Contacts of the helix formed by residues 225 - 239 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224I GLY* 1.3 76.3 - - - -
226I THR* 1.3 54.7 + - - +
227I PRO* 3.5 11.3 - - - +
228I ILE* 3.1 30.0 + - - +
229I ALA* 2.8 32.4 + - - +
247I GLY* 3.9 0.4 - - - -
248I GLY* 4.3 1.1 - - - +
382I GLU* 5.6 1.3 - - - -
501I NAD 2.5 38.1 + - - -
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Residues in contact with THR 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I SER* 1.3 71.8 - - - +
227I PRO* 1.4 61.2 - - - +
229I ALA* 3.1 2.9 + - - +
230I GLU* 2.7 33.6 + - - +
247I GLY* 3.5 5.7 - - - -
248I GLY* 2.8 26.5 + - - +
407I GLU* 4.5 0.7 - - - +
408I TYR* 3.2 20.2 + - + -
454I ARG* 2.9 62.7 + - + +
457I PHE* 4.0 7.9 - - + -
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Residues in contact with PRO 227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I SER* 3.5 13.9 - - - +
226I THR* 1.4 98.0 - - + +
228I ILE* 1.3 64.4 + - + +
230I GLU* 3.8 11.2 + - + +
231I TYR* 3.4 19.1 + - - +
408I TYR* 5.1 5.4 - - - +
454I ARG* 5.4 4.0 - - - +
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Residues in contact with ILE 228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222I PHE* 3.5 23.6 - - + -
225I SER* 3.1 19.4 + - - +
226I THR 3.3 0.4 - - - -
227I PRO* 1.3 79.7 - - + +
229I ALA* 1.3 69.7 + - - +
230I GLU 3.1 1.1 - - - -
231I TYR* 2.9 8.9 + - + +
232I ILE* 2.8 33.4 + - + +
501I NAD 3.5 72.2 - - + +
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Residues in contact with ALA 229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222I PHE* 3.6 16.9 - - + -
225I SER 2.8 22.7 + - - +
226I THR* 3.4 8.7 - - - +
228I ILE* 1.3 73.3 - - - +
230I GLU* 1.3 54.7 + - - +
232I ILE* 3.4 0.4 + - - -
233I TYR* 2.9 32.2 + - - +
245I ALA* 3.5 7.7 - - + +
246I LEU 3.7 21.1 - - - +
247I GLY* 4.1 0.2 - - - -
457I PHE* 3.9 20.4 - - + -
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Residues in contact with GLU 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I THR 2.7 19.0 + - - +
227I PRO* 3.9 9.4 - - - +
229I ALA* 1.3 70.3 - - - +
231I TYR* 1.3 65.7 + - - +
233I TYR* 3.9 2.2 - - - +
234I ARG* 3.0 51.3 + - + +
454I ARG* 2.9 37.4 + - - -
457I PHE* 4.0 22.5 - - + -
237L SER 5.5 2.8 - - - +
238L ALA 4.2 11.6 - - - +
239L ASN 5.5 1.0 - - - -
240L GLY* 5.4 1.9 + - - -
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Residues in contact with TYR 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205I LYS* 3.4 24.5 + - - -
209I ASP* 2.6 33.7 + - - -
212I LEU* 4.2 7.1 - - + +
213I HIS* 4.9 1.9 - - - -
227I PRO 3.4 12.0 + - - +
228I ILE* 2.9 11.1 + - + +
230I GLU* 1.3 78.2 - - - +
232I ILE* 1.3 80.4 + - + +
234I ARG* 3.9 19.2 - - - +
235I THR* 2.8 65.0 + - + +
501I NAD 4.0 15.9 - + - -
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Residues in contact with ILE 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145I ILE* 4.4 5.2 - - + -
208I VAL* 3.5 32.1 - - + -
212I LEU* 4.0 17.1 - - + +
220I VAL* 4.1 12.1 - - + -
222I PHE* 3.8 39.9 - - + -
228I ILE* 2.8 23.6 + - + +
229I ALA 3.7 3.8 - - - +
231I TYR* 1.3 94.6 - - + +
233I TYR* 1.3 57.5 + - - +
235I THR* 3.8 2.5 - - - -
236I ALA* 2.9 31.2 + - - +
243I CYS* 4.3 6.3 - - - -
245I ALA* 4.8 0.2 - - + -
501I NAD 4.1 7.6 - - + +
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Residues in contact with TYR 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229I ALA 2.9 18.4 + - - +
230I GLU* 3.9 2.9 - - - +
232I ILE* 1.3 77.7 - - - +
234I ARG* 1.3 58.0 + - - +
236I ALA* 4.2 0.3 - - - +
237I SER* 2.6 39.8 + - - -
243I CYS* 3.5 40.3 - - + +
245I ALA* 4.1 3.1 - - + +
457I PHE* 3.5 48.7 - + + -
458I GLY* 3.7 16.2 - - - -
459I ASP* 6.1 0.3 - - - -
233L TYR* 4.7 10.1 + - - -
237L SER* 3.7 41.7 + - - -
240L GLY 4.7 4.3 - - - -
241L LYS 4.4 5.6 + - - -
242L ARG* 4.3 14.6 - - - +
243L CYS* 4.8 3.3 + - - +
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Residues in contact with ARG 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230I GLU* 3.0 49.3 + - - +
231I TYR* 3.9 25.6 + - - +
233I TYR* 1.3 76.8 - - - +
235I THR* 1.3 60.4 + - - +
237I SER* 3.5 4.7 + - - -
238I ALA* 3.0 29.5 + - + +
234L ARG* 5.2 5.4 - - + +
237L SER* 4.5 8.9 - - - +
238L ALA* 3.9 42.6 + - + +
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Residues in contact with THR 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212I LEU* 3.9 25.1 - - + -
213I HIS* 4.0 24.7 - - + +
231I TYR* 2.8 45.2 + - + +
232I ILE 3.9 2.0 - - - -
234I ARG* 1.3 78.8 - - - +
236I ALA* 1.3 62.5 + - - +
238I ALA* 3.3 5.3 + - - +
239I ASN* 2.7 37.7 + - - +
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Residues in contact with ALA 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212I LEU* 4.0 19.7 - - + +
220I VAL* 4.3 4.0 - - + -
232I ILE 2.9 20.4 + - - +
233I TYR 4.2 0.2 - - - +
235I THR* 1.3 73.3 - - - +
237I SER* 1.3 58.7 + - - +
239I ASN* 2.9 21.0 + - - +
240I GLY 3.1 8.8 + - - -
241I LYS* 3.3 35.0 + - + +
243I CYS* 4.0 18.6 - - + -
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Residues in contact with SER 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233I TYR* 2.6 35.5 + - - -
234I ARG 3.7 1.6 - - - -
236I ALA* 1.3 77.6 - - - +
238I ALA* 1.3 59.0 + - - +
240I GLY* 3.4 9.1 + - - +
241I LYS 3.9 5.3 + - - -
243I CYS* 4.8 2.9 - - - +
230L GLU* 5.6 3.1 - - - +
233L TYR* 3.5 36.0 + - - -
234L ARG* 4.7 5.6 - - - +
237L SER* 3.3 34.8 + - - -
457L PHE* 5.5 0.3 - - - -
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Residues in contact with ALA 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234I ARG* 3.0 19.5 + - + +
235I THR* 3.7 8.3 - - - +
236I ALA 3.2 0.4 - - - -
237I SER* 1.3 75.9 - - - +
239I ASN* 1.3 62.2 - - - +
240I GLY 3.2 3.9 + - - -
230L GLU* 4.3 7.9 - - - +
234L ARG* 4.0 44.7 + - + +
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Residues in contact with ASN 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212I LEU 3.4 24.4 + - - +
213I HIS* 3.5 31.9 + - - +
215I ASP* 5.4 5.9 - - - +
235I THR* 2.7 32.9 + - - +
236I ALA 2.9 8.3 + - - +
238I ALA* 1.3 80.1 - - - +
240I GLY* 1.3 55.5 + - - +
241I LYS* 3.2 20.0 + - - -
230L GLU* 6.0 0.2 - - - -
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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