Contacts of the helix formed by residues 229 - 239 (chain A) in PDB entry 4Z4H
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 PRO 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A GLN* 1.3 94.1 - - + +
230A VAL* 1.3 65.6 + - - +
231A ILE* 4.1 12.6 - - + +
232A GLU* 2.9 35.1 + - + +
233A PHE 3.0 9.0 + - - -
341A LEU 5.7 0.2 - - - +
342A GLU 5.7 3.4 - - - +
344A CYS 3.5 11.2 - - - +
345A ASN* 3.9 11.2 - - - +
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Residues in contact with VAL 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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228A GLN 3.5 1.2 + - - -
229A PRO* 1.3 70.5 - - - +
231A ILE* 1.3 53.1 + - - +
233A PHE* 3.1 9.0 + - + +
234A VAL* 2.8 33.1 + - + +
258A PHE* 4.0 8.5 - - + -
262A ILE* 3.9 20.4 - - + -
267A VAL* 4.2 11.4 - - + -
328A LEU* 4.0 9.0 - - + -
341A LEU* 3.6 35.4 - - + +
344A CYS* 2.9 42.1 + - + +
345A ASN 4.2 4.5 - - - +
346A ILE* 4.4 6.7 - - + -
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Residues in contact with ILE 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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229A PRO* 3.0 9.2 - - + -
230A VAL* 1.3 77.0 - - - +
232A GLU* 1.3 65.5 + - + +
234A VAL* 3.4 7.7 + - + +
235A CYS* 3.3 23.3 + - - -
243A ILE* 4.0 44.1 - - + +
322A TYR* 4.3 8.5 - - + -
325A LEU* 4.3 8.1 - - + -
341A LEU* 3.6 38.1 - - + +
342A GLU* 3.9 24.5 - - + +
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Residues in contact with GLU 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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226A LYS* 5.4 0.5 - - - -
228A GLN* 3.1 32.2 - - + +
229A PRO* 2.9 26.3 + - + +
231A ILE* 1.3 78.8 - - + +
233A PHE* 1.3 64.7 + - - +
235A CYS* 3.3 9.3 + - - +
236A GLU* 3.2 27.5 + - - +
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Residues in contact with PHE 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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194A GLY 3.7 18.2 - - - -
195A GLY* 3.9 7.4 - - - -
225A TYR* 4.0 20.4 - + - -
226A LYS 5.5 0.7 - - - -
228A GLN* 3.6 21.9 - - - +
229A PRO 3.0 11.2 + - - +
230A VAL* 3.3 12.6 - - - +
232A GLU* 1.3 75.3 - - - +
234A VAL* 1.3 64.3 + - - +
236A GLU* 3.5 2.4 + - - +
237A VAL* 3.1 45.4 + - + +
258A PHE* 3.8 17.0 - + - -
261A GLU* 4.0 22.4 - - + -
262A ILE* 3.8 32.8 - - + -
265A LEU* 4.0 9.4 - - + -
346A ILE* 4.3 16.6 - - + -
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Residues in contact with VAL 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 VAL 2.8 20.9 + - - +
231A ILE* 3.5 10.5 - - + +
233A PHE* 1.3 76.9 - - - +
235A CYS* 1.3 59.6 + - - +
237A VAL* 3.2 1.2 + - - +
238A LEU* 2.9 55.3 + - + +
240A PHE* 4.7 7.4 - - + -
250A LEU* 5.1 8.3 - - + -
258A PHE* 3.4 38.1 - - + -
325A LEU* 5.9 5.8 - - + -
341A LEU* 3.8 20.9 - - + -
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Residues in contact with CYS 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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231A ILE* 3.3 17.3 + - - -
232A GLU* 3.7 10.8 - - - +
233A PHE 3.3 0.2 - - - -
234A VAL* 1.3 80.1 - - - +
236A GLU* 1.3 59.3 + - + +
239A ASP* 2.8 10.4 + - - -
240A PHE* 2.7 54.1 + - + +
242A SER* 3.8 7.9 - - - -
243A ILE* 3.5 38.4 - - - -
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Residues in contact with GLU 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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191A PRO* 6.0 1.4 - - - +
193A GLY* 3.9 9.5 - - - -
194A GLY* 3.7 16.9 + - - +
195A GLY* 2.8 36.5 + - - +
226A LYS* 3.6 17.0 - - - +
228A GLN* 3.6 18.5 - - - +
232A GLU* 3.2 13.0 + - - +
233A PHE 4.0 2.7 - - - +
235A CYS* 1.3 80.2 - - + +
237A VAL* 1.3 62.5 + - - +
239A ASP* 3.6 9.8 + - - +
240A PHE 5.3 0.4 - - - -
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Residues in contact with VAL 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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194A GLY* 3.9 17.7 - - - +
233A PHE* 3.1 48.1 + - + +
234A VAL* 3.6 4.9 - - - +
236A GLU* 1.3 81.1 - - - +
238A LEU* 1.3 74.9 + - + +
239A ASP* 3.3 1.8 + - - +
257A LYS* 3.2 26.9 - - + +
258A PHE* 4.0 14.8 - - + -
261A GLU* 3.7 30.1 - - + -
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Residues in contact with LEU 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 VAL* 2.9 40.7 + - + +
237A VAL* 1.3 91.4 - - + +
239A ASP* 1.3 71.5 + - - +
240A PHE* 3.4 39.4 + - + -
250A LEU* 4.0 19.1 - - + -
254A GLN* 3.4 36.8 + - + +
257A LYS* 4.1 15.7 - - + -
258A PHE* 4.2 5.6 - - + -
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Residues in contact with ASP 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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235A CYS 2.8 10.0 + - - -
236A GLU* 3.6 8.1 + - - +
237A VAL 3.3 4.5 - - - +
238A LEU* 1.3 82.5 - - - +
240A PHE* 1.3 62.5 + - - +
241A LYS* 4.0 1.9 + - - +
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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