Contacts of the strand formed by residues 231 - 239 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B GLN* 3.8 2.1 - - - +
212B TRP* 3.6 28.3 - - - +
213B ALA 3.8 0.4 - - - +
214B GLY* 3.6 17.0 - - - +
215B ALA* 4.0 0.9 - - - -
227B VAL* 3.3 29.2 - - - +
228B LEU* 3.3 13.2 + - - +
229B ALA 3.5 0.6 - - - -
230B GLN* 1.3 79.6 - - - +
232B ASN* 1.3 65.5 + - - +
235B GLY* 4.1 0.9 - - - -
236B CYS 3.4 38.6 - - - +
237B VAL* 3.4 24.0 - - + -
258B ARG* 3.6 24.3 + - - -
260B VAL* 3.6 27.6 - - + -
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Residues in contact with ASN 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ASP 4.0 10.1 + - - -
148B GLY* 5.0 2.6 - - - -
210B GLN* 3.4 18.0 - - - +
211B LEU 3.4 24.1 + - - -
212B TRP 2.8 18.9 + - - +
213B ALA* 3.4 29.9 - - - +
230B GLN 3.6 0.2 + - - -
231B MSE 1.3 76.6 - - - +
233B TYR* 1.3 72.2 + - - +
234B GLY 3.2 0.7 + - - -
235B GLY* 2.8 16.3 + - - +
260B VAL* 3.9 5.9 - - - +
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Residues in contact with TYR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASP* 2.6 37.6 + - - +
269A MSE 3.8 42.7 - - + -
270A THR* 4.0 3.6 + - - -
271A PRO* 5.0 7.5 - - + +
210B GLN* 2.9 20.2 + - - +
231B MSE 3.7 0.2 + - - -
232B ASN* 1.3 76.8 - - - +
234B GLY* 1.3 64.5 + - - +
235B GLY 3.3 0.2 + - - -
257B LEU 3.7 13.5 - - - -
258B ARG* 3.3 30.5 - - + +
259B ASN* 3.8 18.5 + - + +
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Residues in contact with GLY 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ALA* 5.0 4.5 - - - +
143B ILE* 4.0 12.0 - - - +
233B TYR* 1.3 79.9 - - - +
235B GLY* 1.3 64.6 + - - +
236B CYS* 5.2 0.3 - - - +
258B ARG 2.7 14.8 + - - -
259B ASN* 3.4 21.8 - - - -
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Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ILE* 4.3 2.0 - - - -
213B ALA* 3.3 17.9 - - - -
231B MSE 4.1 10.1 - - - -
232B ASN* 2.8 18.8 + - - -
233B TYR 3.2 1.2 + - - -
234B GLY* 1.3 81.7 - - - +
236B CYS* 1.3 60.9 + - - +
260B VAL* 3.5 7.5 - - - +
261B ARG* 3.0 23.6 + - - +
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Residues in contact with CYS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ALA 4.2 8.7 - - - -
138B LEU* 3.3 12.8 - - + +
141B ALA* 3.4 33.9 - - + -
143B ILE* 4.0 9.1 - - + +
213B ALA 3.4 6.3 + - - -
214B GLY* 3.2 6.6 - - - -
215B ALA 3.1 21.5 + - - -
231B MSE 3.4 1.6 - - - +
235B GLY* 1.3 75.9 - - - +
237B VAL* 1.3 76.1 + - - +
238B ALA* 4.5 0.7 - - - -
261B ARG* 3.3 26.0 - - + +
263B GLN* 4.4 6.7 - - - -
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ALA* 3.6 16.6 - - + +
217B ASP* 4.5 4.5 - - + -
224B LEU* 3.8 26.9 - - + -
227B VAL* 4.2 5.4 - - + -
228B LEU* 3.9 14.4 - - + -
231B MSE 3.4 40.4 - - + -
236B CYS* 1.3 76.3 - - - +
238B ALA* 1.3 64.9 + - - +
260B VAL* 4.9 0.4 - - + -
261B ARG 2.8 11.4 + - - +
262B LEU* 3.5 15.0 - - + +
263B GLN* 2.7 32.4 + - - +
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B CYS* 3.7 46.8 - - + +
137B ALA* 4.1 12.3 - - + -
138B LEU* 4.3 5.3 - - + +
215B ALA 2.8 15.2 + - - +
216B ILE* 3.4 2.9 - - + -
217B ASP 2.9 26.0 + - - +
236B CYS 4.1 0.6 + - - -
237B VAL* 1.3 71.3 - - - +
239B ALA* 1.3 60.7 + - - +
240B CYS 4.1 0.2 + - - -
263B GLN* 3.3 8.3 - - - +
265B VAL* 4.3 1.1 - - + -
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A VAL* 5.8 1.3 - - + -
255A PHE* 4.9 6.7 - - + -
256A ILE* 3.7 12.7 - - + +
217B ASP* 3.7 9.0 - - + +
224B LEU* 4.2 22.9 - - + -
237B VAL 3.8 0.6 + - - -
238B ALA* 1.3 71.9 - - - +
240B CYS* 1.3 59.9 + - - +
241B GLY 3.9 1.1 - - - +
262B LEU* 3.7 24.9 - - + -
263B GLN 2.9 8.9 + - - +
264B GLY* 3.6 2.6 - - - -
265B VAL* 2.9 28.2 + - - +
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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