Contacts of the helix formed by residues 232 - 237 (chain E) in PDB entry 4QOZ
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 232 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D C 5.5 0.3 + - - -
25D C 3.2 20.3 + - - -
229E THR* 4.8 0.2 - - - -
231E GLY* 1.3 73.2 - - - -
233E TRP* 1.3 59.8 + - - +
234E ASP* 3.5 2.2 - - - -
235E MET 4.0 2.2 + - - -
236E SER* 2.4 36.1 + - - -
257E TRP* 4.1 7.3 - - - +
259E ASN* 3.9 2.7 - - - +
320E GLU* 3.0 34.3 - - - -
327E LEU* 3.6 21.0 - - - +
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Residues in contact with TRP 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D C 5.5 4.5 - + - -
25D C 3.0 98.9 + + + +
232E SER* 1.3 86.4 + - - +
234E ASP* 1.3 67.4 + - - +
235E MET 3.2 2.0 - - - -
236E SER* 3.7 9.0 - - - -
237E LYS* 2.9 62.5 + - + +
238E PHE* 2.9 20.1 + + + -
327E LEU* 5.9 0.8 - - + +
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Residues in contact with ASP 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D C 4.5 3.8 + - - +
26D A 5.8 1.4 - - - +
133E ILE 3.6 17.9 - - - +
134E ASP* 4.1 9.9 - - - +
135E PHE* 3.3 46.6 + - + +
229E THR* 3.8 28.5 - - + -
230E ASP 4.1 14.6 + - - +
232E SER 3.5 0.2 - - - -
233E TRP* 1.3 76.5 - - - +
235E MET* 1.3 60.4 + - + +
238E PHE* 3.8 10.1 - - - +
239E LEU* 3.0 28.4 + - - +
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Residues in contact with MET 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E ILE* 4.0 22.9 - - + -
135E PHE* 3.7 27.6 - - + -
227E LEU* 4.5 8.5 - - + -
229E THR* 3.7 28.5 - - + -
232E SER 4.0 2.2 + - - -
233E TRP 3.2 0.2 - - - -
234E ASP* 1.3 76.0 - - + +
236E SER* 1.3 60.1 + - - +
237E LYS 3.3 1.6 - - - -
239E LEU* 3.7 21.5 - - - -
240E ASN* 3.1 28.1 + - - +
250E TYR* 3.3 23.0 + - - +
254E ALA* 4.4 11.0 - - - +
257E TRP* 3.8 40.6 - - + -
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Residues in contact with SER 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLU* 3.5 12.9 - - - +
232E SER* 2.4 30.3 + - - -
233E TRP* 3.7 8.8 - - - -
235E MET* 1.3 78.6 - - - +
237E LYS* 1.3 58.9 + - - +
240E ASN* 3.0 22.1 + - - -
257E TRP* 4.5 0.9 - - - -
322E MET* 3.6 26.7 - - - -
327E LEU* 4.1 24.6 - - - +
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Residues in contact with LYS 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLU* 3.1 37.9 + - - +
149E HIS* 5.2 10.8 - - + +
233E TRP* 2.9 73.5 + - + +
235E MET 3.3 0.2 - - - -
236E SER* 1.3 81.8 + - - +
238E PHE* 1.3 76.8 + - + +
239E LEU 3.5 0.9 - - - -
240E ASN* 3.4 0.2 - - - +
241E ILE* 2.9 39.7 + - + +
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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