Contacts of the strand formed by residues 225 - 232 (chain A) in PDB entry 1QQJ
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 ILE 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TRP* 3.6 11.7 - - - -
204A PHE* 3.8 36.1 - - + -
205A PHE 3.9 2.0 - - - -
221A ALA 3.7 9.6 - - - +
222A HIS 3.5 7.4 + - - +
223A GLU 3.5 1.8 - - - -
224A HIS* 1.3 82.9 - - - +
226A PHE* 1.3 63.2 + - - +
266A MET* 3.3 38.3 - - + +
293A TYR* 3.8 13.7 - - + +
326A MET* 4.0 30.5 - - + +
327A LEU* 3.9 28.5 - - + -
330A LEU* 4.3 5.8 - - + -
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Residues in contact with PHE 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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19A TYR* 3.7 33.2 - + + -
67A LEU* 4.9 2.0 - - + -
70A PHE* 3.7 30.3 - + - -
71A MET* 3.8 35.7 - - + -
78A TRP* 3.4 49.3 - + + -
205A PHE* 2.9 20.8 + - + +
207A GLY 4.4 3.1 - - - +
224A HIS 3.8 1.2 + - - -
225A ILE* 1.3 73.3 - - - +
227A GLY* 1.3 61.1 + - - +
263A VAL* 3.6 29.2 - - + -
265A PRO* 3.5 9.7 - - + +
266A MET* 3.1 18.4 + - - -
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Residues in contact with GLY 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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204A PHE* 3.2 5.2 - - - +
205A PHE* 2.9 26.2 + - - +
225A ILE* 3.6 1.6 - - - +
226A PHE* 1.3 83.2 - - - +
228A MET* 1.3 63.6 + - - -
263A VAL* 3.8 13.4 - - - +
264A VAL 3.0 14.6 - - - -
265A PRO* 3.9 1.3 - - - -
266A MET* 3.9 11.0 - - - +
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Residues in contact with MET 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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202A MET* 3.7 26.7 - - + -
203A ALA* 3.2 11.7 - - - +
204A PHE* 4.2 6.5 - - + -
205A PHE* 5.1 0.7 - - - +
227A GLY* 1.3 79.0 - - - +
229A VAL* 1.3 68.1 + - - +
262A TRP 3.7 1.2 - - - +
263A VAL* 3.5 2.4 - - - +
264A VAL 2.9 27.5 + - - -
266A MET* 3.8 13.2 - - - +
269A LEU* 3.7 22.0 - - + -
295A PHE* 5.2 1.1 - - - -
297A ILE* 4.3 9.2 - - - -
319A PHE* 3.5 34.1 - - + -
326A MET* 3.8 23.6 - - - -
405A PHE* 3.6 19.5 - - + -
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO* 4.9 0.9 - - + -
202A MET* 3.4 13.4 - - - +
203A ALA* 2.9 40.8 + - + +
205A PHE* 3.9 19.1 - - + -
228A MET* 1.3 79.6 - - - +
230A LEU* 1.3 68.3 + - - +
259A ILE* 4.0 18.4 - - + -
260A SER* 3.4 26.5 - - - +
262A TRP 3.9 8.3 - - - +
263A VAL* 3.8 25.4 - - + -
345A LEU* 4.2 6.7 - - + -
405A PHE* 4.4 3.6 - - - -
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Residues in contact with LEU 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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201A GLU 3.9 3.1 - - - +
202A MET* 3.9 16.4 - - + -
229A VAL* 1.3 74.5 - - - +
231A MET* 1.3 61.9 + - - +
259A ILE* 3.2 7.6 - - - +
260A SER* 2.8 34.8 + - - +
299A LEU* 3.6 31.4 - - + -
392A ILE* 3.7 33.4 - - + +
393A THR* 3.9 6.3 - - - -
394A GLY 4.3 2.5 - - - +
405A PHE* 3.7 33.2 - - + +
406A GLY 3.8 11.7 - - - +
408A CYS* 3.8 15.9 - - + +
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Residues in contact with MET 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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124A TYR* 3.8 21.1 - - + -
166A ILE* 5.3 0.9 - - + -
199A GLU 3.4 0.5 - - - +
201A GLU* 2.9 53.4 + - + +
202A MET* 4.7 4.7 - - - +
203A ALA* 4.1 3.4 - - + -
230A LEU* 1.3 76.6 - - - +
232A ASN* 1.3 66.5 + - - +
233A ASP* 4.0 2.5 - - - +
257A THR* 3.8 26.7 - - + -
258A THR 3.2 11.0 - - - +
259A ILE* 3.6 10.3 - - + -
345A LEU* 3.5 32.1 - - + -
347A ALA* 3.6 25.6 - - + -
392A ILE* 3.4 8.0 - - - +
408A CYS* 3.9 4.0 - - - -
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Residues in contact with ASN 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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198A MET* 3.4 21.4 - - - +
199A GLU 3.0 23.8 + - - -
231A MET* 1.3 73.1 - - - +
233A ASP* 1.3 58.7 + - - +
234A TRP* 3.1 54.5 + - + +
257A THR* 3.5 0.3 - - - -
258A THR* 2.8 36.2 + - - +
390A VAL* 3.8 13.9 + - - +
392A ILE* 3.7 14.6 - - + +
408A CYS* 3.6 11.6 + - - +
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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