Contacts of the helix formed by residues 222 - 235 (chain B) in PDB entry 3NJ4
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 222 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A TYR* 3.7 8.1 - - - -
220B GLY 3.8 1.2 - - - -
221B TYR* 1.3 75.9 - - - +
223B ASP* 1.3 57.6 + - - -
224B VAL 3.2 2.5 - - - -
225B GLY 3.9 4.8 - - - +
226B LYS* 2.7 40.1 + - - +
248B ASN* 3.8 0.2 - - - -
275B THR* 4.8 0.6 + - - -
502B NAD 3.1 31.7 + - - -
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Residues in contact with ASP 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A TYR* 4.0 15.1 + - - -
432A TYR 3.7 21.0 - - - +
187B SER* 3.5 31.7 - - - +
188B LYS* 4.2 10.8 + - - +
191B ASN* 3.4 25.1 - - + +
192B LEU* 3.4 19.7 - - + +
222B GLY* 1.3 71.6 - - - +
224B VAL* 1.3 63.3 + - - +
226B LYS* 4.4 7.8 - - - +
227B GLY 3.1 17.0 + - - -
502B NAD 3.1 13.0 + - - +
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Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASN* 3.5 11.9 - - + +
195B CYS* 3.7 18.1 - - - +
223B ASP* 1.3 71.0 - - - +
225B GLY* 1.3 67.6 + - - +
227B GLY* 3.0 2.8 + - - -
228B CYS* 2.9 28.6 + - - -
275B THR* 3.5 26.2 - - + -
299B ILE* 3.5 18.6 - - + -
502B NAD 2.8 67.8 + - + +
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Residues in contact with GLY 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B VAL* 4.0 3.8 - - - +
220B GLY 3.8 11.7 - - - -
221B TYR* 4.2 6.5 - - - -
222B GLY* 3.2 10.3 + - - +
224B VAL* 1.3 78.4 - - - +
226B LYS* 1.3 63.0 + - - +
228B CYS* 3.5 1.4 + - - +
229B ALA* 3.0 26.3 + - - +
275B THR* 3.5 28.1 + - - -
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Residues in contact with LYS 226 (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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430A TYR* 4.9 0.6 + - - -
432A TYR* 3.3 28.1 + - - +
188B LYS* 5.8 2.2 - - - +
192B LEU* 3.4 21.3 - - + -
221B TYR* 3.2 51.0 + - + +
222B GLY 2.7 31.0 + - - +
223B ASP* 4.6 6.3 - - - +
225B GLY* 1.3 72.4 - - - +
227B GLY* 1.3 63.1 + - - +
229B ALA* 3.7 1.7 - - - +
230B GLN* 3.1 26.3 + - - +
248B ASN* 3.8 4.2 + - - -
251B GLN* 2.9 33.5 - - - +
257B TYR* 5.0 0.2 + - - -
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Residues in contact with GLY 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASN 4.9 0.7 - - - -
192B LEU* 3.3 30.3 - - - +
196B ARG* 3.3 24.5 - - - +
223B ASP 3.1 5.5 + - - -
224B VAL 3.0 6.6 + - - -
226B LYS* 1.3 80.9 - - - +
228B CYS* 1.3 60.6 - - - +
230B GLN* 3.5 2.3 + - - +
231B ALA 3.2 16.1 + - - -
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Residues in contact with CYS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B CYS* 3.9 13.7 - - - -
199B LEU* 3.4 30.7 - - + -
218B VAL* 4.5 12.3 - - + -
224B VAL* 2.9 37.5 + - - +
225B GLY 3.9 3.1 - - - +
227B GLY* 1.3 72.3 - - - +
229B ALA* 1.3 67.1 - - - +
231B ALA* 3.0 14.7 + - - +
232B LEU* 3.0 18.7 + - - +
273B VAL* 4.4 3.6 - - + -
275B THR* 3.8 9.6 - - - -
299B ILE* 4.1 10.8 - - - -
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B VAL* 4.3 5.5 - - + +
221B TYR* 4.0 12.6 - - + -
225B GLY 3.0 19.3 + - - +
226B LYS 3.7 3.4 - - - +
228B CYS* 1.3 78.7 - - - +
230B GLN* 1.3 62.9 + - - +
232B LEU* 3.4 1.4 + - - -
233B ARG* 3.2 18.9 + - - +
239B VAL* 3.6 16.2 - - + +
241B ILE* 4.0 11.7 - - + -
257B TYR* 3.4 29.2 + - + +
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Residues in contact with GLN 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 6.1 0.6 - - - +
255A GLU* 4.3 8.7 + - - +
192B LEU* 5.2 8.5 - - - +
196B ARG* 3.3 38.1 + - - +
226B LYS 3.1 17.1 + - - +
227B GLY* 3.8 6.1 - - - +
228B CYS 3.2 0.2 - - - -
229B ALA* 1.3 77.3 - - - +
231B ALA* 1.3 63.7 + - - +
233B ARG* 3.5 21.6 - - - +
234B GLY* 3.0 21.0 + - - -
257B TYR* 3.4 10.0 + - - +
234D GLY 4.6 9.5 + - - +
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Residues in contact with ALA 231 (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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196B ARG* 3.2 33.8 - - - +
199B LEU* 4.8 2.0 - - + -
200B ILE* 3.8 21.3 - - + -
227B GLY 3.2 8.8 + - - +
228B CYS* 3.0 11.8 + - - +
230B GLN* 1.3 77.0 - - - +
232B LEU* 1.3 63.5 + - - +
234B GLY* 2.9 12.7 + - - -
235B PHE* 3.2 17.5 + - - -
234D GLY 5.9 2.0 - - - -
235D PHE* 4.7 5.8 - - + -
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU* 4.0 14.1 - - + -
200B ILE* 3.2 25.4 - - + -
203B ILE* 4.8 8.1 - - + -
211B ILE* 3.4 21.1 - - + +
216B ALA* 3.7 24.7 - - + -
218B VAL* 3.5 32.3 - - + -
228B CYS 3.0 13.5 + - - +
229B ALA* 3.8 2.0 - - - +
231B ALA* 1.3 75.5 - - - +
233B ARG* 1.3 59.8 + - - +
235B PHE 3.3 6.2 + - - -
237B ALA* 3.0 26.2 + - + +
239B VAL* 3.6 13.0 - - + -
271B ILE* 5.1 4.9 - - + -
273B VAL* 4.7 6.5 - - + -
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Residues in contact with ARG 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLN* 5.4 5.1 + - - -
229B ALA 3.2 9.3 + - - +
230B GLN* 3.5 24.0 - - - +
232B LEU* 1.3 74.9 - - - +
234B GLY* 1.3 67.2 + - - +
235B PHE 3.0 2.5 - - - -
236B GLY* 3.1 12.9 + - - -
237B ALA 3.1 19.7 - - - +
239B VAL* 3.7 11.2 - - + +
255B GLU* 2.8 40.0 + - - +
256B GLY* 4.8 2.2 - - - -
257B TYR* 3.2 34.6 + - + -
233C ARG* 5.6 13.9 + - - +
255C GLU 5.0 2.9 - - - +
256C GLY* 5.6 0.6 - - - -
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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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230B GLN 3.0 12.4 + - - -
231B ALA 2.9 10.0 + - - -
233B ARG* 1.3 78.8 - - - +
235B PHE* 1.3 63.9 + - - +
236B GLY 3.3 1.0 + - - -
196D ARG* 4.4 13.2 + - - +
230D GLN* 5.2 6.6 - - - +
231D ALA* 6.1 0.9 - - - -
234D GLY* 5.7 12.0 - - - -
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Residues in contact with PHE 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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200B ILE* 3.5 39.5 - - + -
204B LYS* 5.6 0.9 - - - -
211B ILE* 3.6 23.8 - - + -
212B ALA* 3.1 18.2 - - - +
231B ALA 3.2 15.6 + - - -
232B LEU 3.3 0.6 + - - +
233B ARG 3.0 0.4 - - - -
234B GLY* 1.3 81.5 - - - +
236B GLY* 1.3 56.3 + - - +
237B ALA 3.5 0.4 - - - -
196D ARG* 3.0 48.0 + - + +
197D GLU* 3.3 29.3 - - + +
200D ILE* 5.0 6.1 - - + -
231D ALA* 4.9 6.3 - - + -
235D PHE* 3.3 43.1 - + - -
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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
------------------------------------------------------------
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