Contacts of the strand formed by residues 244 - 249 (chain B) in PDB entry 3PU3
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 SER 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B VAL* 4.0 1.1 - - - -
189B VAL* 3.7 14.4 - - - -
191B ASN* 2.9 43.1 + - - -
240B CYS* 3.3 2.1 - - - +
241B VAL 2.9 19.0 + - - -
243B ASP* 1.3 80.8 - - - +
245B TYR* 1.3 59.5 + - - +
324B LEU* 3.5 6.2 - - - +
325B THR* 3.0 42.3 + - - -
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Residues in contact with TYR 245 (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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84B ASN* 4.4 2.0 - - + -
85B GLY* 3.8 14.4 - - - -
89B PHE* 3.4 37.3 - + - -
90B ILE* 4.2 13.5 - - + -
93B LEU* 3.7 24.5 - - + -
162B THR* 5.5 2.3 - - - +
164B VAL* 3.7 28.4 - - + +
167B GLN* 4.2 9.9 + - - -
191B ASN* 4.6 1.7 + - - +
244B SER* 1.3 79.0 - - - +
246B THR* 1.3 70.5 + - - +
247B ASP* 2.9 46.9 + - + -
248B PHE* 4.0 0.9 - - - -
269B TYR* 5.2 2.2 - + - -
294B PHE* 3.8 11.9 - + - -
322B ALA* 3.8 12.8 - - + +
323B THR 3.1 23.3 - - - -
324B LEU* 4.4 3.6 - - + -
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Residues in contact with THR 246 (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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2B OGA 2.9 34.3 + - - +
167B GLN* 5.7 0.2 - - - +
191B ASN* 4.9 3.8 + - - -
193B THR* 4.6 5.3 - - - +
245B TYR* 1.3 77.9 + - - +
247B ASP* 1.3 69.4 + - - +
249B HIS* 4.1 14.6 - - + +
322B ALA* 2.9 9.7 - - - +
323B THR* 2.8 48.7 + - - +
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Residues in contact with ASP 247 (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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84B ASN* 3.1 31.5 + - - +
167B GLN* 4.5 16.8 + - - +
245B TYR* 2.9 33.2 + - + -
246B THR* 1.3 82.6 - - - +
248B PHE* 1.3 85.0 + - - +
249B HIS* 3.2 16.1 + - - +
284B TRP* 3.5 19.6 - - + -
285B ARG* 5.3 5.0 + - - +
290B HIS* 4.6 6.4 + - - +
291B SER* 4.8 1.2 - - - -
294B PHE* 5.3 1.2 - - - -
295B PHE 5.4 0.3 + - - -
321B TYR 3.5 0.3 - - - +
322B ALA* 3.7 0.2 - - - -
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Residues in contact with PHE 248 (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 TYR* 4.0 3.4 - - - -
247B ASP* 1.3 92.4 + - - +
249B HIS* 1.3 59.7 + - - +
269B TYR* 3.7 24.0 - + + -
271B ILE* 3.7 22.0 - - + -
281B TYR* 4.0 1.1 - - - -
284B TRP* 3.5 30.0 - - + -
285B ARG* 4.9 5.5 + - - -
294B PHE* 3.6 28.9 - + - -
295B PHE* 3.8 19.1 - + + -
296B ALA* 3.6 29.4 - - + -
302B CYS* 4.0 8.3 - - - -
320B ILE* 4.0 12.8 - - + -
321B TYR* 3.1 13.9 - - - -
322B ALA* 3.5 21.0 - - + +
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Residues in contact with HIS 249 (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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2B OGA 3.2 43.6 + - - -
246B THR* 4.1 12.1 - - + +
247B ASP 3.2 10.0 + - - +
248B PHE* 1.3 76.1 - - - +
250B ILE* 1.3 71.2 + - - +
251B ASP* 3.3 17.1 + - - -
281B TYR* 3.6 15.3 - - - +
285B ARG* 5.6 5.8 - - - +
319B TRP 3.7 1.7 - - - +
320B ILE* 3.5 2.4 - - - +
321B TYR* 2.9 56.3 + + - +
322B ALA* 5.3 0.4 - - - -
323B THR* 6.3 0.2 - - + -
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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