Contacts of the strand formed by residues 224 - 230 (chain A) in PDB entry 5C58
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 GLY 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A ILE* 4.1 8.9 - - - +
172A ARG 3.8 1.0 + - - -
173A VAL* 3.4 4.0 - - - +
174A ASN 3.2 21.1 + - - -
209A ASP 3.1 12.1 - - - -
211A GLY 3.3 11.7 + - - -
213A THR* 5.1 0.4 - - - -
221A THR* 3.3 14.5 - - - +
223A GLY* 1.3 81.3 - - - +
225A ILE* 1.3 65.5 + - - +
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Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ILE* 4.3 2.2 - - - +
173A VAL* 4.7 1.1 - - - -
174A ASN* 3.8 13.2 - - + +
176A ASN* 3.6 11.7 - - - +
207A THR 3.8 1.6 - - - +
208A ILE* 3.5 2.3 - - - +
209A ASP* 2.8 47.6 + - + +
213A THR* 3.3 32.8 - - + +
215A GLY* 5.8 1.1 - - - +
216A MET 5.6 2.7 - - - +
217A GLY* 3.2 31.4 - - - +
218A SER* 4.1 2.2 - - - -
221A THR* 4.2 5.2 - - - +
224A GLY* 1.3 79.0 - - - +
226A ALA* 1.3 62.4 + - - +
227A THR* 3.6 20.6 + - - +
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Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A VAL* 4.0 29.8 - - + -
173A VAL* 4.3 6.1 - - + +
174A ASN 3.0 11.2 + - - +
175A MET* 3.5 3.4 - - - -
176A ASN* 2.7 36.4 + - - +
207A THR 3.8 3.8 - - - -
208A ILE* 4.5 12.3 - - + -
225A ILE* 1.3 71.1 - - - +
227A THR* 1.3 55.0 + - - +
228A PHE* 3.8 20.8 - - + -
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Residues in contact with THR 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ASN* 3.0 30.7 + - - +
178A ASP* 4.7 3.8 - - - +
179A GLY 4.7 2.5 - - - +
206A VAL* 3.3 6.1 - - - +
207A THR* 2.9 50.3 + - - +
225A ILE* 3.6 12.7 + - - +
226A ALA* 1.3 69.7 - - - +
228A PHE* 1.3 63.7 + - - +
229A ASN* 3.7 26.5 + - - +
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Residues in contact with PHE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ILE* 4.2 16.2 - - + -
143A LEU* 5.4 5.2 - - + -
160A LEU* 3.5 29.2 - - + -
162A VAL* 4.1 13.7 - - + -
175A MET* 5.0 0.9 - - + -
176A ASN 2.8 20.1 + - - +
177A ILE* 3.3 16.7 - - + +
178A ASP 3.0 21.8 + - - -
196A MET* 4.0 21.5 - - + -
198A ILE* 4.3 9.0 - - + -
203A LEU* 3.8 22.6 - - + +
206A VAL* 3.5 33.2 - - + -
208A ILE* 5.9 0.9 - - + -
226A ALA* 3.8 25.8 - - + -
227A THR* 1.3 72.8 - - - +
229A ASN* 1.3 62.5 + - - +
230A THR 3.8 1.9 + - - -
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Residues in contact with ASN 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP* 3.2 16.8 - - - +
203A LEU* 3.3 8.5 - - - +
204A SER* 3.0 34.2 + - - +
205A GLY* 3.0 22.8 + - - +
207A THR* 4.4 16.0 - - - +
227A THR* 3.9 25.8 + - - +
228A PHE* 1.3 72.5 - - - +
230A THR* 1.3 62.7 + - - +
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ILE* 3.8 20.4 - - + -
178A ASP* 2.3 37.9 + - - +
198A ILE* 4.6 2.7 - - + -
202A LEU* 3.2 13.2 - - + +
203A LEU* 4.2 9.9 - - + -
204A SER* 3.6 7.6 + - - -
229A ASN* 1.3 77.9 - - - +
231A VAL* 1.3 65.0 + - - +
232A SER* 3.5 6.1 + - - -
235A ASP* 4.9 0.2 - - - +
328A LEU* 4.0 15.4 - - + +
330A LYS* 2.9 27.4 + - - -
346A LEU* 4.1 16.4 - - + -
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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