Contacts of the strand formed by residues 453 - 457 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C ARG* 2.8 16.1 + - - -
399C TYR* 3.7 34.1 - - + -
409C VAL* 3.5 9.0 - - + +
411C ASP* 3.9 26.9 - - + +
447C ASP* 4.3 6.7 - - + +
450C HIS* 3.1 15.0 + - + +
451C PRO 3.1 1.2 - - - -
452C SER* 1.3 77.0 + - - +
454C ILE* 1.3 57.9 + - - +
455C ILE 3.9 11.7 - - - +
456C TRP* 4.1 11.0 - - + -
482C ARG* 2.7 44.7 + - - +
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Residues in contact with ILE 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C TRP* 4.6 0.9 - - + -
333C ARG* 4.5 2.0 - - - +
335C VAL* 3.7 30.1 - - + +
342C LEU* 4.7 3.1 - - + -
344C LEU* 4.0 13.7 - - + -
349C LEU* 3.9 25.6 - - + -
351C ILE* 4.7 4.3 - - + -
408C TYR* 3.7 34.3 - - + -
409C VAL 3.0 15.3 + - - +
410C VAL* 5.6 0.7 - - + -
451C PRO 4.0 8.5 - - - +
452C SER 3.1 8.6 + - - +
453C VAL* 1.3 79.4 - - - +
455C ILE* 1.3 81.8 + - + +
482C ARG* 3.4 10.5 - - - +
483C PRO* 3.3 23.7 - - - +
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Residues in contact with ILE 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LEU* 4.0 18.6 - - + -
351C ILE* 6.0 2.7 - - + -
409C VAL 3.6 1.1 + - - +
410C VAL* 3.3 25.3 - - + -
411C ASP 3.1 24.3 + - - -
453C VAL* 3.8 6.0 - - - +
454C ILE* 1.3 97.6 - - + +
456C TRP* 1.3 76.3 + - - +
482C ARG* 4.4 1.1 - - - -
483C PRO* 3.4 21.3 - - + +
485C GLN* 3.8 31.0 - - + +
498C ILE* 3.7 24.5 - - + -
534C ILE* 5.1 3.4 - - + -
566C PHE* 5.6 3.6 - - + -
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Residues in contact with TRP 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C ASP* 3.5 35.7 - - + -
443C MET* 3.8 21.3 - - + -
444C VAL* 3.8 30.7 - - + +
447C ASP* 3.9 5.8 - - + -
448C ARG* 3.7 31.4 - - + -
453C VAL* 4.1 5.8 - - + -
455C ILE* 1.3 76.6 - - - +
457C SER* 1.4 55.5 + - - +
475C ILE* 3.4 41.6 - - + +
479C ASP* 2.8 24.0 + - - +
482C ARG* 3.3 47.5 - - + +
483C PRO 3.1 7.0 + - - +
484C VAL* 3.3 5.3 - - + +
485C GLN 2.8 30.8 + - - -
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Residues in contact with SER 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ARG* 4.7 0.3 + - - -
410C VAL* 3.8 19.3 - - - -
411C ASP 2.8 9.8 + - - +
412C GLU* 2.5 34.9 + - - -
413C ALA 3.0 24.9 + - - -
443C MET* 3.9 7.4 - - - +
455C ILE 4.2 0.2 + - - -
456C TRP* 1.4 75.9 - - - +
458C LEU* 1.3 61.5 + - - +
459C GLY 3.1 10.7 + - - -
475C ILE* 5.8 0.2 - - - -
485C GLN* 3.2 17.3 + - - +
486C TYR* 4.8 1.9 - - - -
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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