Contacts of the strand formed by residues 237 - 244 (chain B) in PDB entry 4PIM
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 PHE 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B ARG* 2.9 28.6 + - + -
221B LEU* 3.7 21.3 - - + -
232B PHE* 3.8 28.0 - + - -
233B ASP 3.4 22.7 - - - -
234B LEU 3.3 6.5 + - - +
235B ASP 3.3 1.6 - - - -
236B ALA* 1.3 79.0 - - + +
238B GLU* 1.3 61.0 + - - +
254B LEU* 4.2 24.7 - - + -
255B ARG 3.4 5.2 - - - +
256B ALA* 3.9 28.7 - - + -
257B ARG* 3.8 6.9 + - - -
260B GLN* 4.2 22.7 - - + -
262B VAL* 5.0 0.9 - - + -
273B PHE* 3.9 34.8 - + - -
279B MSE 4.7 3.8 - - + -
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Residues in contact with GLU 238 (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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235A ASP* 3.7 24.7 - - - +
218B ARG* 4.0 2.7 - - - +
237B PHE* 1.3 73.6 - - - +
239B HIS* 1.3 73.4 + - - +
240B VAL* 3.6 7.1 + - + +
254B LEU* 3.4 6.9 - - - -
255B ARG* 2.8 74.2 + - + +
257B ARG* 3.8 21.3 + - + +
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Residues in contact with HIS 239 (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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235A ASP* 5.1 0.8 + - - -
206B TYR 2.8 28.8 + - - -
207B ASP* 3.4 27.2 - - - +
213B THR* 3.7 19.1 - - + +
214B ALA* 3.5 35.0 - - + +
217B ASN* 3.0 34.9 + - + +
218B ARG* 3.6 10.1 - - - +
238B GLU* 1.3 81.0 - - - +
240B VAL* 1.3 68.3 + - - +
241B ALA* 4.3 3.4 - - - +
252B MSE 4.0 13.9 - - + -
253B TRP 3.8 3.4 - - - -
254B LEU* 4.5 2.2 - - + -
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Residues in contact with VAL 240 (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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207B ASP* 6.0 0.2 - - - -
238B GLU* 4.0 16.2 - - - +
239B HIS* 1.3 85.0 - - - +
241B ALA* 1.3 63.0 + - - +
242B LYS* 3.7 36.3 - - + -
251B GLU 3.8 0.9 - - - +
252B MSE 3.4 3.5 - - - +
253B TRP* 2.7 46.4 + - + +
255B ARG* 3.7 42.6 - - + +
278B GLU* 4.5 0.4 - - - +
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Residues in contact with ALA 241 (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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203B VAL* 3.8 21.3 - - + +
206B TYR* 3.5 41.3 - - + +
207B ASP* 4.1 14.6 - - + +
239B HIS* 4.3 3.4 + - - +
240B VAL* 1.3 76.7 - - - +
242B LYS* 1.3 63.6 + - - +
250B ILE* 4.8 2.9 - - + -
251B GLU 3.4 5.8 - - - +
252B MSE 4.5 4.3 - - + +
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Residues in contact with LYS 242 (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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203B VAL* 4.6 2.0 - - - -
240B VAL* 3.7 25.1 - - + -
241B ALA* 1.3 78.6 - - - +
243B TRP* 1.3 63.1 + - - +
244B ASN 3.9 0.3 + - - -
250B ILE* 3.4 9.8 - - - +
251B GLU* 2.8 40.2 + - + +
253B TRP* 3.9 22.4 - - + +
255B ARG* 4.2 4.8 - - - +
278B GLU* 2.7 35.2 + - - -
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Residues in contact with TRP 243 (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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196B VAL* 4.5 13.7 - - + -
199B THR* 3.5 33.9 - - + +
202B LEU* 3.6 29.2 - - + -
203B VAL* 4.1 19.5 - - + +
242B LYS* 1.3 75.7 - - - +
244B ASN* 1.3 64.2 + - - +
245B SER* 3.6 26.3 + - - +
248B GLU* 3.3 39.5 - - + -
249B ARG* 3.4 33.2 - - - -
250B ILE* 3.7 14.4 - - + -
286B LYS* 3.8 16.4 - - + -
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Residues in contact with ASN 244 (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 LYS 3.9 0.8 + - - -
243B TRP* 1.3 70.4 - - - +
245B SER* 1.3 58.0 + - - +
246B ASP* 3.1 13.7 + - - +
247B GLU* 3.0 34.1 + - - +
248B GLU* 2.8 26.0 + - - -
249B ARG* 2.9 27.0 + - + +
251B GLU* 3.0 37.7 + - - +
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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