Contacts of the strand formed by residues 231 - 239 (chain A) in PDB entry 3NX4
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 MSE 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A GLN* 3.6 13.2 - - - +
212A TRP* 3.3 33.7 - - + +
213A ALA 3.7 4.0 - - - +
214A GLY* 3.7 29.8 - - - +
215A ALA* 4.1 2.0 - - - -
227A VAL* 3.2 29.6 - - - +
228A LEU* 3.4 13.1 + - - +
229A ALA 3.5 0.6 - - - -
230A GLN* 1.3 78.7 - - - +
232A ASN* 1.3 66.3 + - - +
235A GLY* 4.1 0.9 - - - -
236A CYS 3.7 18.4 - - - +
237A VAL* 3.6 25.6 - - + -
258A ARG* 3.6 12.5 + - - -
260A VAL* 3.6 27.6 - - + -
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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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147A ASP 4.4 8.7 + - - -
148A GLY* 5.1 2.6 - - - -
210A GLN* 3.5 27.1 - - - +
211A LEU 3.5 3.8 + - - -
212A TRP* 2.8 31.5 + - - +
213A ALA* 3.5 28.1 - - - +
230A GLN 3.6 0.4 + - - -
231A MSE 1.3 78.2 - - - +
233A TYR* 1.3 70.9 + - - +
234A GLY 3.2 0.3 + - - -
235A GLY* 2.9 16.7 + - - +
258A ARG* 4.9 0.4 - - - -
260A VAL* 4.1 3.6 - - - +
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Residues in contact with TYR 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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210A GLN* 2.8 20.6 + - - +
231A MSE 3.7 0.4 + - - -
232A ASN* 1.3 77.4 - - - +
234A GLY* 1.3 62.7 + - - +
235A GLY 3.3 0.2 + - - -
257A LEU 3.6 11.2 - - - -
258A ARG* 3.4 28.9 - - + +
259A ASN* 4.0 16.9 + - + +
266B ASP* 2.5 36.5 + - - +
269B MSE 3.4 47.8 - - + -
270B THR* 3.5 6.2 + - - -
271B PRO* 4.5 15.1 - - + +
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Residues in contact with GLY 234 (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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141A ALA* 5.2 2.9 - - - +
143A ILE* 4.2 11.7 - - - +
233A TYR* 1.3 78.9 - - - +
235A GLY* 1.3 66.4 + - - +
236A CYS* 5.1 0.5 - - - +
258A ARG 2.8 14.1 + - - -
259A ASN* 3.6 19.7 - - - -
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Residues in contact with GLY 235 (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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143A ILE* 4.6 1.1 - - - -
212A TRP 4.7 0.2 - - - -
213A ALA* 3.3 18.4 - - - -
231A MSE 4.1 10.5 - - - -
232A ASN* 2.9 19.7 + - - -
233A TYR 3.2 1.2 + - - -
234A GLY* 1.3 82.3 - - - +
236A CYS* 1.3 58.3 + - - +
237A VAL 4.4 0.2 - - - -
259A ASN 4.6 0.4 + - - -
260A VAL* 3.5 7.7 - - - +
261A ARG* 3.0 23.7 + - - +
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Residues in contact with CYS 236 (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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137A ALA 4.3 7.6 - - - -
138A LEU* 3.3 19.9 - - + +
141A ALA* 3.5 33.0 - - + -
143A ILE* 4.1 5.5 - - + +
213A ALA 3.3 7.9 + - - -
214A GLY* 3.2 5.9 - - - -
215A ALA 3.0 22.5 + - - -
231A MSE 3.8 1.5 - - - +
234A GLY 5.1 0.2 - - - +
235A GLY* 1.3 75.0 - - - +
237A VAL* 1.3 74.0 + - - +
238A ALA* 4.5 0.4 - - - -
261A ARG* 3.4 27.1 - - + +
263A GLN* 4.4 7.9 - - - -
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Residues in contact with VAL 237 (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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215A ALA* 3.5 16.8 - - + +
217A ASP* 4.3 6.3 - - + -
224A LEU* 3.9 24.5 - - + -
227A VAL* 4.3 5.2 - - + -
228A LEU* 3.8 22.2 - - + -
231A MSE 3.6 32.3 - - + -
236A CYS* 1.3 75.4 - - - +
238A ALA* 1.3 68.8 + - - +
260A VAL* 4.8 0.9 - - + -
261A ARG 2.8 12.0 + - - +
262A LEU* 3.5 15.8 - - + +
263A GLN 2.9 27.9 + - - +
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Residues in contact with ALA 238 (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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134A CYS* 3.7 45.0 - - + +
137A ALA* 4.1 12.3 - - + -
138A LEU* 4.3 6.1 - - + +
215A ALA 2.8 13.7 + - - +
216A ILE* 3.4 5.0 - - + +
217A ASP 2.8 26.0 + - - +
236A CYS* 4.1 1.4 + - - -
237A VAL* 1.3 70.4 - - - +
239A ALA* 1.3 60.3 + - - +
240A CYS 4.1 0.2 + - - -
263A GLN* 3.4 8.3 - - - +
265A VAL* 4.3 1.6 - - + -
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Residues in contact with ALA 239 (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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217A ASP* 3.6 11.9 - - + +
224A LEU* 4.5 17.3 - - + -
237A VAL* 3.7 1.0 + - + -
238A ALA* 1.3 72.6 - - - +
240A CYS* 1.3 61.0 + - - +
241A GLY 5.2 0.9 - - - +
262A LEU* 3.7 25.1 - - + -
263A GLN 3.0 8.2 + - - +
264A GLY* 3.6 2.9 - - - -
265A VAL* 2.9 24.5 + - - -
252B VAL* 5.7 1.6 - - + -
255B PHE* 4.9 7.4 - - + -
256B ILE* 3.6 12.3 - - + +
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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