Contacts of the helix formed by residues 231 - 243 (chain B) in PDB entry 1ZJA
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 ASN 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B ASP* 4.2 7.5 + - - -
206B SER* 3.0 12.9 + - - +
207B LYS 5.3 2.2 + - - -
209B PRO* 5.4 4.2 - - - +
230B PRO* 1.3 93.7 - - - +
232B LEU* 1.3 65.3 + - - +
233B HIS 3.5 2.0 - - - -
234B ARG* 3.3 24.3 + - - +
235B TYR* 3.0 56.0 + - + -
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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
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202B VAL 3.5 21.5 - - - +
203B ALA* 3.5 24.7 - - - +
205B TYR* 4.1 18.6 - - + +
206B SER* 3.4 11.8 - - - +
227B THR 3.9 13.0 - - - +
229B GLY 3.5 11.9 + - - +
230B PRO 3.5 2.8 - - - -
231B ASN* 1.3 77.5 - - - +
233B HIS* 1.3 71.0 + - + +
235B TYR* 3.2 6.4 + - - +
236B LEU* 3.0 42.6 + - + +
266B PHE* 3.5 28.9 - - + -
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Residues in contact with HIS 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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230B PRO 5.5 0.2 + - - -
231B ASN 3.5 0.4 - - - -
232B LEU* 1.3 84.6 - - + +
234B ARG* 1.3 61.7 + - - +
236B LEU* 3.8 2.2 - - + +
237B GLN* 2.9 40.3 + - - +
262B GLN* 5.8 1.0 + - - +
265B LEU* 3.4 42.4 + - + +
266B PHE* 3.6 39.5 - + - -
271B ARG* 3.7 11.7 - - - +
273B GLU* 2.6 37.9 + - - +
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Residues in contact with ARG 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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179B ARG* 5.9 2.8 - - - +
231B ASN* 3.3 29.4 + - - +
232B LEU 3.3 0.2 - - - -
233B HIS* 1.3 78.5 - - - +
235B TYR* 1.3 74.9 + - + +
237B GLN* 3.4 8.1 + - - +
238B GLU* 3.0 29.5 + - + +
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Residues in contact with TYR 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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173B TRP* 3.4 52.6 - + + -
174B ASP* 2.7 33.7 + - - -
179B ARG* 3.7 29.9 + - - -
183B TYR* 4.0 3.5 + - - -
205B TYR* 4.9 3.6 - - + -
206B SER* 4.2 17.3 - - - -
231B ASN* 3.0 46.4 + - + +
232B LEU* 3.5 6.7 - - - +
234B ARG* 1.3 92.7 - - + +
236B LEU* 1.3 65.3 + - + +
238B GLU* 3.2 6.6 + - + +
239B MET* 3.0 23.2 + - - +
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B TRP* 5.6 0.2 - - + -
202B VAL* 3.8 14.4 - - + +
205B TYR* 3.6 38.1 - - + -
232B LEU* 3.0 21.9 + - + +
233B HIS* 3.4 3.5 + - - +
235B TYR* 1.3 75.4 - - - +
237B GLN* 1.3 61.7 + - - +
239B MET* 3.3 19.1 + - + +
240B HIS* 3.1 22.5 + - - +
266B PHE* 3.6 33.4 - - + -
272B LYS 4.4 0.3 - - - +
273B GLU* 3.5 35.5 - - + +
274B LEU* 4.9 9.1 - - + +
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Residues in contact with GLN 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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233B HIS* 2.9 26.9 + - - +
234B ARG* 3.8 6.6 - - - +
236B LEU* 1.3 74.0 - - - +
238B GLU* 1.3 61.0 - - - +
240B HIS* 3.4 2.9 + - - +
241B GLU* 3.0 27.0 + - - +
271B ARG* 3.4 34.7 + - - +
272B LYS* 3.8 8.4 - - - +
273B GLU* 3.0 33.2 + - + -
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Residues in contact with GLU 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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179B ARG* 2.7 36.3 + - - +
180B GLU* 5.2 2.1 - - - +
183B TYR* 2.6 32.0 + - + +
234B ARG* 3.0 19.3 + - + +
235B TYR* 3.6 7.6 - - + +
237B GLN* 1.3 74.0 - - - +
239B MET* 1.3 61.0 + - - +
241B GLU* 3.1 11.1 + - - +
242B LYS* 2.9 49.6 + - + +
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Residues in contact with MET 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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102B ILE* 4.2 2.7 - - - -
173B TRP* 4.1 17.9 - - + -
183B TYR* 3.7 26.6 + - + -
186B LEU* 3.7 16.4 - - + -
199B PHE* 3.7 41.3 - - + -
205B TYR* 4.7 2.5 - - + -
235B TYR 3.0 13.1 + - - +
236B LEU* 3.6 31.4 - - + +
238B GLU* 1.3 78.2 - - - +
240B HIS* 1.3 56.5 + - - +
243B VAL* 2.9 28.6 + - + +
244B PHE* 3.5 15.3 + - + -
274B LEU* 4.7 10.5 - - + -
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Residues in contact with HIS 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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236B LEU 3.1 10.7 + - - +
237B GLN 3.7 3.4 - - - +
238B GLU 3.2 0.2 - - - -
239B MET* 1.3 76.5 - - - +
241B GLU* 1.3 66.0 + - - +
244B PHE* 3.2 24.3 + - + +
245B ASP* 2.9 58.6 + - + +
272B LYS* 3.1 56.5 + - + +
273B GLU 3.4 21.6 + - - +
275B ASP* 5.9 3.1 - - - -
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Residues in contact with GLU 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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237B GLN 3.0 18.0 + - - +
238B GLU* 3.6 10.5 - - - +
240B HIS* 1.3 83.9 - - - +
242B LYS* 1.3 82.8 + - + +
245B ASP* 4.0 8.9 - - - +
246B HIS* 3.1 22.2 + - - -
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Residues in contact with LYS 242 (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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180B GLU* 3.5 29.6 - - - +
183B TYR* 3.8 25.8 - - + -
187B ARG* 2.9 28.6 + - - +
238B GLU* 2.9 36.4 + - + +
241B GLU* 1.3 95.8 + - + +
243B VAL* 1.3 60.9 + - + +
246B HIS* 3.3 16.0 + - - -
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 3.5 45.3 - - + +
186B LEU* 4.0 16.6 - - + -
187B ARG* 4.3 6.7 - - + +
190B LEU* 3.4 31.4 - - + -
239B MET 2.9 15.0 + - - +
241B GLU 3.5 0.2 - - - -
242B LYS* 1.3 82.6 - - - +
244B PHE* 1.3 76.5 + - + +
245B ASP 3.3 2.0 - - - -
246B HIS* 3.0 17.1 + - - +
247B TYR* 3.3 20.5 - - + -
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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