Contacts of the strand formed by residues 276 - 281 (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 VAL 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B GLU* 3.3 19.1 - - - +
246B VAL* 3.4 35.3 - - + +
247B ALA 3.2 18.7 + - - +
250B GLN 3.7 31.2 - - - +
251B LYS 4.1 2.2 - - - +
271B ALA* 4.6 2.9 - - + -
272B HIS* 3.6 29.6 - - + -
274B ALA 3.7 3.8 - - - +
275B GLU* 1.3 75.8 - - - +
277B ASN* 1.3 59.6 + - - +
278B CYS 3.6 0.2 - - - -
291B THR* 3.9 10.1 - - + -
292B GLY 3.6 13.5 - - - +
293B SER* 4.2 0.4 - - - +
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Residues in contact with ASN 277 (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* 5.6 1.6 + - - -
231B GLU* 3.2 41.9 - - + +
232B ASP* 3.5 12.3 - - - +
246B VAL* 4.0 1.3 - - - -
248B ASP* 4.3 1.4 - - - +
275B GLU* 4.3 4.2 - - - +
276B VAL* 1.3 75.5 - - - +
278B CYS* 1.3 59.1 + - - +
292B GLY 2.8 9.5 + - - -
294B ALA* 3.9 10.7 - - - +
319B GLU* 3.1 28.8 + - - +
320B ILE 3.0 28.1 + - - +
321B PHE* 3.6 29.6 - - + +
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Residues in contact with CYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ASP* 3.4 13.0 - - - +
246B VAL* 3.5 8.7 - - - +
277B ASN* 1.3 81.1 - - - +
279B LEU* 1.3 61.7 + - - +
291B THR* 3.2 7.8 - - - -
292B GLY* 3.0 43.7 + - - +
320B ILE* 4.2 2.2 - - - -
321B PHE* 3.4 22.9 - - - +
322B GLN* 3.7 9.0 - - - +
323B VAL* 3.3 35.9 - - + +
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Residues in contact with LEU 279 (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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232B ASP* 3.1 35.2 + - + +
233B VAL* 3.8 28.0 - - - +
234B SER* 4.1 13.3 + - - -
244B GLY* 3.6 32.3 - - - +
245B SER 4.0 2.0 - - - +
246B VAL* 4.0 9.0 - - + -
252B LEU* 4.0 16.6 - - + -
278B CYS* 1.3 74.7 - - - +
280B SER* 1.3 63.7 + - - +
281B PHE* 4.2 14.1 - - + -
289B LEU* 4.3 5.4 - - + -
290B ALA 3.2 12.3 - - - +
291B THR* 4.1 9.0 - - + -
322B GLN* 5.4 0.5 - - - +
323B VAL* 4.0 6.7 - - - +
324B GLN* 5.0 2.9 - - - +
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Residues in contact with SER 280 (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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234B SER* 5.0 2.9 - - - -
279B LEU* 1.3 74.7 - - - +
281B PHE* 1.3 65.8 + - - +
289B LEU* 3.4 3.4 - - - +
290B ALA 3.0 29.9 + - - -
323B VAL* 3.3 30.9 - - - +
324B GLN* 3.9 7.5 + - - -
325B TRP* 3.1 38.2 + - - +
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Residues in contact with PHE 281 (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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234B SER* 3.4 34.2 + - - +
235B TRP 3.6 20.2 - - - +
236B HIS* 3.5 40.6 - + + +
237B LEU* 4.9 6.5 - - + +
242B LEU* 5.7 2.9 - - + -
243B PHE 4.5 3.8 - - - -
244B GLY* 4.0 16.6 - - - -
254B ILE* 4.6 6.3 - - + -
279B LEU* 4.2 10.8 - - + -
280B SER* 1.3 78.5 + - - +
282B ASN* 1.3 67.5 + - - +
283B PRO* 3.3 7.3 - - - +
288B ILE 4.0 6.5 - - - -
289B LEU* 3.9 29.4 - - + -
303B LEU* 4.3 16.4 - - + -
325B TRP* 3.2 9.7 - - - +
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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