Contacts of the strand formed by residues 327 - 333 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B CYS* 1.3 73.9 - - - +
328B TRP* 1.3 61.4 + - - +
329B HIS* 4.0 4.4 - - + +
344B ASP* 6.1 1.1 - - + +
345B VAL 3.3 12.2 + - - +
346B ASP* 3.7 19.5 + - - +
376B ILE* 3.3 10.2 - - - +
377B SER* 2.8 36.0 + - - +
378B PRO 3.6 2.2 - - - +
379B PRO* 3.4 3.8 - - - +
380B SER* 2.6 48.2 + - - -
4C GAL 2.7 27.4 + - - +
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Residues in contact with TRP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B PHE* 3.7 26.5 - + - -
321B PRO* 3.3 47.3 - - + -
323B LEU* 2.8 40.6 + - + +
326B CYS* 3.6 20.1 + - - -
327B ASP* 1.3 72.7 - - - +
329B HIS* 1.3 73.4 + - - +
330B ILE* 3.9 20.9 - - + -
343B TYR 3.6 0.2 - - - +
345B VAL* 2.8 53.4 + - + -
347B THR* 3.7 14.4 - - + +
352B PHE* 3.9 19.5 - + - -
359B ILE* 6.1 0.4 - - + -
373B LEU* 3.8 18.6 - - + -
375B TRP 4.1 2.5 - - - -
376B ILE* 4.5 1.3 - - + -
393B PRO* 3.9 7.0 - - + -
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Residues in contact with HIS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ASP* 4.0 5.7 - - + +
328B TRP* 1.3 85.7 + - - +
330B ILE* 1.3 61.6 + - - +
342B GLN* 3.9 8.3 - - + -
343B TYR 3.4 2.9 - - - -
344B ASP* 2.7 28.6 - - + +
373B LEU* 3.9 1.0 - - - +
374B SER* 2.9 27.5 + - - -
375B TRP* 2.9 65.2 + + + +
376B ILE* 3.9 1.4 - - - -
377B SER* 2.7 38.1 - - - -
4C GAL 3.2 7.7 + - - -
5C FUC 3.1 22.9 + - - -
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Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLN* 5.1 0.4 - - - -
288B ALA 5.7 0.2 - - - +
290B ILE* 4.2 28.0 - - + -
321B PRO* 4.4 7.4 - - + -
328B TRP* 3.9 35.4 - - + -
329B HIS* 1.3 75.8 - - - +
331B ASN* 1.3 63.4 + - - +
332B MET* 3.5 13.1 + - - -
341B THR 3.4 1.0 - - - +
342B GLN* 3.6 2.6 - - - -
343B TYR* 2.8 44.2 + - + +
345B VAL* 4.0 11.9 - - + -
359B ILE* 6.2 0.4 - - + -
371B GLY* 3.6 14.6 - - - -
372B VAL 3.4 24.5 - - - +
373B LEU* 4.1 12.8 - - + +
374B SER* 4.9 0.4 - - - -
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Residues in contact with ASN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASN* 3.6 28.4 - - - +
340A GLN* 2.8 23.9 + - - +
374A SER* 3.0 17.2 + - - -
329B HIS 4.0 1.4 + - - -
330B ILE* 1.3 70.1 - - - +
332B MET* 1.3 61.4 + - - +
333B THR* 4.0 3.1 + - - +
340B GLN* 2.9 40.9 - - - +
341B THR 3.7 3.0 - - - +
370B VAL 3.8 1.0 - - - +
371B GLY* 3.2 2.8 - - - -
372B VAL* 2.8 46.4 + - + +
374B SER* 4.3 2.6 - - - -
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Residues in contact with MET 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ILE* 3.9 12.6 - - + -
292B GLY 5.9 0.2 - - - +
299B ILE* 3.9 30.7 - - + -
330B ILE* 3.8 21.3 - - - -
331B ASN* 1.3 74.4 + - - +
333B THR* 1.3 60.7 + - - +
339B SER 4.1 0.2 - - - +
340B GLN* 3.1 7.8 - - - -
341B THR* 2.8 46.2 + - - +
343B TYR* 3.6 23.6 - - + -
364B ILE* 4.3 10.8 - - + -
369B TYR* 3.7 45.7 - - + -
370B VAL 3.4 5.2 - - - +
371B GLY* 3.8 10.3 - - - -
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Residues in contact with THR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A SER* 3.2 35.3 + - - +
375A TRP* 4.2 4.9 - - + -
426A PRO* 3.7 18.9 - - - +
331B ASN* 4.4 4.9 + - - +
332B MET* 1.3 79.5 - - - +
334B GLN* 1.3 66.2 + - - +
339B SER 4.0 11.2 - - - +
340B GLN* 3.9 11.2 - - + -
369B TYR* 3.3 7.1 - - - +
370B VAL* 2.9 47.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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