Contacts of the strand formed by residues 227 - 233 (chain A) in PDB entry 2A7P
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 LYS 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.6 43.7 + - + +
69A LYS* 6.0 4.3 - - - +
151A THR 4.2 2.7 - - - +
152A THR* 3.3 25.2 - - + +
153A LEU 3.0 15.8 + - - -
224A TRP* 2.8 17.0 + - - -
226A HIS* 1.3 78.3 - - + +
228A LEU* 1.3 58.9 + - - +
248A ASP* 3.1 29.7 + - + +
279A LYS* 5.9 2.6 - - - +
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Residues in contact with LEU 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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153A LEU* 3.4 33.0 - - + +
155A LEU* 4.7 3.8 - - + +
217A LEU* 4.5 14.4 - - + -
220A LEU* 4.4 16.8 - - + +
221A ARG* 3.8 59.0 - - + +
224A TRP* 4.0 5.6 - - + -
227A LYS* 1.3 75.8 - - - +
229A LEU* 1.3 82.9 + - - +
230A VAL* 5.5 0.2 - - + -
247A ALA* 3.7 9.9 - - + -
248A ASP* 2.7 37.3 + - - +
249A GLY 3.6 0.2 + - - -
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Residues in contact with LEU 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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67A LEU* 3.9 28.3 - - + -
127A TRP* 3.8 29.2 - - + -
152A THR* 4.4 5.8 - - + -
153A LEU 2.9 7.5 + - - +
154A VAL* 3.3 13.2 - - + -
155A LEU* 2.9 26.2 + - - +
228A LEU* 1.3 83.2 - - - +
230A VAL* 1.3 63.5 + - - +
248A ASP* 3.9 1.6 - - + -
249A GLY* 3.2 41.5 - - - +
250A VAL 4.0 0.2 - - - +
251A ILE* 4.2 23.8 - - + -
282A LEU* 4.3 13.2 - - + -
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Residues in contact with VAL 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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155A LEU* 3.5 9.0 - - + +
157A THR* 3.9 25.1 - - + -
217A LEU* 4.1 26.7 - - + -
228A LEU* 5.5 1.8 - - + -
229A LEU* 1.3 76.4 - - - +
231A LYS* 1.3 60.9 + - - +
233A LEU* 4.0 16.0 - - + +
242A CYS* 3.7 39.9 - - + -
247A ALA* 4.3 9.4 - - + -
249A GLY 3.4 5.1 + - - -
250A VAL* 3.4 6.8 - - + +
251A ILE* 2.8 24.5 + - - +
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Residues in contact with LYS 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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79A PRO* 3.8 14.4 - - + -
154A VAL* 3.6 25.6 - - + -
155A LEU 2.7 10.8 + - - +
156A THR* 3.7 17.2 + - + +
157A THR* 2.9 32.3 + - - -
158A ASP* 5.3 0.8 + - - +
229A LEU 4.0 0.4 + - - -
230A VAL* 1.3 74.5 - - - +
232A GLY* 1.3 63.6 + - - +
233A LEU 3.6 1.3 - - - -
251A ILE* 3.6 27.6 - - + -
253A SER* 4.9 4.3 + - - +
255A HIS* 4.3 8.1 + - - -
284A ASP* 3.6 17.7 - - - +
305A LEU* 5.0 1.1 - - - -
390A FMN 2.9 60.5 + - - +
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Residues in contact with GLY 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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157A THR* 4.1 7.1 + - - -
158A ASP* 3.2 36.1 - - - +
231A LYS* 1.3 79.8 - - - +
233A LEU* 1.3 65.2 + - - +
234A LEU* 3.8 6.9 + - - +
251A ILE 3.1 7.3 + - - -
253A SER* 3.5 13.9 - - - +
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Residues in contact with LEU 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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157A THR* 4.5 6.3 - - - +
214A TRP* 5.4 2.0 - - + -
230A VAL* 4.0 25.8 - - + +
232A GLY* 1.3 81.6 - - - +
234A LEU* 1.3 63.3 + - - +
235A SER 3.8 3.6 - - - +
238A ASP* 3.9 23.3 - - + +
239A ALA* 3.4 31.2 - - + -
242A CYS* 3.6 20.4 - - - -
250A VAL* 3.6 20.4 - - + -
251A ILE 3.5 4.0 + - - +
252A LEU* 3.3 20.6 - - + +
253A SER 3.0 22.0 + - - -
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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