Contacts of the strand formed by residues 224 - 232 (chain A) in PDB entry 4JF7
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 ARG 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ASN* 3.2 23.9 + - - -
191A SER* 3.6 3.1 + - - -
192A ASN 5.7 0.6 - - - -
193A GLN* 3.9 10.4 - - + +
218A LEU* 3.7 44.2 + - - +
220A ASP* 2.4 43.1 + - - +
222A VAL* 3.1 25.6 + - + +
223A ASN* 1.3 72.7 - - - +
225A LYS* 1.3 60.9 + - - +
227A CYS* 4.2 4.3 - - - -
240A CYS* 4.1 21.3 - - + -
241A PHE 3.7 4.7 - - - -
242A VAL* 4.6 7.2 - - + +
260A ARG* 3.4 11.3 - - - +
262A ILE* 3.9 15.9 - - - -
272A GLU* 3.0 41.2 + - - +
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Residues in contact with LYS 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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179A ASN* 2.9 27.3 + - - +
181A ILE* 3.8 16.0 - - - +
187A ASP 4.5 0.4 + - - -
188A HIS* 3.9 26.6 + - - +
191A SER* 3.4 20.8 + - - -
223A ASN* 3.5 20.2 - - - +
224A ARG* 1.3 78.8 - - - +
226A SER* 1.3 73.0 + - - +
227A CYS* 3.1 7.3 + - - -
240A CYS* 3.9 1.2 - - - -
241A PHE* 2.9 50.1 + - + +
243A SER* 3.9 12.6 - - - -
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Residues in contact with SER 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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164A ILE* 4.5 10.0 - - - +
179A ASN* 6.1 1.4 - - - +
193A GLN* 5.8 0.2 + - - -
225A LYS* 1.3 76.2 - - - +
227A CYS* 1.3 63.1 + - - +
241A PHE* 3.7 21.1 - - - -
288A ASN* 4.0 7.2 + - - +
289A PRO* 2.9 39.9 + - - +
291A THR* 3.3 23.9 - - - +
306A TYR* 4.6 5.2 + - - -
390A GLU* 5.1 0.5 + - - -
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Residues in contact with CYS 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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164A ILE* 4.7 8.3 - - - +
166A SER* 3.6 15.6 - - - -
177A THR* 4.5 1.5 - - + +
193A GLN* 3.5 41.8 + - - +
224A ARG* 4.2 2.2 - - - -
225A LYS 3.1 13.3 + - - -
226A SER* 1.3 78.0 - - - +
228A SER* 1.3 58.6 + - - +
238A MET* 3.8 8.7 - - - -
239A TYR 3.1 7.2 - - - +
240A CYS* 2.1 45.1 - - - -
291A THR* 3.7 8.5 - - - -
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Residues in contact with SER 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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166A SER* 3.4 5.6 - - - -
226A SER 3.5 1.4 + - - -
227A CYS* 1.3 72.8 - - - +
229A ILE* 1.3 59.8 + - - +
238A MET* 3.4 5.3 - - - +
239A TYR 2.9 31.6 + - - -
289A PRO* 4.0 8.5 - - - +
290A GLY 3.7 6.8 + - - -
291A THR 2.9 23.6 + - - -
292A GLY 2.7 25.0 + - - -
303A PHE* 3.7 22.2 - - - -
304A PRO* 4.0 3.4 - - - +
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Residues in contact with ILE 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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166A SER* 3.0 38.7 + - - +
167A PHE* 3.9 4.0 - - - +
168A SER* 3.7 2.6 - - - +
175A CYS* 3.8 33.9 - - + +
176A TYR 4.2 8.7 - - - +
177A THR* 4.0 12.6 - - + -
195A VAL* 4.1 21.5 - - + -
228A SER* 1.3 76.1 - - - +
230A SER* 1.3 69.6 + - - +
236A CYS* 3.9 13.2 - - + -
237A MET 3.5 11.7 - - - +
238A MET* 4.1 11.4 - - + -
293A SER* 3.2 10.9 - - - -
294A GLY 2.8 20.1 + - - -
303A PHE* 3.9 1.3 - - - -
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Residues in contact with SER 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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168A SER* 3.5 9.3 + - - -
175A CYS* 4.4 3.1 - - - -
229A ILE* 1.3 75.5 - - - +
231A THR* 1.3 79.8 + - - +
236A CYS* 3.3 4.7 - - - +
237A MET 2.9 32.1 + - - -
294A GLY* 3.5 20.6 + - - -
295A VAL* 3.5 21.3 - - - -
296A TYR 3.6 0.5 + - - -
301A VAL* 3.6 21.0 - - - +
303A PHE* 4.0 2.5 - - - -
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Residues in contact with THR 231 (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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168A SER* 3.0 35.1 + - - +
170A THR* 2.8 35.0 + - - +
173A HIS* 3.6 31.6 - - - +
175A CYS* 3.8 15.7 - - - +
230A SER* 1.3 89.3 + - - +
232A VAL* 1.3 66.3 + - - +
235A GLY 3.5 4.9 - - - -
296A TYR* 3.8 10.3 + - - +
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Residues in contact with VAL 232 (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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173A HIS* 3.1 10.5 - - - -
231A THR* 1.3 80.7 - - - +
233A PRO* 1.3 85.0 - - + +
234A GLY 3.0 2.8 + - - -
235A GLY* 2.8 36.3 + - - +
236A CYS 3.7 9.4 - - - +
237A MET* 3.9 17.5 - - + -
263A ILE* 4.8 1.6 - - + -
265A TYR* 4.3 12.6 - - + -
296A TYR* 4.6 4.5 - - + -
301A VAL* 3.9 27.4 - - + -
367A LEU* 4.0 17.9 - - + -
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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