Contacts of the helix formed by residues 229 - 242 (chain E) in PDB entry 4CQM
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 ASP 229 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202E ILE* 3.4 5.2 - - - +
203E ALA* 3.9 12.0 - - - +
227E LEU 4.0 3.0 + - - +
228E GLY* 1.3 79.8 - - - +
230E PRO* 1.3 67.8 - - + +
231E GLU* 3.0 10.0 - - + +
232E ASP* 2.8 43.2 + - - +
233E VAL* 3.6 2.9 + - - +
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Residues in contact with PRO 230 (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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22E GLY* 4.0 15.0 - - - +
23E ILE* 4.5 6.2 - - + +
26E ALA* 3.5 28.6 - - + +
202E ILE* 3.4 11.0 - - + -
203E ALA* 3.5 26.9 - - + +
204E THR* 3.9 11.9 - - + -
229E ASP* 1.3 91.8 - - + +
231E GLU* 1.3 55.1 + - - +
233E VAL* 3.3 8.5 + - + +
234E ALA 3.1 20.6 + - - -
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Residues in contact with GLU 231 (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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26E ALA* 4.2 4.2 - - + +
30E ARG* 4.8 2.6 + - - -
229E ASP* 3.0 8.8 + - + +
230E PRO* 1.3 79.1 - - - +
232E ASP* 1.3 63.1 + - - +
234E ALA* 3.2 9.4 + - + +
235E ASP* 2.9 29.6 + - - +
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Residues in contact with ASP 232 (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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202E ILE* 6.1 0.4 - - + -
226E HIS* 5.6 4.2 - - - -
228E GLY* 4.1 6.4 - - - -
229E ASP* 2.8 36.8 + - - +
231E GLU* 1.3 78.7 - - - +
233E VAL* 1.3 61.1 + - + +
235E ASP* 3.6 7.9 + - - +
236E VAL* 3.4 23.7 + - - +
255E VAL* 4.1 17.7 - - + +
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Residues in contact with VAL 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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23E ILE* 3.6 31.2 - - + -
27E VAL* 5.0 0.2 - - - -
154E ILE* 4.5 8.1 - - + -
197E VAL* 4.0 23.8 - - + -
199E PRO* 4.2 13.7 - - + -
202E ILE* 4.0 34.8 - - + -
229E ASP 4.1 7.9 - - - +
230E PRO 3.7 6.5 - - - +
231E GLU 3.2 0.4 - - - -
232E ASP* 1.3 75.6 - - + +
234E ALA* 1.3 64.4 + - - +
235E ASP 3.2 0.4 - - - -
236E VAL* 3.3 7.6 + - - +
237E VAL* 3.1 22.5 + - + +
255E VAL* 5.0 6.3 - - + -
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Residues in contact with ALA 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E ALA 3.5 30.5 - - - +
27E VAL* 3.8 14.7 - - + +
30E ARG* 3.7 17.0 - - + +
31E LEU* 5.4 0.9 - - - +
230E PRO 3.1 13.7 + - - +
231E GLU* 3.2 12.1 + - - +
233E VAL* 1.3 75.7 - - - +
235E ASP* 1.3 58.5 + - - +
237E VAL* 3.8 1.8 - - - +
238E ALA* 2.9 30.8 + - - +
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Residues in contact with ASP 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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8E ARG* 4.7 1.7 + - - -
30E ARG* 3.0 37.2 + - - +
231E GLU 2.9 15.0 + - - +
232E ASP* 3.7 10.5 - - - +
234E ALA* 1.3 77.7 - - - +
236E VAL* 1.3 61.9 + - - +
238E ALA* 3.5 2.1 + - - +
239E PHE* 3.1 22.3 + - - +
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Residues in contact with VAL 236 (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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197E VAL* 4.1 21.3 - - + -
232E ASP 3.4 16.4 - - - +
233E VAL 3.3 6.8 + - - +
235E ASP* 1.3 78.1 - - + +
237E VAL* 1.3 59.6 + - - +
239E PHE* 3.1 10.4 + - + +
240E LEU* 2.9 34.3 + - + +
253E VAL* 3.7 29.6 - - + -
255E VAL* 3.6 25.1 - - + -
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Residues in contact with VAL 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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27E VAL* 3.9 26.0 - - + -
31E LEU* 4.6 6.3 - - + -
101E VAL* 3.7 31.6 - - + -
152E ILE* 3.3 19.1 - - + +
154E ILE* 3.8 28.9 - - + -
197E VAL* 4.4 4.5 - - + -
233E VAL 3.1 16.7 + - - +
234E ALA 3.8 5.2 - - - +
235E ASP 3.4 0.2 - - - -
236E VAL* 1.3 76.0 - - - +
238E ALA* 1.3 57.8 + - - +
240E LEU* 3.3 2.0 + - - -
241E ALA* 2.8 28.8 + - - +
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Residues in contact with ALA 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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8E ARG* 3.4 20.0 + - - +
9E LEU* 4.4 2.6 - - - +
30E ARG* 3.8 21.3 - - + +
31E LEU* 4.0 15.7 - - + +
34E GLU* 3.8 8.5 - - - +
234E ALA 2.9 18.7 + - - +
235E ASP 3.5 5.8 - - - +
236E VAL 3.2 0.2 - - - -
237E VAL* 1.3 77.4 - - - +
239E PHE* 1.3 55.8 + - - +
241E ALA* 3.5 2.0 + - - +
242E SER* 3.0 29.8 + - - -
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Residues in contact with PHE 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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8E ARG* 3.7 13.2 - - - +
235E ASP* 3.1 12.9 + - - +
236E VAL* 3.1 13.7 + - + +
238E ALA* 1.3 77.3 - - - +
240E LEU* 1.3 63.8 + - + +
242E SER* 2.6 20.5 + - - -
244E ASP* 3.7 35.4 - - + -
245E SER* 2.6 33.7 + - - -
248E ILE* 3.6 27.8 - - + -
253E VAL* 6.3 1.3 - - + -
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Residues in contact with LEU 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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150E SER* 2.8 17.4 + - - +
152E ILE* 3.7 35.4 - - + -
193E ARG* 2.9 20.6 + - - -
195E ASN* 3.9 34.3 - - + +
196E SER 4.9 0.2 - - - +
197E VAL* 3.8 18.2 - - + -
236E VAL* 2.9 24.7 + - + +
239E PHE* 1.3 91.6 - - + +
241E ALA* 1.3 58.3 + - - +
245E SER* 3.2 10.3 - - - +
248E ILE* 4.4 8.3 - - + -
253E VAL* 4.4 20.2 - - + -
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Residues in contact with ALA 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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9E LEU* 4.0 18.9 - - + +
31E LEU* 4.4 3.6 - - + -
99E VAL* 3.9 30.7 - - + +
150E SER* 3.8 9.9 - - - -
152E ILE* 3.5 13.0 - - + +
193E ARG* 3.8 5.5 + - - -
237E VAL 2.8 18.0 + - - +
238E ALA 3.8 4.3 - - - +
240E LEU* 1.3 74.1 - - - +
242E SER* 1.3 66.5 + - - +
243E GLU* 4.6 3.3 - - - +
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Residues in contact with SER 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ARG* 3.6 34.2 + - - -
9E LEU* 3.6 11.4 - - - +
193E ARG* 2.9 20.7 + - - -
238E ALA 3.0 13.2 + - - -
239E PHE* 2.6 27.5 + - - -
241E ALA* 1.3 77.7 - - - +
243E GLU* 1.3 60.9 + - - +
244E ASP* 3.1 15.8 + - - +
245E SER* 3.1 10.9 + - - -
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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
------------------------------------------------------------
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