Contacts of the helix formed by residues 230 - 241 (chain B) in PDB entry 3N4E
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 HIS 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A GLN* 3.6 23.2 - - + +
258A LYS* 5.6 4.3 - - - +
226B VAL* 3.9 7.4 - - + +
227B GLN* 3.0 36.4 + - + +
228B HIS 4.3 0.7 - - - -
229B TYR* 1.3 100.5 - + - +
231B VAL* 1.3 57.7 + - - +
232B GLY 3.3 2.5 - - - -
233B ALA* 3.3 20.1 + - + +
234B MSE 2.9 27.6 + - - +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 5.3 1.0 - - - +
259A ASP* 4.5 17.8 + - - +
228B HIS 3.8 16.8 - - - +
229B TYR* 3.4 7.7 + - - +
230B HIS* 1.3 67.7 - - - +
232B GLY* 1.3 66.2 + - - +
234B MSE 3.2 8.2 + - - +
235B GLY 3.1 19.2 + - - -
256B ALA 5.7 0.4 - - - +
259B ASP* 4.2 8.7 - - + +
260B LEU* 4.2 27.1 - - + +
263B SER* 3.6 22.0 - - - +
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Residues in contact with GLY 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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258A LYS* 4.3 18.2 - - - +
259A ASP* 5.0 2.5 + - - -
230B HIS 3.3 0.8 - - - -
231B VAL* 1.3 80.2 - - - +
233B ALA* 1.3 56.5 + - - +
235B GLY* 3.3 1.4 + - - -
236B GLU* 3.0 28.3 + - - +
263B SER* 4.8 7.2 - - - +
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Residues in contact with ALA 233 (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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258A LYS* 5.4 1.2 - - - +
204B VAL* 3.6 27.6 - - + -
226B VAL* 4.2 8.7 - - + -
230B HIS* 3.3 25.7 + - + +
232B GLY* 1.3 72.1 - - - +
234B MSE 1.3 65.7 + - - +
236B GLU* 3.3 10.1 + - - +
237B VAL* 2.9 30.0 + - - +
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Residues in contact with MSE 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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224B GLU* 4.0 10.8 - - - +
225B PRO* 3.6 31.0 - - - -
226B VAL* 3.4 35.6 - - + +
227B GLN 3.9 0.2 - - - +
228B HIS* 3.8 23.8 - - + +
230B HIS 2.9 17.2 + - - +
231B VAL* 3.2 14.1 + - - +
233B ALA* 1.3 72.2 - - - +
235B GLY* 1.3 57.9 + - - +
237B VAL* 3.5 4.5 + - - +
238B ALA* 3.0 26.0 + - - +
245B VAL* 4.0 6.9 - - + +
247B ALA* 3.9 33.7 - - + -
260B LEU* 4.4 6.5 - - + -
265B VAL* 3.9 11.9 - - + -
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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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231B VAL 3.1 10.1 + - - -
232B GLY 3.8 1.1 - - - -
234B MSE 1.3 73.8 - - - +
236B GLU* 1.3 59.9 + - - +
238B ALA* 3.3 9.3 + - - +
239B GLN* 2.9 34.1 + - - +
263B SER* 3.2 37.1 + - - -
264B GLY* 3.9 1.1 - - - -
265B VAL* 4.1 2.5 - - - -
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Residues in contact with GLU 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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204B VAL* 3.8 17.0 - - + +
232B GLY 3.0 17.8 + - - +
233B ALA* 3.3 10.5 + - - +
235B GLY* 1.3 73.2 - - - +
237B VAL* 1.3 60.7 + - - +
239B GLN* 3.3 5.3 + - - +
240B ARG* 2.9 72.1 + - + +
263B SER 4.0 1.0 + - - -
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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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204B VAL* 4.1 26.5 - - + +
207B ALA* 4.1 20.2 - - + -
208B ILE* 4.8 4.7 - - + -
225B PRO* 4.1 8.5 - - + -
226B VAL* 4.3 16.8 - - + -
233B ALA 2.9 22.2 + - - +
234B MSE 3.7 4.3 - - - +
236B GLU* 1.3 72.9 - - - +
238B ALA* 1.3 66.1 + - - +
240B ARG* 4.5 5.6 - - - +
241B LEU* 3.1 48.7 + - + +
245B VAL* 3.9 9.4 - - + -
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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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234B MSE 3.0 16.6 + - - +
235B GLY* 3.3 7.0 - - - +
236B GLU 3.2 0.2 - - - -
237B VAL* 1.3 79.3 - - - +
239B GLN* 1.3 60.5 + - - +
241B LEU* 3.4 14.7 - - - +
243B ILE 4.7 3.6 - - - +
245B VAL* 3.6 28.1 + - + +
264B GLY 3.3 27.4 - - - +
265B VAL* 3.9 9.0 - - - -
266B ARG* 5.0 1.3 - - + +
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Residues in contact with GLN 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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235B GLY 2.9 19.2 + - - +
236B GLU* 3.3 5.4 + - - +
237B VAL 3.3 0.2 - - - -
238B ALA* 1.3 73.7 - - - +
240B ARG* 1.3 63.7 + - + +
241B LEU 3.4 3.7 + - - +
263B SER 4.6 2.5 - - - +
264B GLY* 2.8 36.8 + - - -
266B ARG* 3.7 24.8 - - - +
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Residues in contact with ARG 240 (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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204B VAL* 4.1 4.9 - - - +
208B ILE* 3.2 39.9 - - + +
212B ARG* 3.2 22.9 + - - +
236B GLU* 2.9 53.8 + - + +
237B VAL* 3.2 5.6 + - - +
239B GLN* 1.3 79.7 - - + +
241B LEU* 1.3 60.0 + - - +
242B ASP* 4.8 1.7 - - - +
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Residues in contact with LEU 241 (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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207B ALA 4.2 2.9 - - - +
208B ILE* 4.0 31.0 - - + +
211B GLY* 4.1 9.4 - - - -
212B ARG* 3.9 19.1 - - - +
215B GLU* 3.6 14.4 - - - +
222B PHE* 3.9 26.2 - - + -
237B VAL* 3.1 38.1 + - + +
238B ALA 3.4 13.0 - - - +
239B GLN 3.4 3.5 - - - +
240B ARG* 1.3 81.6 - - - +
242B ASP* 1.3 65.4 + - - +
243B ILE* 3.8 14.4 - - + +
245B VAL* 3.9 5.2 - - + -
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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