Contacts of the strand formed by residues 225 - 230 (chain B) in PDB entry 6A5T
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 ILE 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B LYS* 3.9 13.7 - - + +
223B SER* 3.0 17.2 - - - +
224B PRO* 1.3 81.1 - - - +
226B SER* 1.3 57.6 + - - +
227B HIS 3.6 23.8 - - - +
228B VAL* 3.8 18.8 - - + -
248B LYS* 3.5 37.9 - - + -
249B LEU 3.2 12.6 - - - +
250B TYR* 3.6 25.4 - - + +
252B ARG* 2.5 31.5 + - - -
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Residues in contact with SER 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LYS* 3.3 26.7 - - - +
219B LYS 3.6 4.4 + - - +
224B PRO 4.2 0.6 + - - -
225B ILE* 1.3 76.0 - - - +
227B HIS* 1.3 102.1 + - - +
249B LEU* 3.4 20.0 + - - +
251B GLY 5.1 9.5 + - - -
252B ARG* 3.4 15.9 - - - +
382B ALA* 4.3 0.9 - - - +
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Residues in contact with HIS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B VAL* 5.0 0.2 - - + -
217B PHE 3.4 5.6 - - - +
218B LYS* 3.5 28.5 - - + +
225B ILE* 3.6 2.6 - - - +
226B SER* 1.3 117.3 + - - +
228B VAL* 1.3 63.4 + - - +
249B LEU* 3.3 26.1 + - + +
378B LEU* 3.4 27.4 - - + +
381B CYS* 2.7 42.8 + - - -
382B ALA* 3.3 31.5 - - + -
384B GLU* 5.0 7.9 - - + +
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Residues in contact with VAL 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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215B GLN 3.5 1.6 - - - +
216B VAL* 3.4 3.8 - - - -
217B PHE* 2.9 42.8 + - + +
218B LYS 5.2 0.7 - - - -
219B LYS* 4.6 20.2 - - + +
225B ILE* 3.8 21.1 - - + -
227B HIS* 1.3 77.1 - - - +
229B ALA* 1.3 64.3 + - - +
230B GLU* 3.7 14.6 + - + +
246B GLN* 4.7 16.4 - - - +
247B ILE 3.2 19.5 - - - +
248B LYS* 4.9 4.7 - - + -
378B LEU* 4.3 3.1 - - - -
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Residues in contact with ALA 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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214B VAL* 5.1 6.3 - - + -
215B GLN 3.4 7.9 - - - +
216B VAL* 4.6 7.4 - - + +
228B VAL* 1.3 69.7 - - - +
230B GLU* 1.3 59.1 + - - +
245B MET 4.1 2.8 - - - +
246B GLN 4.1 0.9 - - - -
247B ILE* 3.2 43.2 + - + +
374B MET* 4.3 20.2 - - + +
378B LEU* 4.0 29.1 - - + +
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Residues in contact with GLU 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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213B ILE 3.7 0.5 - - - +
214B VAL* 3.8 1.6 - - - -
215B GLN* 2.9 45.3 + - + +
217B PHE* 4.5 15.3 - - + -
228B VAL* 3.7 15.1 + - + +
229B ALA* 1.3 74.6 - - - +
231B ILE* 1.3 73.2 + - - +
232B ARG* 3.8 30.1 + - + +
244B THR* 4.0 13.8 - - + +
245B MET 4.2 4.3 - - - +
246B GLN* 4.6 24.5 + - + +
374B MET* 5.2 1.8 - - - -
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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