Contacts of the strand formed by residues 453 - 457 (chain D) in PDB entry 1JZ3
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 VAL 453 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D ARG* 2.9 15.9 + - - -
399D TYR* 3.8 33.0 - - + -
409D VAL* 3.5 9.6 - - + +
411D ASP* 3.8 28.0 - - + +
447D ASP 4.3 6.1 - - - +
450D HIS* 3.2 18.6 + - + +
451D PRO 3.1 1.0 - - - -
452D SER* 1.4 76.9 + - - +
454D ILE* 1.3 60.1 + - - +
455D ILE 3.9 12.6 - - - +
456D TRP* 4.1 9.4 - - + -
482D ARG* 2.8 38.6 + - - +
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Residues in contact with ILE 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D TRP* 4.6 1.6 - - + -
333D ARG* 4.4 2.2 - - - +
335D VAL* 3.6 30.4 - - + +
342D LEU* 4.8 2.2 - - + -
344D LEU* 4.2 11.7 - - + -
349D LEU* 4.0 21.3 - - + -
351D ILE* 4.7 4.7 - - + -
408D TYR* 3.6 36.8 - - + -
409D VAL 3.0 12.5 + - - +
410D VAL* 5.7 0.4 - - + -
451D PRO 4.0 8.3 - - - +
452D SER 3.1 7.8 + - - +
453D VAL* 1.3 78.4 - - - +
455D ILE* 1.3 86.0 + - + +
482D ARG* 3.4 10.0 - - - +
483D PRO* 3.3 19.4 - - - +
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Residues in contact with ILE 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D LEU* 4.2 13.5 - - + -
351D ILE* 5.8 2.5 - - + -
409D VAL 3.6 1.0 + - - +
410D VAL* 3.5 24.1 - - + -
411D ASP 3.1 23.6 + - - -
453D VAL* 3.7 5.9 - - - +
454D ILE* 1.3 105.1 - - + +
456D TRP* 1.3 77.5 + - - +
482D ARG* 4.4 0.9 - - - -
483D PRO* 3.5 20.4 - - + +
485D GLN* 3.8 28.0 - - + +
498D ILE* 3.8 24.0 - - + -
534D ILE* 5.0 4.7 - - + -
566D PHE* 5.6 4.5 - - + -
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Residues in contact with TRP 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411D ASP* 3.5 34.1 - - + -
443D MET* 3.8 28.7 - - + -
444D VAL* 3.7 33.7 - - + -
447D ASP* 3.9 7.9 - - + -
448D ARG* 3.8 18.6 - - - -
453D VAL* 4.1 6.7 - - + -
455D ILE* 1.3 78.8 - - - +
457D SER* 1.4 58.7 + - - +
475D ILE* 3.4 40.9 - - + +
479D ASP* 2.8 30.4 + - - +
482D ARG* 3.4 39.8 - - + +
483D PRO 2.9 8.9 + - - +
484D VAL* 3.4 4.8 - - + +
485D GLN 2.9 25.5 + - - -
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Residues in contact with SER 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410D VAL* 3.7 18.4 - - - -
411D ASP 2.8 11.2 + - - +
412D GLU* 2.5 33.6 + - - -
413D ALA* 3.0 26.9 + - - +
443D MET* 3.9 5.8 - - - +
456D TRP* 1.4 74.0 - - - +
458D LEU* 1.3 60.7 + - - +
459D GLY 3.2 8.3 + - - -
475D ILE* 5.7 0.2 - - - -
485D GLN* 3.2 18.5 + - - +
486D TYR* 4.8 2.1 - - - -
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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