Contacts of the helix formed by residues 234 - 248 (chain E) in PDB entry 2CNW
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 GLN 234 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B MET 4.7 2.9 - - - +
40B ASP* 3.9 40.3 - - - +
42B ASP* 3.0 18.8 + - - +
43E ASP* 2.9 32.9 + - - +
44E VAL 4.3 2.3 - - - +
45E GLY* 3.4 28.4 - - - +
46E LEU 4.8 0.2 + - - -
47E SER* 5.3 3.5 + - - -
233E GLY* 1.3 70.7 - - - -
235E ASN* 1.3 64.1 + - - +
236E GLY 3.1 1.4 + - - -
237E LEU* 3.4 18.8 + - - +
238E GLU* 3.8 6.4 + - - +
265E VAL* 4.3 8.5 - - - +
268E PRO* 5.0 3.8 - - - +
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Residues in contact with ASN 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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42B ASP* 4.3 4.1 + - - +
221B MET* 4.1 16.7 - - + +
250B ASP* 2.6 32.0 + - - +
251B ALA* 3.4 33.7 + - + +
196E LEU* 5.7 2.8 - - - +
197E HIS* 3.5 15.1 + - - -
232E THR* 4.5 1.1 - - + -
233E GLY 3.1 1.0 + - - -
234E GLN* 1.3 75.2 - - - +
236E GLY* 1.3 54.3 + - - +
238E GLU* 3.0 9.6 + - - +
239E GLN* 2.8 53.4 + - - +
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Residues in contact with GLY 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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228E LEU* 3.9 15.7 - - - +
232E THR* 3.5 14.7 - - - +
233E GLY 3.0 14.8 + - - -
235E ASN* 1.3 78.0 - - - +
237E LEU* 1.3 55.1 + - - +
239E GLN* 3.4 7.1 + - - +
240E ALA* 3.0 23.4 + - - +
265E VAL* 4.2 4.9 - - - -
269E ILE* 3.5 14.3 - - - +
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Residues in contact with LEU 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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47E SER* 5.6 4.7 - - - +
234E GLN* 3.4 13.4 + - - +
235E ASN 3.3 0.8 - - - -
236E GLY* 1.3 71.2 - - - +
238E GLU* 1.3 65.8 + - - +
240E ALA* 3.3 0.3 + - - +
241E LYS* 3.0 54.3 + - + +
265E VAL* 3.8 12.1 - - + +
268E PRO* 3.8 35.4 - - + +
269E ILE* 3.7 23.6 - - + +
272E THR* 4.0 14.8 - - + +
273E LEU* 4.7 3.6 - - + -
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Residues in contact with GLU 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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250B ASP* 3.5 25.6 - - - +
197E HIS* 3.5 9.0 - - + +
234E GLN 3.8 3.3 + - - +
235E ASN* 3.0 22.4 + - - +
237E LEU* 1.3 79.2 - - - +
239E GLN* 1.3 61.8 + - - +
241E LYS* 3.5 20.1 + - - +
242E LYS* 3.2 55.4 + - - +
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Residues in contact with GLN 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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221B MET* 3.2 25.4 - - - +
110E VAL* 3.4 30.9 + - + +
113E VAL* 4.8 2.1 - - - +
196E LEU* 6.4 0.2 - - - +
197E HIS* 3.6 28.0 + - + +
226E LEU* 4.9 5.4 - - + +
227E VAL 4.8 5.5 - - - +
228E LEU* 4.2 15.4 - - + +
229E ASP 5.7 0.3 + - - -
232E THR* 3.7 10.0 + - - +
235E ASN* 2.8 33.5 + - - +
236E GLY* 3.5 9.6 - - - +
238E GLU* 1.3 75.7 - - - +
240E ALA* 1.3 61.5 + - - +
242E LYS* 3.4 1.2 + - - +
243E PHE* 3.1 38.5 + - + -
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Residues in contact with ALA 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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226E LEU* 3.9 21.9 - - + +
236E GLY 3.0 16.7 + - - +
237E LEU 3.8 3.6 - - - +
238E GLU 3.3 0.2 - - - -
239E GLN* 1.3 77.6 - - - +
241E LYS* 1.3 61.3 + - - +
244E HIS* 3.0 27.5 + - - +
249E LEU* 3.6 5.6 - - + +
252E VAL* 5.9 0.2 - - + -
269E ILE* 3.8 23.6 - - + -
273E LEU* 3.6 19.5 - - + +
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Residues in contact with LYS 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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237E LEU* 3.0 49.2 + - + +
238E GLU* 3.9 24.1 + - - +
239E GLN 3.4 0.2 - - - -
240E ALA* 1.3 74.6 - - - +
242E LYS* 1.3 59.2 + - + +
244E HIS* 3.6 2.4 - - - +
245E GLU* 2.9 30.8 + - - +
272E THR* 4.5 12.1 - - + -
273E LEU* 3.7 24.8 - - + +
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Residues in contact with LYS 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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197E HIS* 3.6 44.3 + - + +
203E MET* 3.7 6.9 - - + +
238E GLU* 3.2 38.4 + - - +
239E GLN 3.9 0.7 - - - +
241E LYS* 1.3 76.5 - - - +
243E PHE* 1.3 61.0 + - - +
245E GLU* 3.4 9.0 + - + +
246E ALA* 3.0 29.5 + - - +
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Residues in contact with PHE 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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108E VAL* 3.7 17.5 - - + -
109E GLY* 3.6 24.0 - - - -
110E VAL* 3.9 20.0 - - + -
195E ARG* 3.6 31.4 - - + -
197E HIS* 4.3 12.1 - - + -
203E MET* 3.5 23.3 - - + -
206E LEU* 3.7 21.5 - - + -
226E LEU* 4.0 14.6 - - + -
239E GLN* 3.1 31.0 + - + +
240E ALA 4.4 1.1 - - - +
242E LYS* 1.3 73.4 - - - +
244E HIS* 1.3 66.0 + - - +
246E ALA* 3.1 1.1 + - - -
247E VAL* 2.9 29.9 + - + +
249E LEU* 4.0 18.4 - - + -
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Residues in contact with HIS 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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240E ALA 3.0 21.5 + - - +
241E LYS 3.6 4.5 - - - +
243E PHE* 1.3 76.5 - - - +
245E GLU* 1.3 59.3 + - - +
248E GLY* 2.8 32.4 + - - -
249E LEU* 3.0 56.0 + - + +
273E LEU* 3.6 35.0 + - + +
275E VAL* 4.1 12.6 - - + +
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Residues in contact with GLU 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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207E LYS* 4.8 10.5 + - - -
241E LYS 2.9 19.2 + - - +
242E LYS* 3.8 8.6 - - + +
243E PHE 3.3 0.2 - - - -
244E HIS* 1.3 78.4 - - - +
246E ALA* 1.3 68.8 + - - +
248E GLY 5.0 0.2 + - - -
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Residues in contact with ALA 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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203E MET* 3.8 32.8 - - + +
206E LEU* 5.6 0.4 - - + -
207E LYS* 3.4 31.4 - - - +
242E LYS 3.0 18.6 + - - +
243E PHE* 3.1 3.5 + - - +
245E GLU* 1.3 85.7 + - - +
247E VAL* 1.3 71.8 + - + +
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Residues in contact with VAL 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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106E LEU* 5.2 1.8 - - + -
108E VAL* 4.6 4.5 - - + -
206E LEU* 4.1 30.5 - - + +
207E LYS* 4.1 26.5 - - + +
210E LYS* 2.8 44.8 + - + +
224E VAL* 3.8 26.4 - - + +
243E PHE* 2.9 21.3 + - - +
246E ALA* 1.3 87.6 - - + +
248E GLY* 1.3 68.9 + - - +
249E LEU* 4.7 2.2 - - + -
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Residues in contact with GLY 248 (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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210E LYS* 4.9 1.9 + - - -
224E VAL* 3.4 14.8 - - - +
243E PHE 3.8 0.6 + - - -
244E HIS* 2.8 30.4 + - - -
247E VAL* 1.3 77.4 - - - +
249E LEU* 1.3 65.0 + - - +
250E THR* 3.8 6.1 + - - +
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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