Contacts of the strand formed by residues 251 - 256 (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 LYS 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B HIS* 3.8 10.1 - - + -
246B VAL* 3.5 6.9 - - - +
247B ALA 3.4 22.4 + - - +
249B ASP* 3.0 38.2 + - + +
250B GLN* 1.3 80.0 - - - +
252B LEU* 1.3 61.0 + - - +
253B MET* 4.1 15.0 - - + -
268B SER* 4.0 15.5 - - - +
269B VAL 3.2 13.2 - - - +
270B ASP* 2.6 32.3 + - - +
271B ALA* 4.5 1.8 - - - -
276B VAL* 4.4 2.1 - - - +
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Residues in contact with LEU 252 (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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245B SER 3.4 15.3 - - - +
246B VAL* 3.8 15.9 - - + -
251B LYS* 1.3 74.1 - - - +
253B MET* 1.3 67.1 + - - +
254B ILE* 4.1 10.4 + - + +
267B HIS 4.1 0.7 - - - +
268B SER* 3.5 1.7 + - - -
269B VAL* 2.8 58.2 + - + +
271B ALA* 3.9 10.6 - - + +
279B LEU* 4.0 18.4 - - + -
289B LEU* 4.0 16.4 - - + -
291B THR* 4.1 2.9 - - + -
301B TRP* 3.8 36.1 - - + +
306B LEU* 4.5 7.1 - - + +
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Residues in contact with MET 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLY* 3.5 24.9 - - - +
226B HIS* 3.3 38.4 - - + +
244B GLY* 3.3 4.7 - - - -
245B SER* 2.9 41.8 + - - +
249B ASP* 4.2 0.2 - - - +
251B LYS* 4.1 17.3 - - + -
252B LEU* 1.3 77.5 - - - +
254B ILE* 1.3 64.1 + - - +
255B TRP* 3.6 26.2 - - - +
265B PRO* 3.7 24.0 - - + -
267B HIS 3.4 3.6 - - - -
268B SER* 3.9 18.4 - - - +
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Residues in contact with ILE 254 (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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242B LEU* 4.0 31.2 - - + -
243B PHE 3.5 5.8 - - - +
244B GLY* 4.3 9.4 - - - -
252B LEU* 4.1 20.6 - - + +
253B MET* 1.3 78.4 - - - +
255B TRP* 1.3 62.9 + - - +
265B PRO* 3.4 1.9 - - - +
266B SER* 2.9 28.6 + - - -
267B HIS* 3.0 26.3 + - + +
281B PHE* 4.6 4.7 - - + -
289B LEU* 4.6 8.1 - - + -
303B LEU* 4.0 21.3 - - + -
306B LEU* 3.6 28.0 - - + -
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Residues in contact with TRP 255 (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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202B ILE* 3.8 12.8 - - + +
223B PHE* 3.8 33.9 - + + -
225B GLY* 3.8 27.1 - - - -
226B HIS* 5.0 1.3 - + - -
241B SER 3.6 0.7 - - - +
242B LEU* 3.4 10.3 - - - +
243B PHE* 2.7 77.5 + + + +
245B SER* 2.9 25.0 + - - -
253B MET* 3.6 31.6 - - - +
254B ILE* 1.3 74.2 - - - +
256B ASP* 1.3 61.6 + - - +
257B THR 4.2 0.7 - - - -
261B ASN 5.1 1.3 - - - -
262B THR* 4.2 7.0 - - - -
263B SER 4.4 0.4 - - - -
264B LYS 3.7 12.6 - - - -
265B PRO* 3.5 36.8 - - + -
266B SER* 4.5 2.0 - - - +
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Residues in contact with ASP 256 (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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223B PHE* 5.2 4.8 - - - -
241B SER* 3.4 10.2 - - - -
242B LEU* 4.1 14.1 - - + +
243B PHE* 5.2 0.7 - - - -
255B TRP* 1.3 76.8 - - - +
257B THR* 1.3 63.0 + - - +
258B ARG* 2.7 58.8 + - - +
259B SER* 3.2 25.2 + - - +
266B SER* 3.7 20.3 + - - +
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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