Contacts of the strand formed by residues 320 - 325 (chain B) in PDB entry 4PBY
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 ILE 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277B ASN* 3.0 24.8 + - - +
278B CYS* 4.2 0.9 - - - -
292B GLY* 4.1 16.1 - - - -
293B SER 3.1 17.4 + - - +
296B LYS 3.5 20.6 - - - +
297B THR 3.3 28.5 - - - +
298B VAL* 4.0 5.2 - - + -
316B HIS* 3.5 36.8 - - + +
318B ASP 4.0 2.0 - - - +
319B GLU* 1.3 76.3 - - - +
321B PHE* 1.3 63.2 + - - +
322B GLN 3.7 16.2 - - - +
323B VAL* 5.3 0.2 - - + -
335B SER* 4.3 8.7 - - - -
336B SER 3.5 13.7 - - - +
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Residues in contact with PHE 321 (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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129B ARG* 4.9 7.1 + - - -
231B GLU* 5.5 3.8 - - - -
277B ASN* 3.6 30.2 - - + +
278B CYS* 3.4 18.5 - - - +
319B GLU* 3.2 30.9 + - + -
320B ILE* 1.3 74.3 - - - +
322B GLN* 1.3 65.2 + - + +
336B SER 3.0 7.2 + - - +
337B GLY* 4.6 4.3 - - - -
338B THR* 3.4 27.8 - - - -
376B LYS* 3.5 34.3 - - - -
377B ILE 5.0 5.6 - - - +
378B SER* 5.1 6.1 - - - +
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Residues in contact with GLN 322 (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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129B ARG* 3.7 23.8 - - - +
131B ARG* 4.0 8.5 - - - +
232B ASP* 5.0 3.3 - - - +
278B CYS* 3.7 10.8 - - - +
279B LEU 5.4 0.9 - - - +
320B ILE* 3.7 1.9 - - - +
321B PHE* 1.3 81.7 - - + +
323B VAL* 1.3 77.1 + - - +
324B GLN* 3.1 26.6 + - + +
335B SER* 3.2 6.8 - - - -
336B SER* 3.0 42.8 + - - +
378B SER 4.8 8.7 - - - +
379B ASP* 2.8 30.4 + - - +
380B PHE* 3.6 20.4 - - + +
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Residues in contact with VAL 323 (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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278B CYS* 3.3 38.1 - - + +
279B LEU* 4.0 13.1 - - - +
280B SER* 3.3 9.4 - - - +
290B ALA* 4.1 15.9 - - + +
292B GLY* 4.2 6.7 - - - +
298B VAL* 4.3 10.8 - - + -
322B GLN* 1.3 78.7 + - - +
324B GLN* 1.3 79.7 + - - +
333B LEU* 3.6 24.7 - - + -
334B ALA 3.3 13.7 - - - +
335B SER* 4.5 4.9 - - - -
380B PHE* 4.5 0.2 - - - -
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Residues in contact with GLN 324 (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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131B ARG* 6.2 1.1 - - - +
279B LEU 5.0 2.4 - - - +
280B SER* 3.9 9.2 + - - -
322B GLN* 3.1 21.4 + - + +
323B VAL* 1.3 87.1 - - - +
325B TRP* 1.3 60.5 + - - +
333B LEU* 4.2 3.1 - - - -
334B ALA 3.0 24.9 + - - +
380B PHE* 3.6 41.8 + - + +
381B SER* 5.4 5.8 + - - +
382B TRP* 2.9 30.7 + - + +
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Residues in contact with TRP 325 (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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280B SER* 3.1 50.2 + - - +
281B PHE 3.2 13.9 - - - +
282B ASN* 3.2 37.3 - - + +
283B PRO* 3.6 20.0 - - + +
288B ILE* 4.0 8.7 - - + -
289B LEU 4.2 1.3 - - - -
290B ALA* 3.9 7.8 - - + +
300B LEU* 3.7 31.2 - - + -
324B GLN* 1.3 75.1 + - - +
326B SER* 1.3 65.7 + - - +
327B PRO* 3.6 2.6 - - - +
329B ASN 5.3 0.2 - - - -
330B GLU* 3.8 10.5 - - - -
332B ILE 3.4 21.1 - - - -
333B LEU* 3.5 31.7 - - + +
347B LEU* 3.8 21.8 - - + -
382B TRP* 3.4 9.5 - - - -
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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