Contacts of the strand formed by residues 227 - 233 (chain A) in PDB entry 1PJX
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 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A THR* 3.4 12.5 - - - +
198A LYS* 3.9 11.7 - - - -
220A ILE* 4.4 0.2 - - - -
224A HIS* 3.7 0.8 + - - -
226A GLY* 1.3 74.5 - - - -
228A ALA* 1.3 67.7 + - - -
229A ASP 3.3 0.7 + - - -
243A ASN* 3.4 16.8 - - - -
244A TRP* 2.9 33.2 + - - +
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Residues in contact with ALA 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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193A ALA* 3.6 23.2 - - + +
194A GLU 5.2 0.4 + - - +
195A THR* 2.7 36.6 + - - -
199A LYS 4.8 2.5 - - - +
200A LEU* 3.8 12.1 - - + -
220A ILE* 3.8 18.8 - - + +
227A GLY* 1.3 69.9 - - - -
229A ASP* 1.3 57.8 + - - +
241A VAL* 3.5 23.3 - - + -
242A ALA 3.3 7.6 - - - -
243A ASN* 4.5 1.3 - - - +
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Residues in contact with ASP 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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21A GLU* 3.5 3.6 - - - +
175A ASN* 3.0 15.0 + - - +
176A GLY* 2.8 26.4 + - - -
193A ALA* 3.9 3.5 - - - +
195A THR* 5.8 0.7 - - + -
227A GLY 3.3 0.4 + - - +
228A ALA* 1.3 75.6 - - - +
230A GLY* 1.3 61.4 + - - +
231A MET* 4.7 0.9 - - - +
241A VAL* 4.6 0.2 - - - +
242A ALA 2.9 11.8 + - - +
244A TRP* 4.0 21.1 - - + -
271A SER* 2.8 43.7 + - - +
287A HIS* 4.5 2.8 - - - -
491A CA 2.4 29.4 - - - -
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Residues in contact with GLY 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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121A ASP* 4.3 0.7 - - - -
176A GLY* 4.2 5.8 - - - -
229A ASP* 1.3 75.2 + - - +
231A MET* 1.3 62.1 + - - +
240A LEU 4.0 0.2 - - - +
241A VAL* 3.4 1.9 - - - +
242A ALA* 2.9 27.9 + - - +
271A SER 2.8 17.6 + - - -
272A ASN* 3.3 26.9 - - - -
273A LEU* 4.4 4.1 - - - +
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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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121A ASP* 5.0 2.2 + - - +
176A GLY* 4.0 4.4 - - - -
177A ILE* 3.7 41.8 - - - +
178A ALA* 3.7 14.9 - - + +
191A ILE* 3.9 17.7 - - + +
193A ALA* 3.8 35.4 - - + +
200A LEU* 3.9 17.9 - - + -
229A ASP 4.7 0.4 - - - +
230A GLY* 1.3 73.7 - - - +
232A ASP* 1.3 75.4 + - - +
239A LEU* 4.0 10.8 - - + -
240A LEU 3.1 13.7 - - - +
241A VAL* 4.0 12.1 - - + -
272A ASN* 3.9 3.7 + - - +
273A LEU* 4.1 5.4 - - - -
492A CA 4.2 3.3 - - - -
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Residues in contact with ASP 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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77A GLN* 5.4 1.4 + - - -
177A ILE 5.5 0.9 - - - +
178A ALA* 5.0 5.4 - - - +
231A MET* 1.3 80.9 - - - +
233A PHE* 1.3 68.0 + - - +
239A LEU* 3.8 8.5 - - - -
240A LEU* 2.9 35.5 + - - +
273A LEU* 3.1 19.6 - - + +
274A HIS* 3.2 12.5 + - - -
275A PHE* 4.6 11.4 + - + -
304A GLN* 3.4 23.7 + - - -
492A CA 2.2 28.0 - - - -
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Residues in contact with PHE 233 (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 ALA* 3.7 21.3 - - + -
179A VAL 3.3 34.8 - - - -
180A ARG* 3.5 49.6 - - + -
191A ILE* 4.4 9.0 - - + -
232A ASP* 1.3 76.8 + - - +
234A ASP* 1.3 67.6 + - - +
237A ASN* 3.5 20.0 - - + -
238A ASN 3.2 14.8 - - - -
239A LEU* 3.7 20.4 - - + -
275A PHE* 3.7 12.9 - - - -
302A LYS* 3.0 34.9 + - + +
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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