Contacts of the strand formed by residues 225 - 228 (chain B) in PDB entry 1OOA
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 PHE 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PRO* 3.8 22.2 - - + -
91B ALA* 3.7 24.5 - - - -
92B LYS* 3.9 37.2 + - + +
124B THR* 5.0 8.5 - - - -
180B GLY* 5.7 0.3 - - - -
217B PHE* 3.6 36.1 - - + +
218B LEU 3.9 4.5 - - - -
219B PRO* 3.6 28.5 - - + -
223B GLY 3.6 7.6 + - - -
224B SER* 1.3 66.6 - - - +
226B THR* 1.3 61.1 + - - +
227B ARG 3.9 0.9 - - - -
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Residues in contact with THR 226 (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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178B ALA* 5.7 3.3 - - - +
179B GLU* 5.0 2.2 - - - -
180B GLY* 3.7 34.8 + - - -
217B PHE* 4.1 8.9 - - - -
218B LEU 3.4 0.2 + - - -
220B ASP* 3.3 25.0 + - - +
224B SER* 2.7 28.2 + - - +
225B PHE* 1.3 79.9 - - - +
227B ARG* 1.3 68.1 + - - +
228B ARG* 3.1 6.4 + - - +
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Residues in contact with ARG 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PRO* 6.2 0.6 - - - +
87B TYR* 4.5 9.5 - - - -
216B ALA 3.8 0.2 - - - +
217B PHE* 3.1 4.7 - - - -
218B LEU* 2.6 71.4 + - + +
219B PRO* 3.0 31.8 + - - +
220B ASP* 4.6 12.3 - - + +
226B THR* 1.3 77.0 + - - +
228B ARG* 1.3 61.4 - - - +
229B LEU* 4.0 1.5 + - + -
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Residues in contact with ARG 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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163B TYR 4.4 7.5 + - - -
164B ASN* 2.5 42.4 + - - +
167B LEU* 5.5 1.0 - - - +
177B GLN* 5.2 8.3 + - - +
178B ALA* 5.9 7.0 - - + -
213B MET* 6.2 0.8 - - - +
215B THR* 3.7 17.3 + - + +
216B ALA 3.7 2.7 - - - -
217B PHE* 3.5 27.6 - - + -
226B THR 3.1 6.0 + - - +
227B ARG* 1.3 73.3 - - - +
229B LEU* 1.3 77.8 + - - +
230B GLU* 4.6 8.9 + - - +
231B PRO* 4.1 24.5 - - - +
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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