Contacts of the strand formed by residues 271 - 278 (chain B) in PDB entry 4BLU
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 HIS 271 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B ARG* 4.3 8.5 - - - -
223B GLU* 2.8 31.6 + - - -
224B LEU* 3.6 0.2 - - - -
225B ALA* 2.8 53.4 + - + +
227B LEU 5.3 1.1 + - - -
228B PRO* 5.7 3.2 - - + +
229B ASP* 4.8 5.6 - - - -
261B HIS* 3.4 13.6 + - - -
270B GLY* 1.3 77.5 - - - +
272B ALA* 1.3 63.8 + - - +
273B THR* 4.1 26.2 + - + -
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Residues in contact with ALA 272 (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 GLU 3.3 8.1 - - - +
224B LEU* 4.5 3.6 - - + -
257B LEU* 4.0 44.2 - - + +
258B PRO* 5.1 1.3 - - + +
261B HIS* 4.0 14.5 - - + -
271B HIS* 1.3 77.8 - - - +
273B THR* 1.3 64.0 + - - +
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Residues in contact with THR 273 (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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221B GLN 3.8 1.3 + - - +
222B ILE* 3.5 2.8 - - - -
223B GLU* 2.9 47.3 + - - +
257B LEU* 3.7 3.9 - - - +
271B HIS* 4.1 21.6 + - + -
272B ALA* 1.3 78.9 - - - +
274B VAL* 1.3 68.9 + - - +
275B SER* 5.3 4.2 + - - -
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Residues in contact with VAL 274 (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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220B LEU* 3.8 25.6 - - + -
221B GLN 3.4 3.6 - - - -
222B ILE* 4.1 16.2 - - + -
250B GLU* 4.1 23.2 - - + +
253B MET* 3.5 19.5 - - + -
254B ASN* 4.1 24.3 + - - +
257B LEU* 3.4 27.1 - - + -
273B THR* 1.3 74.5 - - - +
275B SER* 1.3 66.7 + - - +
1292B EDO 4.0 6.8 + - - -
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Residues in contact with SER 275 (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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220B LEU* 3.5 6.2 - - - +
221B GLN* 2.7 49.4 + - - +
250B GLU* 5.3 0.2 - - - -
273B THR* 5.3 5.1 + - - -
274B VAL* 1.3 79.1 - - - +
276B TRP* 1.3 64.9 + - - +
1292B EDO 3.7 22.0 - - - -
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Residues in contact with TRP 276 (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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218B LYS* 4.0 21.5 - - + -
219B ILE 3.5 19.1 - - - -
220B LEU* 3.6 15.3 - - + -
245B PRO* 3.7 32.1 - - + -
250B GLU* 3.0 37.8 + - + -
275B SER* 1.3 76.9 - - - +
277B ILE* 1.3 62.7 + - - +
278B VAL 3.7 10.3 - - - -
279B PRO* 4.0 31.7 - - + +
280B GLU 5.3 3.8 - - - -
1292B EDO 2.7 39.9 + - - +
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Residues in contact with ILE 277 (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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208B ILE* 3.8 28.7 - - + -
211B LEU* 5.0 3.4 - - + -
212B GLU* 3.6 38.4 - - + +
219B ILE* 2.8 34.0 + - + +
221B GLN* 3.6 38.8 - - + +
241B ILE* 4.2 16.4 - - + -
275B SER 3.9 0.8 + - - -
276B TRP* 1.3 73.8 - - - +
278B VAL* 1.3 66.5 + - + +
279B PRO* 4.1 4.1 - - - +
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Residues in contact with VAL 278 (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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212B GLU* 4.1 20.0 - - + +
216B ILE 3.9 14.8 - - - +
217B ARG* 3.5 47.3 - - - +
218B LYS* 3.2 5.9 + - - +
219B ILE* 2.8 39.9 + - + +
276B TRP* 3.7 1.8 - - - -
277B ILE* 1.3 95.3 - - + +
279B PRO* 1.3 69.4 - - + +
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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