Contacts of the strand formed by residues 341 - 344 (chain B) in PDB entry 1PZY
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 LYS 341 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257B PRO* 3.9 1.2 - - - +
258B MET* 3.0 46.0 + - + +
259B ASN* 4.4 1.4 + - - +
262B ASN* 4.9 0.5 + - - -
276B ALA* 3.2 9.0 - - + +
282B PHE* 3.5 40.3 - - + -
337B ALA 3.3 18.6 + - - +
338B VAL* 3.4 27.4 + - + +
339B ILE 3.5 1.5 - - - +
340B GLY* 1.3 78.0 - - - +
342B THR* 1.3 63.6 + - - +
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Residues in contact with THR 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 3.8 26.7 - - + -
256B ILE 3.5 16.6 - - - +
257B PRO* 4.2 5.9 - - - +
258B MET* 2.9 9.7 - - - +
262B ASN* 4.7 2.3 + - - -
264B TYR* 5.9 1.1 - - - +
273B ILE* 4.5 1.4 + - - +
274B SER* 3.8 21.2 - - - -
276B ALA 2.8 12.0 + - - -
277B MET* 3.3 12.8 - - + +
278B ASP 3.0 26.2 + - - -
293B VAL* 5.7 0.7 - - + -
340B GLY 3.2 9.8 + - - -
341B LYS* 1.3 76.9 + - - +
343B ARG* 1.3 71.5 + - - +
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Residues in contact with ARG 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 3.4 33.7 + - + +
149B PHE* 4.1 23.6 - - + -
254B ASP 3.4 1.2 - - - +
255B LEU* 3.4 3.6 - - - -
256B ILE* 2.8 39.9 + - - +
258B MET* 3.2 30.2 - - + +
278B ASP* 3.0 19.7 + - - +
282B PHE* 3.8 22.8 - - - -
342B THR* 1.3 75.2 - - - +
344B MET* 1.3 60.4 + - - +
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Residues in contact with MET 344 (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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149B PHE* 4.5 6.2 - - - -
254B ASP* 3.2 9.2 - - - +
255B LEU* 3.5 22.7 - - + -
277B MET* 4.3 6.7 - - + -
278B ASP* 3.1 21.7 + - - +
279B LYS* 3.6 42.2 - - + -
342B THR 5.5 0.2 - - - +
343B ARG* 1.3 74.7 - - - +
345B ILE* 1.3 71.7 + - - +
346B ARG* 3.2 20.2 + - + +
347B HIS* 4.8 4.3 - - - +
407B UDP 4.7 2.5 - - - +
408B MN 3.4 22.7 - - - +
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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