Contacts of the helix formed by residues 225 - 239 (chain A) in PDB entry 4ZZ7
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 SER 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A PHE* 4.1 0.2 - - - -
224A GLY* 1.3 72.3 - - - -
226A THR* 1.3 54.5 + - - +
227A PRO* 3.8 11.1 - - - +
228A ILE* 3.3 18.9 + - - +
229A ALA* 2.7 36.6 + - - +
247A GLY* 3.9 0.7 - - - -
248A GLY* 5.0 0.2 - - - -
501A NAD 2.4 56.0 + - - -
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Residues in contact with THR 226 (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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225A SER* 1.3 70.8 - - - +
227A PRO* 1.4 73.5 - - - +
229A ALA* 3.5 2.5 - - - +
230A GLU* 2.8 22.9 + - - +
247A GLY* 4.0 5.4 - - - -
248A GLY* 2.8 27.2 + - - +
407A GLU* 4.4 0.9 - - - +
408A TYR* 3.1 25.2 + - + -
454A ARG* 3.2 58.3 + - - +
457A PHE* 4.1 6.3 - - + -
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Residues in contact with PRO 227 (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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225A SER* 3.6 13.9 - - - +
226A THR* 1.4 97.7 - - + +
228A ILE* 1.3 62.4 + - + +
230A GLU* 3.4 13.1 - - + +
231A TYR* 3.1 22.2 + - - +
408A TYR* 5.1 4.5 - - - +
454A ARG* 5.6 3.4 - - - +
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PHE* 3.5 24.2 - - + -
225A SER* 3.3 19.8 + - - +
226A THR 3.3 0.4 - - - -
227A PRO* 1.3 79.5 - - + +
229A ALA* 1.3 61.2 + - - +
230A GLU 3.2 0.2 - - - -
231A TYR* 3.1 9.2 + - + +
232A ILE* 2.8 40.8 + - + +
501A NAD 3.5 68.9 - - + +
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Residues in contact with ALA 229 (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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222A PHE* 3.4 22.5 - - + -
225A SER 2.7 22.7 + - - +
226A THR* 3.5 5.6 - - - +
228A ILE* 1.3 72.0 - - - +
230A GLU* 1.3 54.3 + - - +
232A ILE* 3.3 0.3 + - - +
233A TYR* 2.8 36.6 + - - +
245A ALA* 3.3 16.0 - - + +
246A LEU 3.7 16.2 - - - +
457A PHE* 3.9 14.4 - - + -
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Residues in contact with GLU 230 (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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226A THR 2.8 12.2 + - - +
227A PRO* 3.4 13.8 - - - +
229A ALA* 1.3 74.5 - - - +
231A TYR* 1.3 59.8 + - - +
233A TYR* 3.6 3.0 + - - +
234A ARG* 2.9 62.0 + - - +
454A ARG* 3.5 29.8 + - - +
457A PHE* 3.8 27.1 - - + -
237B SER 5.9 2.0 - - - +
238B ALA 4.3 7.0 - - - +
239B ASN 5.9 0.9 - - - -
240B GLY* 6.0 1.6 - - - -
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Residues in contact with TYR 231 (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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205A LYS* 3.5 21.9 + - - -
209A ASP* 2.4 38.3 + - - -
212A LEU* 4.1 10.3 - - + -
213A HIS* 4.8 2.3 - - - -
227A PRO 3.1 9.8 + - - +
228A ILE* 3.1 15.5 + - + +
230A GLU* 1.3 79.3 - - - +
232A ILE* 1.3 66.6 + - + +
234A ARG* 3.2 16.5 + - - +
235A THR* 2.7 62.6 + - + +
501A NAD 4.3 15.5 - + - -
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Residues in contact with ILE 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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145A ILE* 4.1 8.3 - - + -
208A VAL* 3.4 33.9 - - + -
212A LEU* 4.0 15.7 - - + +
220A VAL* 4.0 22.0 - - + -
222A PHE* 3.7 39.5 - - + -
228A ILE* 2.8 32.6 + - + +
229A ALA 3.7 3.4 - - - +
231A TYR* 1.3 81.6 - - + +
233A TYR* 1.3 57.3 + - - +
235A THR* 3.9 0.5 - - - -
236A ALA* 2.9 29.3 + - - +
243A CYS* 4.1 5.4 - - - -
501A NAD 4.5 1.6 - - + +
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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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229A ALA 2.8 20.8 + - - +
230A GLU* 3.9 3.6 - - - +
232A ILE* 1.3 72.1 - - - +
234A ARG* 1.3 62.4 + - - +
236A ALA* 3.9 0.9 - - - +
237A SER* 2.7 40.2 + - - -
243A CYS* 3.5 46.1 + - + -
245A ALA* 4.2 1.8 - - + -
457A PHE* 3.5 45.3 - + + -
458A GLY* 3.7 17.3 - - - -
459A ASP* 6.0 0.5 - - - -
233B TYR* 4.8 9.2 + - - -
237B SER* 3.7 43.0 + - - -
240B GLY 5.2 2.7 - - - -
241B LYS 4.6 4.9 - - - -
242B ARG* 4.4 14.3 - - - -
243B CYS 4.8 2.9 + - - -
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Residues in contact with ARG 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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230A GLU* 2.9 63.7 + - + +
231A TYR* 3.6 19.4 - - + +
233A TYR* 1.3 77.7 - - - +
235A THR* 1.3 59.5 + - - +
237A SER* 3.2 7.2 + - - -
238A ALA* 2.9 30.4 + - + +
234B ARG* 5.4 4.7 - - + +
237B SER* 5.1 4.6 + - - +
238B ALA* 3.8 42.3 + - + +
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Residues in contact with THR 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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212A LEU* 3.8 23.1 - - + -
213A HIS* 3.6 32.8 - - + +
231A TYR* 2.7 49.2 + - - +
232A ILE 3.9 2.9 - - - -
234A ARG* 1.3 78.0 - - - +
236A ALA* 1.3 62.7 + - - +
238A ALA* 3.1 12.2 + - - +
239A ASN* 3.0 27.5 + - - +
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Residues in contact with ALA 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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212A LEU* 4.2 16.5 - - + +
220A VAL* 4.7 2.2 - - + -
232A ILE 2.9 19.1 + - - +
233A TYR 3.9 0.7 - - - +
235A THR* 1.3 75.8 - - - +
237A SER* 1.3 59.6 + - - +
239A ASN* 3.0 20.2 + - - -
240A GLY 3.4 6.2 + - - -
241A LYS* 3.3 31.8 + - + +
243A CYS* 3.7 27.4 - - + -
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Residues in contact with SER 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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233A TYR* 2.7 33.4 + - - -
234A ARG 3.5 2.9 - - - -
236A ALA* 1.3 76.6 - - - +
238A ALA* 1.3 62.2 + - - +
240A GLY* 3.5 8.7 + - - -
241A LYS 4.2 3.7 + - - -
243A CYS* 5.1 1.6 - - - +
230B GLU* 5.6 1.7 - - - +
233B TYR* 3.6 34.3 + - - -
234B ARG* 4.7 8.5 - - - +
237B SER* 3.2 36.3 + - - -
457B PHE* 5.5 0.3 - - - -
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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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234A ARG* 2.9 14.7 + - + +
235A THR* 3.1 12.3 + - - +
237A SER* 1.3 77.5 - - - +
239A ASN* 1.3 64.5 + - - +
240A GLY 3.4 2.1 + - - -
230B GLU* 4.7 4.9 - - - +
234B ARG* 4.1 41.8 + - + +
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Residues in contact with ASN 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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212A LEU 3.7 21.1 - - - +
213A HIS* 3.6 34.5 + - - +
215A ASP* 5.3 4.3 - - - +
235A THR* 3.0 24.3 + - - +
236A ALA 3.0 8.6 + - - +
238A ALA* 1.3 85.2 - - - +
240A GLY* 1.3 53.6 + - - -
241A LYS* 2.9 24.0 + - - -
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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