Contacts of the helix formed by residues 225 - 239 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222G PHE* 4.1 2.8 - - - -
224G GLY* 1.3 73.7 - - - -
226G THR* 1.3 54.9 + - - +
227G PRO* 3.9 8.8 - - - +
228G ILE* 3.2 27.5 + - - +
229G ALA* 2.8 33.4 + - - +
247G GLY* 4.0 1.6 - - - -
248G GLY* 4.3 4.7 - - - +
382G GLU* 5.4 5.6 - - - -
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Residues in contact with THR 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225G SER* 1.3 69.6 - - - +
227G PRO* 1.3 75.4 - - - +
229G ALA* 3.5 2.3 - - - +
230G GLU* 2.9 22.9 + - - +
247G GLY* 3.5 6.5 - - - -
248G GLY* 2.7 27.9 + - - +
407G GLU* 4.6 0.4 - - - +
408G TYR* 3.1 25.6 + - + -
454G ARG* 3.3 54.6 + - - +
457G PHE* 4.0 7.0 - - + -
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Residues in contact with PRO 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G SER* 3.5 12.8 - - - +
226G THR* 1.3 96.9 - - + +
228G ILE* 1.3 66.9 + - + +
230G GLU* 3.6 10.3 + - + +
231G TYR* 3.3 19.1 + - - +
408G TYR* 5.2 4.3 - - - +
454G ARG* 5.6 3.8 - - - +
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Residues in contact with ILE 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205G LYS* 6.3 0.9 - - - +
222G PHE* 3.5 28.5 - - + -
225G SER* 3.2 22.7 + - - +
227G PRO* 1.3 79.5 - - + +
229G ALA* 1.3 67.9 + - - +
230G GLU 3.1 0.2 - - - -
231G TYR* 3.1 13.4 + - + +
232G ILE* 2.9 35.7 + - + +
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Residues in contact with ALA 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222G PHE* 3.7 14.4 - - + -
225G SER 2.8 16.8 + - - +
226G THR* 3.5 8.5 - - - +
228G ILE* 1.3 76.3 - - - +
230G GLU* 1.3 55.6 + - - +
232G ILE* 3.3 1.1 + - - +
233G TYR* 2.9 30.5 + - - +
245G ALA* 3.5 12.4 - - + +
246G LEU 3.8 22.4 - - - +
457G PHE* 3.8 18.8 - - + -
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Residues in contact with GLU 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226G THR 2.9 17.2 + - - +
227G PRO* 3.7 9.5 - - - +
229G ALA* 1.3 74.3 - - - +
231G TYR* 1.3 65.8 + - - +
233G TYR* 3.9 2.9 - - - +
234G ARG* 3.0 56.5 + - + +
454G ARG* 3.2 33.5 + - - -
457G PHE* 3.9 21.1 - - + -
237H SER 6.0 1.8 - - - +
238H ALA* 4.2 9.9 - - - +
239H ASN 5.9 0.2 - - - -
240H GLY* 5.4 2.6 + - - -
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Residues in contact with TYR 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205G LYS* 3.3 30.5 + - + -
208G VAL* 5.2 1.3 - - + -
209G ASP* 2.6 34.2 + - - -
212G LEU* 4.2 9.9 - - + -
213G HIS* 4.8 2.6 - - - -
227G PRO 3.3 10.2 + - - +
228G ILE* 3.1 17.6 + - + +
230G GLU* 1.3 79.6 - - - +
232G ILE* 1.3 70.2 + - + +
234G ARG* 3.8 17.4 - - + +
235G THR* 2.5 64.8 + - + +
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Residues in contact with ILE 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G ILE* 4.2 8.3 - - + -
208G VAL* 3.4 32.3 - - + -
212G LEU* 3.7 12.9 - - + +
220G VAL* 3.9 27.8 - - + -
222G PHE* 3.9 32.1 - - + -
228G ILE* 2.9 27.8 + - + +
229G ALA 3.7 5.2 - - - +
231G TYR* 1.3 81.5 - - + +
233G TYR* 1.3 67.9 + - - +
235G THR* 3.9 2.5 - - - -
236G ALA* 2.9 24.4 + - - +
243G CYS* 4.0 5.8 - - - -
245G ALA* 5.0 0.2 - - + -
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Residues in contact with TYR 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229G ALA 2.9 17.7 + - - +
230G GLU* 3.9 3.6 - - - +
232G ILE* 1.3 77.9 - - - +
234G ARG* 1.3 59.3 + - - +
236G ALA* 3.8 1.2 - - - +
237G SER* 2.5 35.7 + - - -
243G CYS* 3.5 43.0 - - + +
245G ALA* 4.3 2.0 - - + -
457G PHE* 3.5 33.4 - + + -
458G GLY* 3.6 26.9 + - - -
459G ASP* 6.1 0.3 - - - -
233H TYR* 4.8 10.5 + - - -
237H SER* 3.7 45.9 + - - -
240H GLY 4.8 8.2 + - - -
241H LYS 4.8 1.4 + - - -
242H ARG* 4.5 13.7 - - - +
243H CYS 5.0 2.8 + - - -
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Residues in contact with ARG 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G GLU* 3.0 58.0 + - + +
231G TYR* 3.8 21.2 - - - +
233G TYR* 1.3 81.4 - - - +
235G THR* 1.3 64.3 + - - +
237G SER* 3.3 5.7 + - - -
238G ALA* 3.0 25.5 + - + +
234H ARG* 5.6 4.7 - - + +
237H SER 5.4 0.4 - - - +
238H ALA* 4.0 42.7 + - + +
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Residues in contact with THR 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G LEU* 4.0 22.0 - - + -
213G HIS* 3.8 29.2 - - + +
231G TYR* 2.5 57.3 + - + +
232G ILE 3.9 2.7 - - - -
234G ARG* 1.3 73.8 - - - +
236G ALA* 1.3 64.0 + - - +
238G ALA* 3.3 5.9 + - - +
239G ASN* 2.8 36.1 + - - +
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Residues in contact with ALA 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212G LEU* 4.2 16.8 - - + +
220G VAL* 4.6 2.0 - - + -
232G ILE 2.9 18.1 + - - +
233G TYR 3.8 2.0 - - - +
235G THR* 1.3 77.5 - - - +
237G SER* 1.3 57.5 + - - +
239G ASN* 3.0 19.7 + - - -
240G GLY 3.1 9.4 + - - -
241G LYS* 3.4 31.1 + - + +
243G CYS* 3.9 24.0 - - + -
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Residues in contact with SER 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233G TYR* 2.5 33.1 + - - -
234G ARG 3.5 5.2 - - - -
236G ALA* 1.3 74.4 - - - +
238G ALA* 1.3 62.9 + - - +
240G GLY* 3.4 8.9 + - - -
241G LYS 4.0 3.5 + - - -
243G CYS* 5.2 1.7 - - - +
230H GLU* 5.5 3.3 - - - +
233H TYR* 3.6 34.4 + - - -
234H ARG* 4.8 8.2 - - - +
237H SER* 3.4 34.8 + - - -
457H PHE* 5.3 1.6 - - - -
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Residues in contact with ALA 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234G ARG* 3.0 18.2 + - + +
235G THR* 3.5 7.6 - - - +
237G SER* 1.3 77.5 - - - +
239G ASN* 1.3 66.4 + - - +
240G GLY 3.2 1.3 + - - -
230H GLU* 4.3 8.1 - - - +
234H ARG* 4.0 44.2 + - + +
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Residues in contact with ASN 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G LEU 3.5 21.3 - - - +
213G HIS* 3.3 42.2 + - - +
215G ASP* 5.1 7.7 - - - +
235G THR* 2.8 30.8 + - - +
236G ALA 3.0 9.4 + - - +
238G ALA* 1.3 81.1 - - - +
240G GLY* 1.3 54.6 + - - +
241G LYS* 3.4 17.2 + - - -
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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