Contacts of the strand formed by residues 237 - 243 (chain B) in PDB entry 4BLW
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 ALA 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B HIS* 4.7 3.6 - - - -
198B VAL* 2.8 41.7 + - + -
201B ARG* 4.6 1.8 - - - +
223B GLU* 4.4 9.4 - - + +
224B LEU 3.6 7.0 - - - +
225B ALA* 3.5 24.2 - - + +
226B VAL 4.6 0.7 - - - +
227B LEU 4.9 0.2 - - - +
229B ASP* 5.2 1.1 - - - +
235B MET* 3.1 16.8 - - - +
236B THR* 1.3 82.6 + - - +
238B SER* 1.3 62.2 + - - +
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Residues in contact with SER 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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13B HIS* 4.8 2.3 + - - -
14B ALA* 3.5 21.8 + - - +
17B LEU* 3.6 10.3 - - - +
195B TRP* 3.2 31.8 + - - -
196B TYR* 3.2 16.2 - - - -
197B PRO* 4.4 0.2 - - - -
198B VAL* 4.5 2.2 - - - +
223B GLU* 3.5 7.2 - - - +
224B LEU* 2.9 32.5 + - - +
235B MET* 4.1 2.5 - - - -
237B ALA* 1.3 77.4 - - - +
239B GLY* 1.3 58.6 + - - +
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Residues in contact with GLY 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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17B LEU* 3.9 4.5 - - - -
195B TRP* 3.4 10.2 - - - -
196B TYR* 3.0 53.3 + - - -
222B ILE 3.0 13.2 - - - -
223B GLU* 3.9 0.2 - - - -
238B SER* 1.3 76.7 - - - +
240B MET* 1.3 62.7 + - - -
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Residues in contact with MET 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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17B LEU* 4.4 7.4 - - + -
18B LYS* 3.8 36.1 - - + +
21B VAL* 4.3 26.0 - - + -
22B GLN* 4.9 2.9 - - + +
162B LEU* 3.9 15.5 - - + -
193B ALA* 3.8 27.6 - - + -
194B LEU 3.3 3.6 - - - -
195B TRP* 3.6 35.9 - - + -
196B TYR* 4.3 0.4 - - - -
220B LEU 3.7 0.9 - - - +
221B GLN* 3.7 1.4 - - - -
222B ILE* 2.7 41.0 + - + +
239B GLY* 1.3 74.5 - - - -
241B ILE* 1.3 63.6 + - - +
242B VAL* 3.9 11.1 + - + -
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Residues in contact with ILE 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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180B ILE* 5.8 0.7 - - + -
192B TYR 3.4 2.8 - - - +
194B LEU* 2.7 54.3 + - + +
196B TYR* 3.8 28.7 - - + -
207B MET* 4.0 20.2 - - + -
208B ILE* 4.1 11.7 - - + -
211B LEU* 3.7 17.3 - - + -
219B ILE* 3.6 26.9 - - + -
220B LEU 3.4 3.1 - - - +
221B GLN* 4.2 5.4 - - + -
239B GLY 4.2 0.2 - - - -
240B MET* 1.3 72.5 - - - +
242B VAL* 1.3 62.1 + - - +
243B ILE* 4.2 5.8 + - + +
277B ILE* 3.9 22.9 - - + -
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Residues in contact with VAL 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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21B VAL* 4.1 25.6 - - + -
25B ILE* 4.1 11.7 - - + -
191B ILE* 3.9 15.0 - - + -
192B TYR 3.2 8.7 - - - +
193B ALA* 4.4 7.0 - - + -
219B ILE* 3.6 1.0 - - - -
220B LEU* 2.8 41.6 + - + +
222B ILE* 4.5 4.7 - - + -
240B MET* 4.4 11.2 - - + +
241B ILE* 1.3 78.2 - - - +
243B ILE* 1.3 62.9 + - - +
245B PRO* 3.6 38.2 - - + +
249B LEU* 4.1 7.4 - - + -
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Residues in contact with ILE 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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180B ILE* 3.5 38.4 - - + -
184B TYR* 3.9 19.3 - - + -
191B ILE* 3.4 3.3 - - - +
192B TYR* 2.9 46.6 + - + +
211B LEU* 4.7 6.3 - - + -
216B ILE* 3.7 29.2 - - + -
217B ARG 4.1 5.6 - - - +
218B LYS 3.5 3.1 - - - -
219B ILE* 4.1 22.7 - - + -
241B ILE* 4.8 4.3 - - + +
242B VAL* 1.3 73.6 - - - +
244B ASN* 1.3 78.3 + - - +
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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