Contacts of the helix formed by residues 237 - 247 (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 LYS 237 (chain E).
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Specific contacts
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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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Residues in contact with PHE 238 (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 3.6 22.2 - - - -
26D A 3.5 29.2 - - - -
135E PHE* 4.5 10.1 - - + -
137E ALA* 3.8 18.4 - - + -
149E HIS* 3.5 50.8 - + + +
151E ILE* 3.9 17.0 - - + +
233E TRP* 2.9 38.7 + + + -
234E ASP* 3.8 16.6 - - - +
237E LYS* 1.3 86.7 - - + +
239E LEU* 1.3 57.5 + - - +
241E ILE* 4.0 3.4 - - - +
242E GLN* 2.9 31.0 + - - +
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Residues in contact with LEU 239 (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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135E PHE* 4.0 16.6 - - + -
151E ILE* 4.1 6.2 - - - +
154E PHE* 5.7 1.3 - - + -
203E PHE* 3.5 31.6 - - + -
207E LEU* 5.6 4.0 - - + -
234E ASP 3.0 20.1 + - - +
235E MET* 3.7 21.3 - - + +
238E PHE* 1.3 72.0 - - - +
240E ASN* 1.3 67.2 + - - +
242E GLN* 4.3 0.2 - - - -
243E CYS* 2.9 33.7 + - - +
250E TYR* 3.6 29.4 - - + +
251E PRO* 4.5 10.5 - - + -
254E ALA* 4.0 12.1 - - + -
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Residues in contact with ASN 240 (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* 3.8 13.2 + - - +
235E MET 3.1 13.1 + - - +
236E SER 3.0 28.7 + - - +
237E LYS* 3.4 3.4 - - - +
239E LEU* 1.3 77.5 - - - +
241E ILE* 1.3 63.4 + - + +
243E CYS* 3.3 3.6 + - - +
244E GLN* 3.1 37.6 + - - +
250E TYR* 4.0 15.5 - - + -
322E MET* 3.3 25.3 - - - +
325E GLY* 3.7 14.1 + - - -
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Residues in contact with ILE 241 (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* 3.2 46.0 - - + +
147B PHE 4.8 0.9 - - - +
148B VAL* 3.7 24.5 - - + +
148E VAL* 4.5 7.0 - - + -
149E HIS* 4.0 16.2 - - + +
237E LYS* 2.9 30.2 + - + +
238E PHE* 4.0 2.9 - - - +
240E ASN* 1.3 72.7 - - - +
242E GLN* 1.3 60.9 + - - +
244E GLN* 2.9 11.2 + - - +
245E LEU* 2.9 41.1 + - + +
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Residues in contact with GLN 242 (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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149E HIS 5.1 1.5 + - - +
150E GLU* 3.5 15.0 + - - +
151E ILE* 3.0 40.2 + - + +
203E PHE* 3.5 43.1 - - + +
238E PHE 2.9 19.3 + - - +
239E LEU 3.8 4.0 - - - +
241E ILE* 1.3 76.3 - - - +
243E CYS* 1.3 61.8 + - - +
245E LEU* 3.3 18.1 + - - +
246E SER* 3.0 36.0 + - - -
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Residues in contact with CYS 243 (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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203E PHE* 4.2 10.8 - - - -
207E LEU* 5.3 0.2 - - - -
239E LEU* 2.9 39.1 + - - +
240E ASN* 3.6 5.4 - - - +
242E GLN* 1.3 72.7 - - - +
244E GLN* 1.3 67.6 + - + +
246E SER* 3.2 3.4 + - - +
247E ARG 3.0 3.8 + - - -
248E LEU* 2.9 50.0 + - - +
249E LYS 4.3 3.8 - - - -
250E TYR* 4.3 10.8 - - + +
251E PRO* 3.9 24.9 - - - -
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Residues in contact with GLN 244 (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 2.8 26.0 + - - -
147B PHE* 3.5 19.7 - - + +
148B VAL* 2.8 39.1 + - + +
178B ILE* 3.5 15.8 - - - +
179B ASN* 4.0 12.0 + - - +
240E ASN* 3.1 33.8 + - - +
241E ILE* 2.9 9.2 + - - +
243E CYS* 1.3 75.9 - - + +
245E LEU* 1.3 62.4 + - - +
247E ARG* 3.1 12.3 + - - +
248E LEU 5.0 1.8 - - - -
348E ARG* 5.5 11.0 - - - +
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Residues in contact with LEU 245 (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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148B VAL* 4.2 13.5 - - + -
178B ILE* 3.8 38.4 - - + +
245B LEU* 4.0 10.3 - - + -
148E VAL* 3.7 25.6 - - + -
149E HIS 3.8 14.6 - - - +
150E GLU* 4.1 15.5 - - + -
177E GLU* 5.1 5.2 - - - +
178E ILE* 4.0 17.9 - - + +
241E ILE* 2.9 25.1 + - + +
242E GLN* 3.7 18.4 - - - +
243E CYS 3.3 0.2 - - - -
244E GLN* 1.3 73.5 - - - +
246E SER* 1.3 58.5 + - - +
247E ARG* 3.3 8.6 + - - -
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Residues in contact with SER 246 (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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177E GLU* 5.7 3.8 + - - -
203E PHE* 3.7 13.2 - - - +
204E PRO* 4.1 13.8 - - - +
242E GLN* 3.0 31.7 + - - -
243E CYS 3.2 2.6 + - - -
245E LEU* 1.3 76.3 - - - +
247E ARG* 1.3 75.1 + - - +
248E LEU* 3.2 21.4 + - - -
347E PHE* 3.6 17.0 - - - -
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Residues in contact with ARG 247 (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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177B GLU* 3.1 23.6 + - - +
178B ILE* 3.3 34.6 + - + +
179B ASN* 5.1 2.5 - - - +
180B THR* 5.8 1.4 - - - +
177E GLU* 5.8 2.6 + - - -
243E CYS 3.0 4.8 + - - -
244E GLN* 3.1 9.5 + - - +
245E LEU 4.1 13.3 + - - -
246E SER* 1.3 82.9 + - - +
248E LEU* 1.3 59.9 + - - +
347E PHE* 3.4 13.7 - - + -
348E ARG* 2.7 44.2 + - + +
350E LEU* 5.5 12.0 - - - +
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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