Contacts of the strand formed by residues 227 - 232 (chain B) in PDB entry 2QPA
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 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B SER* 3.8 4.0 + - - -
193B THR* 3.0 28.0 - - - +
195B PHE* 3.3 16.4 - - - -
221B ALA* 3.0 26.1 + - - +
224B ASN 3.5 2.7 - - - -
226B PRO* 1.3 72.1 - - - +
228B ILE* 1.3 72.2 + - - +
269B GLY 3.6 6.2 + - - +
270B VAL* 3.1 20.0 - - - +
271B LEU* 3.8 17.7 + - - +
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Residues in contact with ILE 228 (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 VAL* 5.2 9.0 - - + -
183B ALA 4.3 1.3 - - - +
186B VAL* 3.9 17.0 - - + -
187B ALA* 3.1 47.3 - - + +
190B ALA* 5.6 0.4 - - + -
192B SER* 4.4 5.8 - - - +
193B THR 3.0 6.7 + - - +
194B PHE* 4.9 4.9 - - + -
195B PHE* 3.3 29.8 + - - +
227B SER* 1.3 85.6 - - - +
229B ILE* 1.3 68.2 + - - +
230B PHE* 3.6 5.7 + - + +
270B VAL* 4.7 0.9 - - - -
271B LEU* 3.5 15.7 - - + +
273B LEU* 3.4 31.2 - - + -
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Residues in contact with ILE 229 (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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195B PHE* 3.8 4.0 - - + -
217B LEU* 3.2 48.5 - - + +
218B PHE* 4.0 27.8 - - + -
221B ALA* 3.3 31.9 - - + -
228B ILE* 1.3 76.3 - - - +
230B PHE* 1.3 56.3 + - - +
231B ILE* 3.4 16.8 + - + +
270B VAL* 3.6 19.5 - - + -
271B LEU 3.4 5.3 + - - -
272B VAL* 3.6 14.2 - - + +
273B LEU 3.1 23.0 + - - +
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Residues in contact with PHE 230 (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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171B LEU* 4.7 4.5 - - + -
179B LYS 4.4 1.8 - - - -
180B SER* 3.4 37.2 - - - -
183B ALA* 3.5 21.1 - - + -
194B PHE* 3.7 29.2 - + + -
195B PHE 3.0 12.6 + - - +
196B SER* 3.5 16.1 - - - -
197B VAL* 3.2 28.1 + - - +
228B ILE* 3.6 3.3 + - + -
229B ILE* 1.3 68.4 - - - +
231B ILE* 1.3 59.4 + - - +
232B ASP* 3.0 38.8 - - - -
273B LEU* 3.3 19.1 - - + -
274B GLY 4.8 0.2 - - - -
275B ALA* 3.5 24.0 - - + -
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Residues in contact with ILE 231 (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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197B VAL* 3.7 22.2 - - + +
199B SER* 4.5 9.2 - - - +
202B LEU* 5.7 4.7 - - + -
217B LEU* 4.5 2.5 - - + -
218B PHE* 4.7 2.9 - - + -
229B ILE* 3.7 28.5 - - + +
230B PHE* 1.3 72.3 - - - +
232B ASP* 1.3 64.5 + - - +
234B VAL* 2.8 43.3 - - + +
237B LEU* 5.6 4.3 - - + -
256B LEU* 3.9 31.2 - - + -
272B VAL* 4.0 14.8 - - + -
273B LEU 2.8 11.2 + - - +
274B GLY* 3.6 0.2 - - - -
275B ALA 3.3 9.3 + - - -
290B PHE* 5.4 3.8 - - + -
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Residues in contact with ASP 232 (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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179B LYS* 5.1 0.3 - - - +
180B SER* 4.2 9.9 + - - -
196B SER* 5.1 2.8 + - - +
197B VAL 3.0 15.8 + - - +
198B SER* 4.1 3.8 - - - -
199B SER* 3.0 17.8 + - - -
230B PHE* 3.0 39.2 + - + -
231B ILE* 1.3 74.5 - - - +
233B GLN* 1.3 99.1 + - - +
234B VAL 2.9 1.7 + - - -
275B ALA* 3.7 9.2 - - - +
800B PO4 4.2 12.6 + - - -
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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