.0 19.5 - - + -
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Residues in contact with MET 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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435A ALA* 1.3 74.9 - - - +
437A ASP* 1.3 62.0 + - - +
438A PRO* 4.1 4.5 - - - +
441A GLY* 3.5 11.0 - - - +
442A THR* 3.9 24.7 - - + +
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Residues in contact with ASP 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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435A ALA 4.0 1.6 - - - -
436A MET* 1.3 75.6 - - - +
438A PRO* 1.3 69.0 - - - +
439A GLU* 3.0 35.3 + - - +
440A PHE* 3.1 28.4 + - + +
441A GLY* 2.9 39.7 + - - +
443A VAL* 4.7 11.2 - - + -
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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