Contacts of the strand formed by residues 225 - 230 (chain F) in PDB entry 5IJ7
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 VAL 225 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F ASN* 2.8 20.4 + - - -
195F VAL* 3.3 30.0 - - + +
196F SER 3.0 12.9 + - - +
199F HIS* 3.3 35.0 - - - +
200F ALA 3.9 5.4 - - - +
201F LEU* 4.0 13.2 - - + -
221F HIS* 3.8 30.5 - - + +
224F GLU* 1.4 69.7 - - - +
226F LEU* 1.3 59.4 + - - +
227F SER 4.0 7.0 - - - +
239F SER* 4.1 2.9 - - - -
240F CYS 3.4 15.5 - - - +
241F GLY* 4.2 1.3 - - - -
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Residues in contact with LEU 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180F ASN* 3.7 15.8 - - - +
181F GLU* 4.0 1.6 - - - +
195F VAL* 4.0 3.8 - - - -
224F GLU* 3.8 25.1 - - + +
225F VAL* 1.3 74.6 - - - +
227F SER* 1.3 59.0 + - - +
240F CYS 2.9 6.1 + - - -
241F GLY 4.2 2.7 - - - -
242F MET* 3.7 17.5 - - + +
294F TYR* 4.1 3.8 - - + -
295F VAL 3.4 26.2 - - - +
296F ASP* 3.8 20.2 - - + +
350F TRP* 3.5 44.6 - - + +
351F TYR* 4.6 7.6 - - + -
353F ARG* 2.8 29.8 + - - +
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Residues in contact with SER 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181F GLU* 2.7 26.0 + - - -
195F VAL* 3.8 3.5 - - - +
225F VAL* 3.8 3.0 - - - +
226F LEU* 1.3 80.2 - - - +
228F ALA* 1.3 62.3 + - - +
239F SER* 3.4 2.6 - - - -
240F CYS* 3.0 46.3 + - - +
296F ASP 3.6 13.0 - - - -
297F CYS* 3.6 5.5 - - - -
298F VAL* 3.3 17.6 + - - -
299F ARG* 3.6 7.3 + - - -
353F ARG* 5.0 0.2 + - - -
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Residues in contact with ALA 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F GLU* 3.8 3.5 + - - +
183F LYS* 3.5 17.2 - - + +
193F LEU* 3.9 13.9 - - + -
195F VAL* 3.4 25.8 - - + +
201F LEU* 3.8 14.1 - - + -
227F SER* 1.3 78.2 + - - +
229F ASP* 1.3 61.6 + - - +
237F ILE* 4.2 1.8 - - + -
238F MET 3.2 13.0 - - - +
239F SER* 4.2 1.8 - - - -
298F VAL* 3.8 2.7 - - - -
299F ARG* 3.1 17.2 + - - -
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Residues in contact with ASP 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F LYS* 4.0 18.6 + - - +
193F LEU* 5.0 1.1 - - - +
228F ALA* 1.3 76.6 - - - +
230F TYR* 1.4 74.6 + - - +
237F ILE* 3.4 4.6 - - - -
238F MET* 3.0 32.0 + - + +
298F VAL* 3.5 15.0 - - + +
299F ARG* 3.4 24.2 - - - +
300F TRP* 3.0 38.1 + - + +
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Residues in contact with TYR 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F LYS* 3.6 20.6 - - + +
184F PHE 3.5 17.7 - - - -
185F HIS* 3.4 30.8 - + + +
186F PRO* 3.6 16.6 - - + -
191F LEU 3.6 10.0 + - - -
193F LEU* 3.4 20.4 - - + +
203F LEU* 3.2 26.1 - - + +
229F ASP* 1.4 88.4 + - - +
231F ASP* 1.3 70.0 + - - +
234F GLY* 4.4 4.5 - - - -
236F LYS 3.4 5.4 - - - -
237F ILE* 3.7 20.4 - - + +
251F ILE* 3.6 28.9 - - + -
300F TRP* 3.2 10.1 - - - +
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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