Contacts of the strand formed by residues 351 - 355 (chain B) 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 ILE 351 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342B LEU* 4.9 3.1 - - + -
349B LEU* 4.1 30.5 - - + -
350B LEU* 1.3 70.0 - - - +
352B ARG* 1.3 61.2 + - - +
353B GLY 3.5 5.1 + - - +
385B ASN* 3.8 1.6 - - - -
386B ALA* 3.7 9.9 - - + -
408B TYR* 4.4 15.0 - - + -
454B ILE* 4.8 8.5 - - + -
455B ILE* 5.9 1.8 - - + -
534B ILE* 4.2 19.5 - - + -
553B TRP* 3.6 6.8 - - - -
563B GLN 2.9 18.8 + - - +
564B GLY* 3.4 5.5 - - - -
565B GLY 3.2 35.3 + - - +
566B PHE* 3.7 29.8 - - + -
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Residues in contact with ARG 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B LEU* 3.3 40.3 + - - +
351B ILE* 1.3 68.7 - - - +
353B GLY* 1.3 59.1 + - - +
383B ASN 3.3 26.7 - - - +
384B PHE* 3.2 11.6 - - - -
385B ASN* 2.8 36.2 + - - +
386B ALA 3.3 1.2 + - - -
553B TRP* 3.4 26.7 - - + -
557B ARG* 3.9 2.2 - - - +
624B GLN* 2.8 28.7 + - + +
625B GLN 3.2 8.9 + - - -
626B PHE* 3.4 36.8 - - - -
641B GLU* 3.0 40.8 + - - +
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Residues in contact with GLY 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B ILE* 3.4 0.8 - - - -
352B ARG* 1.3 76.0 - - - +
354B VAL* 1.3 65.0 - - - +
384B PHE* 3.4 12.1 - - - -
386B ALA* 3.1 15.0 - - - -
538B TYR* 4.7 0.4 + - - -
565B GLY 2.9 19.6 + - - +
566B PHE* 3.6 14.6 - - - -
567B VAL* 3.0 18.9 + - - +
624B GLN* 4.5 1.3 + - - +
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B GLY* 1.3 77.1 - - - +
355B ASN* 1.3 75.7 + - - +
356B ARG* 5.1 0.4 - - + -
379B MET* 3.7 30.1 - - + -
384B PHE* 3.7 16.6 - - + -
386B ALA 3.1 3.9 + - - +
387B VAL* 3.3 4.8 - - + +
388B ARG 3.1 19.1 + - - -
566B PHE* 3.6 6.8 - - - -
567B VAL* 3.5 20.2 - - + +
569B ASP 3.8 3.8 - - - +
570B TRP* 3.5 35.9 - - + +
606B LEU* 4.4 4.0 - - + -
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Residues in contact with ASN 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B VAL* 1.3 75.3 - - - +
356B ARG* 1.3 60.2 + - - +
388B ARG* 3.0 42.4 + - - +
390B SER* 3.6 8.6 - - - +
536B CYS 2.9 21.7 + - - -
537B GLU* 3.7 2.0 - - - +
566B PHE* 3.2 22.5 + - - +
567B VAL 2.9 17.3 + - - +
568B TRP* 3.3 36.1 - - + -
569B ASP* 3.4 3.4 - - + +
570B TRP* 2.9 26.2 + - - +
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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