Contacts of the strand formed by residues 228 - 233 (chain C) in PDB entry 5IWG
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 ALA 228 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C GLU* 4.1 9.4 - - + -
193C TYR* 4.0 20.2 - - + +
200C THR* 3.5 16.6 - - - +
218C ASP 3.8 6.8 - - - +
219C ILE* 3.3 40.7 + - - +
220C GLY* 3.8 5.2 - - - +
224C GLY 4.0 0.4 + - - -
226C TYR* 4.4 3.1 - - - -
227C TYR* 1.3 77.9 - - - +
229C VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C GLU* 4.9 0.9 - - - +
199C MET* 3.5 30.5 - - + -
200C THR 2.8 17.2 + - - +
201C VAL* 4.0 24.9 - - + -
202C SER 3.0 24.9 + - - -
218C ASP 5.0 0.2 - - - -
219C ILE* 6.1 0.4 - - - -
226C TYR 4.7 1.8 - - - +
228C ALA* 1.3 78.5 - - - +
230C ASN* 1.3 70.1 + - - +
231C PHE* 5.1 0.9 - - + +
249C ILE* 4.7 6.3 - - + -
253C VAL* 4.9 1.8 - - + -
371C LEU* 3.8 32.3 - - + -
374C ASN* 6.3 3.4 - - + -
375C LEU* 4.3 11.7 - - + -
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Residues in contact with ASN 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C HIS* 3.0 27.4 + - - -
189C GLU* 2.8 23.6 + - - +
202C SER* 3.5 5.1 - - - -
204C HIS* 3.3 4.0 - - + -
214C GLY* 3.6 18.0 - - - +
215C ASP 3.4 20.7 + - - +
216C LEU* 3.8 7.1 + - - +
218C ASP* 3.0 29.7 + - - +
229C VAL* 1.3 80.5 - - - +
231C PHE* 1.3 59.4 - - - +
232C PRO* 3.3 9.5 - - - +
371C LEU* 3.5 23.0 - - - +
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Residues in contact with PHE 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C SER 2.8 9.8 + - - +
203C PHE* 3.6 27.9 - + + -
204C HIS* 3.2 25.8 + - - +
229C VAL* 5.1 0.6 - - + +
230C ASN* 1.3 71.2 - - - +
232C PRO* 1.4 75.9 - - - +
233C MET* 3.6 12.8 + - + +
245C ILE* 3.8 27.8 - - + -
249C ILE* 4.5 4.5 - - + -
364C MET* 3.7 53.4 - - + -
367C ILE* 3.6 23.3 - - + -
368C LYS* 4.1 13.9 - - + -
371C LEU* 3.6 21.8 - - + -
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Residues in contact with PRO 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C HIS* 3.6 8.0 - - - +
206C TYR* 3.3 35.2 - - + -
214C GLY 4.1 5.4 - - - +
216C LEU* 4.1 22.9 - - + +
230C ASN 3.3 13.5 - - - +
231C PHE* 1.4 89.8 - - - +
233C MET* 1.3 56.1 + - - +
363C TYR* 2.7 35.1 + - - +
367C ILE* 4.2 20.9 - - + +
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Residues in contact with MET 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C PHE* 4.0 8.3 - - + -
204C HIS 2.7 21.5 + - - +
205C LYS* 3.3 4.3 - - - +
206C TYR 2.8 29.0 + - - +
231C PHE* 3.9 19.3 - - + +
232C PRO* 1.3 77.3 - - - +
234C ARG* 1.3 65.4 + - - +
237C ILE* 4.4 7.6 - - + -
242C TYR* 3.8 30.7 - - + -
245C ILE* 3.4 35.0 - - + -
279C PHE* 3.7 29.2 - - + -
359C ASN* 3.6 15.7 - - - +
363C TYR* 4.1 1.8 - - - -
364C MET* 4.5 4.7 - - + -
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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