Contacts of the strand formed by residues 332 - 337 (chain B) in PDB entry 3EZE
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 GLU 332 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B THR 3.7 2.1 + - - +
331B SER* 1.3 72.9 - - - +
333B ILE* 1.3 59.1 + - - +
334B THR* 5.4 2.0 - - - +
345B LYS* 6.0 8.5 - - - +
365B ALA* 3.0 8.2 - - - +
366B GLU* 3.0 46.4 + - + +
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Residues in contact with ILE 333 (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 ALA* 3.8 35.9 - - + +
329B PHE* 4.3 4.5 - - + +
331B SER* 3.4 20.5 + - - +
332B GLU* 1.3 82.4 - - - +
334B THR* 1.3 68.9 + - - +
343B SER* 4.0 10.0 + - - -
344B ALA* 3.7 31.5 + - + -
345B LYS* 5.3 7.1 + - + +
363B ILE* 4.2 14.4 - - + -
364B SER 3.7 2.5 - - - -
365B ALA* 3.9 9.9 - - + -
373B ALA* 3.9 18.6 - - + -
377B LEU* 4.0 18.8 - - + -
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Residues in contact with THR 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B GLU* 5.4 2.1 - - - +
333B ILE* 1.3 77.6 + - - +
335B VAL* 1.3 69.5 + - - +
336B THR* 4.1 6.1 - - - +
341B SER* 4.0 23.1 - - - -
342B ALA 3.8 13.0 - - - +
343B SER* 5.0 3.3 + - - -
363B ILE* 3.5 4.7 - - - +
364B SER* 2.7 46.6 + - - +
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Residues in contact with VAL 335 (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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322B PHE* 4.0 32.1 - - + -
334B THR* 1.3 78.6 - - - +
336B THR* 1.3 63.2 + - - +
337B SER* 5.3 0.7 - - - -
341B SER* 3.2 2.3 - - - -
342B ALA 3.1 33.8 + - - +
344B ALA* 4.3 12.1 - - + -
350B LEU* 4.6 6.7 - - + -
353B LEU* 3.7 17.6 - - + +
355B LEU* 4.9 11.4 - - + -
361B VAL* 4.5 21.1 - - + -
362B THR 3.5 6.7 - - - +
363B ILE* 4.6 11.2 - - + -
381B MET* 5.6 2.9 - - + -
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Residues in contact with THR 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B THR* 4.2 4.9 - - - +
335B VAL* 1.3 72.4 - - - +
337B SER* 1.3 67.2 + - - +
338B ASN 5.2 0.4 - - - +
339B GLY* 4.9 9.2 - - - +
340B LYS 3.8 3.4 - - - +
341B SER* 3.4 23.3 + - - +
360B VAL 5.0 0.2 - - - +
361B VAL* 3.7 2.3 - - - -
362B THR* 2.8 47.5 + - - +
364B SER* 4.1 11.0 + - - -
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Residues in contact with SER 337 (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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335B VAL* 3.9 0.9 + - - -
336B THR* 1.3 75.6 - - - +
338B ASN* 1.3 76.9 + - - +
339B GLY 3.4 0.9 - - - -
340B LYS* 2.7 35.1 + - - +
353B LEU* 4.6 9.8 - - - +
354B GLY 4.2 5.9 + - - -
355B LEU* 3.4 31.9 - - - +
359B THR* 4.1 12.8 - - - +
360B VAL 5.2 1.3 + - - -
361B VAL* 4.3 10.8 - - - +
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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