Contacts of the strand formed by residues 486 - 492 (chain B) in PDB entry 1Z3S
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 ALA 486 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328B ARG* 3.2 19.1 - - - +
329B GLU* 3.8 10.3 - - + -
374B HIS 4.6 0.4 - - - -
375B LEU* 3.6 0.9 - - - +
376B LYS* 3.0 62.4 + - + +
484B LEU 3.6 0.4 - - - -
485B LYS* 1.3 86.5 - - + +
487B THR* 1.3 68.5 + - - +
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Residues in contact with THR 487 (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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326B GLN* 2.8 19.4 + - - -
327B ARG* 3.1 4.0 - - - +
328B ARG* 2.7 49.0 + - + +
374B HIS 3.4 6.5 - - - -
375B LEU* 3.5 22.4 - - + -
455B LEU* 3.8 14.3 - - + +
472B ILE* 3.8 27.1 - - + -
484B LEU* 4.0 7.0 - - + -
486B ALA* 1.3 80.4 - - - +
488B THR* 1.3 65.2 + - - +
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Residues in contact with THR 488 (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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324B ILE* 4.2 10.9 - - - +
326B GLN 3.4 10.0 + - - -
327B ARG* 4.8 11.9 + - - -
372B LYS 3.6 1.6 - - - +
373B ILE* 3.5 2.9 - - - -
374B HIS* 2.9 60.3 + - + +
375B LEU* 5.0 0.4 - - - +
376B LYS* 5.3 7.9 - - - +
487B THR* 1.3 79.5 - - - +
489B MET* 1.3 62.0 + - - +
490B MET* 2.8 26.7 + - + +
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Residues in contact with MET 489 (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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324B ILE* 3.5 4.2 - - - +
325B ILE* 2.7 52.8 + - + -
326B GLN* 3.0 38.1 + - + +
354B TRP* 4.4 8.5 - - + -
371B LEU* 4.5 20.6 - - + -
372B LYS 3.6 4.9 - - - -
373B ILE* 4.2 15.0 - - + -
390B PHE* 5.8 0.2 - - + -
416B ILE* 5.5 1.3 - - + -
445B TRP* 4.7 6.5 - - + -
446B TRP* 3.9 31.2 - - + -
455B LEU* 3.9 31.2 - - + -
488B THR* 1.3 75.8 - - - +
490B MET* 1.3 53.7 + - - +
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Residues in contact with MET 490 (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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314B ASP* 4.6 14.4 - - - +
317B ALA* 5.7 2.7 - - + -
322B TRP* 3.8 45.7 - - + -
323B THR 3.3 11.7 - - - +
324B ILE* 4.1 12.6 - - + -
325B ILE 4.3 0.4 - - - +
371B LEU* 3.3 4.5 - - - +
372B LYS* 2.9 50.5 + - + +
374B HIS* 4.7 7.2 - - + -
488B THR* 2.8 43.3 - - + +
489B MET* 1.3 75.3 - - - +
491B ILE* 1.3 65.1 + - - +
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Residues in contact with ILE 491 (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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321B GLY 4.0 1.0 - - - +
322B TRP* 3.7 3.3 - - - -
323B THR* 3.0 48.8 + - + +
325B ILE* 4.2 21.3 - - + -
360B VAL* 4.8 7.0 - - + -
363B LEU* 4.5 18.4 - - + -
364B THR* 4.4 12.1 - - + -
369B TYR* 3.9 27.3 - - + -
370B VAL 3.3 7.4 - - - +
371B LEU* 3.9 9.0 - - + -
390B PHE* 3.6 31.0 - - + -
490B MET* 1.3 79.5 - - - +
492B ARG* 1.3 65.2 + - - +
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Residues in contact with ARG 492 (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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285B ALA* 5.0 0.2 - - + -
318B GLY 2.6 29.7 + - - -
319B GLY* 3.9 5.9 - - - -
320B GLY 3.6 15.7 + - - -
321B GLY 4.1 11.7 - - - +
322B TRP* 3.3 44.2 - - + +
369B TYR* 3.4 6.9 - - - -
370B VAL* 2.7 40.1 + - - +
491B ILE* 1.3 81.4 - - - +
493B PRO* 1.3 90.2 + - + +
495B ASP* 3.2 28.4 + - - +
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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