Contacts of the strand formed by residues 228 - 234 (chain B) in PDB entry 5FJV
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 ASP 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B TYR* 5.0 3.4 - - + -
174B LYS* 3.6 28.0 - - + -
175B PHE 3.1 17.9 - - - +
176B GLY* 4.5 2.5 - - - -
187B LEU* 4.5 4.3 - - - -
214B TYR* 3.5 6.1 - - - -
215B ASN* 2.6 58.1 + - - +
216B SER 4.7 0.2 + - - -
217B LYS* 5.5 2.3 - - - +
219B TYR* 4.1 8.2 + - - +
226B TYR 4.4 3.2 - - - +
227B PRO* 1.3 76.9 - - - +
229B VAL* 1.3 62.7 - - - +
230B THR* 2.8 28.9 + - - -
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 4.4 14.3 - - + -
173B MET 3.7 0.3 - - - +
175B PHE* 2.9 28.1 + - - +
187B LEU* 4.6 14.2 - - + +
189B GLN* 4.3 26.5 - - + -
213B THR 3.5 8.3 - - - +
214B TYR* 4.2 24.0 - - + -
228B ASP* 1.3 78.6 - - - +
230B THR* 1.3 62.6 + - - +
231B TYR* 3.2 44.5 - - + +
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Residues in contact with THR 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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172B LYS* 3.9 32.3 - - + -
173B MET 3.1 17.7 - - - +
174B LYS* 3.5 13.1 - - + +
211B THR 3.8 0.7 - - - +
212B GLY* 3.7 0.9 - - - -
213B THR* 2.9 42.0 + - - +
215B ASN* 4.6 6.3 + - - -
228B ASP* 2.8 18.8 + - - -
229B VAL* 1.3 72.6 - - - +
231B TYR* 1.3 66.3 + - - +
232B ALA* 4.2 0.8 + - + -
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Residues in contact with TYR 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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62B PHE* 3.9 23.5 + + - -
63B GLY* 4.1 1.9 - - - -
64B LEU* 4.0 26.7 + - + -
172B LYS* 3.0 6.6 - - - +
173B MET* 2.7 45.8 + - + +
175B PHE* 4.0 22.2 - + - -
189B GLN* 4.3 5.0 - - - +
192B GLN* 3.9 14.6 + - - -
196B LEU* 4.2 17.0 - - + -
210B ALA* 6.0 1.1 - - + -
211B THR 3.2 7.9 - - - +
212B GLY* 3.6 23.1 - - - -
229B VAL* 3.2 34.3 - - + +
230B THR* 1.3 77.7 - - - +
232B ALA* 1.3 60.1 + - - +
233B PHE* 3.4 24.8 - + + -
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Residues in contact with ALA 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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170B ASN* 4.0 19.3 - - - +
171B CYS 4.0 2.2 - - - -
172B LYS* 4.5 5.8 - - + +
209B ASN 3.8 0.7 - - - +
210B ALA* 3.4 5.2 - - - +
211B THR* 2.9 46.8 + - + +
213B THR* 6.1 1.1 - - + +
230B THR* 4.2 1.1 + - + -
231B TYR* 1.3 73.4 - - - +
233B PHE* 1.3 61.6 + - - +
234B VAL* 5.5 0.8 - - - +
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Residues in contact with PHE 233 (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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64B LEU* 4.3 12.1 - - + -
66B ILE* 4.1 21.8 - - + -
79B MET* 5.3 7.4 - - + -
81B THR* 5.9 2.9 - - + -
169B GLN 3.2 14.0 - - - +
170B ASN* 3.3 9.9 + - - +
171B CYS* 3.0 40.3 + - + +
173B MET* 3.9 29.2 - - + -
196B LEU* 6.1 1.3 - - + -
207B ILE* 4.3 19.5 - - + -
209B ASN 3.4 4.3 - - - -
210B ALA* 4.0 23.1 - - + -
231B TYR* 3.4 33.9 - + + -
232B ALA* 1.3 74.7 - - - +
234B VAL* 1.3 70.4 + - - +
235B ILE* 4.9 8.7 - - + -
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Residues in contact with VAL 234 (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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168B GLN* 4.0 26.2 - - - +
169B GLN* 3.4 7.4 - - - +
170B ASN* 4.6 6.7 - - + +
207B ILE* 3.5 2.9 - - - -
208B VAL* 2.9 31.2 + - + +
209B ASN* 2.9 49.5 + - + +
232B ALA* 5.5 1.1 - - + +
233B PHE* 1.3 81.4 - - - +
235B ILE* 1.3 62.1 + - - +
236B ARG* 4.2 3.4 - - - +
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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