Contacts of the strand formed by residues 226 - 230 (chain B) in PDB entry 3UFJ
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 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASP 2.9 14.4 + - - +
134B ILE* 3.6 5.5 - - + -
135B VAL* 2.9 27.5 + - - +
224B PRO* 4.5 1.9 - - - +
225B ARG* 1.3 85.8 - - + +
227B ALA* 1.3 62.8 + - - +
228B VAL* 3.6 9.2 + - + +
264B THR* 3.8 2.5 - - - -
265B LEU* 3.7 11.9 - - + +
267B TYR* 3.7 29.8 - - + -
292B LEU* 4.4 13.0 - - + -
295B LEU* 3.9 21.1 - - + -
296B ARG* 4.0 21.8 - - + +
299B LEU* 3.8 27.8 - - + -
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Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 4.0 7.0 - - + -
137B ILE* 3.9 19.1 - - + -
224B PRO* 5.1 2.9 - - + -
226B ILE* 1.3 70.8 - - - +
228B VAL* 1.3 60.1 + - - +
229B PHE* 3.5 15.8 - - + -
259B ILE* 3.4 31.0 - - + -
264B THR* 3.3 4.3 - - + +
265B LEU 2.9 11.6 + - - +
267B TYR 3.0 25.8 + - - +
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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
----------------------------------------------------------
134B ILE* 4.8 3.8 - - + -
135B VAL 2.8 19.1 + - - +
136B ILE* 4.1 22.9 - - + -
137B ILE* 3.0 33.6 + - - +
226B ILE* 3.6 9.4 + - + +
227B ALA* 1.3 73.7 - - - +
229B PHE* 1.3 66.5 + - - +
230B ASN* 4.5 2.2 - - - +
267B TYR* 3.3 11.0 - - + +
269B MET* 4.1 26.0 - - + -
292B LEU* 3.5 38.8 - - + -
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Residues in contact with PHE 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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137B ILE* 3.9 17.0 - - + -
192B MET* 5.9 0.9 - - - -
227B ALA* 3.5 32.3 - - + -
228B VAL* 1.3 74.7 - - - +
230B ASN* 1.3 61.7 + - - +
231B GLY 3.1 2.6 + - - +
234B ILE* 3.8 25.4 - - + -
235B TYR* 4.0 33.7 - + + -
238B PHE* 3.5 53.8 - + + -
259B ILE* 6.0 0.4 - - + -
266B CYS* 4.2 15.3 - - + -
267B TYR 2.8 19.5 + - - +
268B VAL* 3.9 4.7 - - + -
269B MET* 2.9 33.3 + - - +
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Residues in contact with ASN 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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136B ILE* 4.5 10.8 - - + +
137B ILE 2.9 25.2 + - - +
138B GLY* 4.2 3.3 - - - -
139B ILE* 3.9 10.7 - - + +
152B TYR* 3.2 37.1 + - - +
159B PHE* 6.1 0.6 - - - -
228B VAL* 3.7 3.5 + - - +
229B PHE* 1.3 70.2 - - - +
231B GLY* 1.3 60.7 + - - +
234B ILE* 3.2 10.4 - - - +
269B MET* 4.0 5.4 - - - +
270B PRO 3.6 5.4 - - - +
271B SER* 3.4 13.7 + - - +
272B SER* 2.8 38.9 + - - +
289B TYR* 4.9 4.5 + - - -
11F UF2 4.8 4.6 - - - -
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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