Contacts of the strand formed by residues 408 - 412 (chain A) 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 TYR 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A TRP* 3.7 21.1 - + - -
302A SER* 3.6 11.3 - - - -
303A ALA* 3.1 38.3 + - + +
304A GLU* 4.5 5.9 + - + +
344A LEU* 3.7 17.2 - - + +
349A LEU* 3.6 28.0 - - + +
351A ILE* 4.3 11.4 - - + -
385A ASN* 2.8 44.3 + - - +
386A ALA* 3.2 9.4 - - + +
387A VAL* 2.9 25.6 + - - +
407A LEU* 1.4 71.5 - - - +
409A VAL* 1.4 59.7 + - - +
452A SER 3.7 3.6 - - - -
454A ILE* 3.7 28.9 - - + -
566A PHE* 5.1 0.8 - - + -
644A PHE* 4.1 4.3 - - - -
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Residues in contact with VAL 409 (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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387A VAL* 3.3 10.3 - - + +
389A CYS* 3.8 19.5 - - - -
398A TRP* 4.9 1.6 - - - +
399A TYR* 4.4 7.2 - - + -
402A CYS* 3.7 38.4 - - + -
407A LEU 3.8 0.4 - - - +
408A TYR* 1.4 79.8 - - - +
410A VAL* 1.4 79.3 + - - +
411A ASP* 3.8 2.5 - - - +
452A SER* 2.6 27.9 + - - +
453A VAL* 3.5 14.7 - - + -
454A ILE* 2.9 26.9 + - - +
455A ILE 3.6 4.3 + - - +
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Residues in contact with VAL 410 (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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387A VAL 2.9 8.5 + - - -
388A ARG* 4.0 20.1 - - + +
389A CYS* 3.0 27.9 + - - +
409A VAL* 1.4 75.7 - - - +
411A ASP* 1.3 58.7 + - - +
412A GLU* 3.8 1.1 + - - +
454A ILE* 5.4 1.1 - - + -
455A ILE* 3.5 38.4 - - + +
457A SER* 3.8 27.6 - - - -
485A GLN* 4.3 11.9 - - - +
566A PHE* 3.5 33.2 - - + -
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Residues in contact with ASP 411 (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 CYS* 4.3 3.0 - - - -
393A PRO* 3.9 8.1 - - - +
399A TYR* 2.6 31.6 + - + -
409A VAL* 3.8 4.4 + - - -
410A VAL* 1.3 71.6 - - - +
412A GLU* 1.3 63.9 + - - +
443A MET* 3.7 12.3 - - - +
447A ASP* 2.4 39.3 - - - +
453A VAL* 3.8 22.8 - - + +
455A ILE 3.1 5.9 + - - -
456A TRP* 3.4 15.4 - - + -
457A SER 2.8 26.0 + - - +
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Residues in contact with GLU 412 (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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388A ARG* 2.8 28.7 + - - +
389A CYS* 3.6 19.3 - - - +
390A SER* 3.9 0.9 - - - -
391A HIS* 2.7 44.2 + - - +
392A TYR* 3.0 30.0 - - - -
393A PRO* 3.0 3.6 - - - +
410A VAL* 3.8 3.7 + - + +
411A ASP* 1.3 77.8 + - - +
413A ALA* 1.3 67.2 - - - +
443A MET* 3.4 5.4 - - - -
457A SER* 2.6 32.8 + - - +
459A GLY* 3.4 22.2 - - - -
460A ASN* 3.8 0.2 - - - +
485A GLN* 5.4 0.2 + - - -
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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