Contacts of the strand formed by residues 327 - 333 (chain A) in PDB entry 2ZL6
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 ASP 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A CYS* 1.3 74.5 - - - +
328A TRP* 1.3 62.0 + - - +
329A HIS* 4.0 8.4 + - + +
345A VAL 3.3 12.7 - - - +
346A ASP* 3.6 18.6 + - - +
376A ILE* 3.3 10.0 - - - +
377A SER* 2.8 45.7 + - - +
378A PRO 3.7 5.0 - - - +
379A PRO* 3.3 3.1 - - - +
380A SER* 2.5 48.6 + - - -
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Residues in contact with TRP 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PHE* 3.7 28.0 - + - -
321A PRO* 3.3 46.9 - - + -
323A LEU* 2.8 37.0 + - + +
326A CYS* 3.6 21.2 + - - -
327A ASP* 1.3 74.6 - - - +
329A HIS* 1.3 70.8 + - - +
330A ILE* 3.9 22.0 - - + -
343A TYR 3.6 0.4 - - - +
345A VAL* 2.8 55.1 + - + -
347A THR* 3.7 14.6 - - + +
352A PHE* 3.8 18.8 - + - -
359A ILE* 6.2 0.4 - - + -
373A LEU* 3.7 21.1 - - + -
375A TRP 4.2 0.7 - - - -
376A ILE* 4.5 1.8 - - + -
393A PRO* 3.9 7.9 - - + -
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Residues in contact with HIS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ASP* 4.1 10.1 + - + +
328A TRP* 1.3 81.6 + - - +
330A ILE* 1.3 61.7 + - - +
342A GLN* 3.8 7.9 - - + -
343A TYR 3.4 2.9 - - - -
344A ASP* 2.8 32.9 - - + +
373A LEU* 3.9 1.2 - - - +
374A SER* 2.9 26.5 + - - -
375A TRP* 2.9 77.9 + + + +
376A ILE* 4.0 1.8 - - - -
377A SER* 2.7 34.2 + - - -
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Residues in contact with ILE 330 (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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290A ILE* 4.2 21.5 - - + -
321A PRO* 4.6 4.9 - - + -
328A TRP* 3.9 26.5 - - + -
329A HIS* 1.3 76.9 - - - +
331A ASN* 1.3 62.4 + - - +
332A MET* 3.5 13.4 + - - -
341A THR 3.4 1.9 - - - +
342A GLN* 3.5 2.6 - - - -
343A TYR* 2.8 49.2 + - + +
345A VAL* 3.8 21.8 - - + -
359A ILE* 6.2 0.7 - - + -
371A GLY* 3.6 30.1 - - - -
372A VAL 3.4 9.4 - - - +
373A LEU* 4.2 13.7 - - + +
374A SER* 4.8 0.7 - - - -
340B GLN* 4.9 0.9 - - - -
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Residues in contact with ASN 331 (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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329A HIS 4.1 1.4 + - - -
330A ILE* 1.3 68.8 - - - +
332A MET* 1.3 61.2 + - - +
333A THR* 4.0 3.1 + - - +
340A GLN* 2.9 42.9 + - - +
341A THR 3.8 3.0 - - - +
370A VAL 3.7 0.9 - - - +
371A GLY* 3.2 2.6 - - - -
372A VAL* 2.8 48.8 + - + +
374A SER* 4.3 2.4 - - - -
331B ASN* 3.6 16.9 - - - +
340B GLN* 2.8 33.3 - - - +
374B SER* 2.9 19.2 + - - -
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Residues in contact with MET 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ILE* 3.9 12.6 - - + -
292A GLY 6.4 0.2 - - - +
299A ILE* 4.0 28.9 - - + -
330A ILE* 3.8 11.2 - - - +
331A ASN* 1.3 72.7 + - - +
333A THR* 1.3 61.1 + - - +
339A SER 4.2 0.2 - - - +
340A GLN* 3.2 8.1 - - - -
341A THR* 2.8 47.8 + - - +
343A TYR* 3.6 24.5 - - + -
364A ILE* 4.3 9.9 - - + -
369A TYR* 3.6 45.5 - - + -
370A VAL 3.4 4.9 - - - -
371A GLY* 3.8 20.4 - - - -
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Residues in contact with THR 333 (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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331A ASN* 4.0 5.3 + - - +
332A MET* 1.3 80.1 - - - +
334A GLN* 1.3 67.2 + - - +
339A SER 4.2 7.4 - - - +
340A GLN* 4.0 10.8 - - + -
369A TYR* 3.3 6.8 - - - -
370A VAL* 2.8 40.8 + - - +
374B SER* 3.2 33.9 + - - +
375B TRP* 4.1 9.2 - - + -
426B PRO* 3.6 23.2 - - - +
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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