Contacts of the helix formed by residues 235 - 247 (chain E) in PDB entry 3KQG
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 235 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233E VAL* 3.7 3.3 - - - +
234E THR* 1.3 87.7 + - - +
236E GLU* 1.3 59.2 - - - +
237E SER* 3.5 19.2 + - - -
238E GLU* 3.5 11.3 + - - +
239E GLN* 2.9 28.4 + - - +
276E GLN* 3.7 11.0 - - - +
280E PHE* 4.2 7.1 - - - -
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Residues in contact with GLU 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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235E SER* 1.3 73.9 - - - +
237E SER* 1.3 52.2 + - - +
239E GLN* 3.3 3.2 + - - +
240E GLU* 2.6 37.2 + - - +
276E GLN* 4.7 2.2 - - + +
279E ARG* 2.8 39.5 + - - -
280E PHE* 4.0 23.0 - - + -
303E LEU* 3.9 20.3 - - + +
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Residues in contact with SER 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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202E PHE* 3.6 11.3 - - - -
203E LYS* 3.8 28.6 + - - +
235E SER* 3.5 12.4 + - - -
236E GLU* 1.3 78.8 - - - +
238E GLU* 1.3 58.3 + - - +
240E GLU* 3.2 12.2 + - - +
241E PHE* 2.8 28.9 + - - +
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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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202E PHE* 3.8 13.7 - - + -
205E ASN* 5.4 1.6 - - - -
207E TYR* 2.7 31.6 + - + +
232E SER 3.1 17.6 - - - +
233E VAL* 3.6 2.4 - - + -
234E THR* 2.6 38.9 + - - -
235E SER* 3.4 14.7 + - - +
236E GLU 3.4 0.2 - - - -
237E SER* 1.3 78.0 + - - +
239E GLN* 1.3 61.1 + - - +
241E PHE* 3.3 2.0 + - + +
242E LEU* 2.9 46.7 + - + +
320E LYS* 2.9 23.2 + - - +
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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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233E VAL* 3.3 21.6 - - + +
235E SER 2.9 17.9 + - - +
236E GLU 3.4 5.2 - - - +
238E GLU* 1.3 78.3 - - - +
240E GLU* 1.3 61.3 + - - +
242E LEU* 3.4 3.0 + - - +
243E TYR* 3.0 25.2 + - + +
280E PHE* 3.7 24.7 + - + +
298E ILE* 4.3 6.6 - - - +
303E LEU* 3.2 39.8 + - + +
305E ALA* 3.7 18.9 - - - +
306E TRP* 3.3 30.7 + - - +
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Residues in contact with GLU 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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236E GLU 2.6 20.5 + - - +
237E SER* 3.5 10.2 - - - +
239E GLN* 1.3 72.0 - - - +
241E PHE* 1.3 66.8 + - - +
243E TYR* 3.7 17.1 + - + -
244E LYS* 3.0 64.5 + - + +
303E LEU* 4.4 4.9 - - + -
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Residues in contact with PHE 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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197D GLN* 3.7 32.8 - - + -
200E LYS* 4.3 10.8 - - + -
201E TYR 4.4 0.9 - - - -
202E PHE* 3.7 44.0 - + + -
207E TYR* 3.4 37.9 - + - -
209E PHE* 4.2 14.6 - + - -
237E SER 2.8 20.1 + - - +
238E GLU 3.5 4.9 - - - +
240E GLU* 1.3 74.5 - - - +
242E LEU* 1.3 73.2 + - + +
244E LYS* 3.8 3.0 - - - +
245E THR* 2.8 58.3 + - + -
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Residues in contact with LEU 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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207E TYR* 4.0 26.7 - - + -
209E PHE* 4.0 18.8 - - + -
231E THR* 4.0 15.5 - - + +
233E VAL* 3.8 29.8 - - + -
238E GLU* 2.9 37.1 + - + +
239E GLN* 3.8 2.5 - - - +
241E PHE* 1.3 82.7 - - + +
243E TYR* 1.3 58.1 + - - +
245E THR* 3.7 0.9 - - - -
246E ALA* 2.8 31.2 + - - +
253E ILE* 5.3 0.2 - - + -
298E ILE* 3.5 21.5 - - + +
318E ILE* 4.1 14.8 - - + -
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Residues in contact with TYR 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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226D ARG* 4.7 5.8 + - - -
239E GLN 3.0 25.6 + - - +
240E GLU* 3.7 20.4 + - + +
242E LEU* 1.3 75.0 - - - +
244E LYS* 1.3 96.1 + - + +
246E ALA* 3.3 15.6 + - - +
247E GLY* 3.4 9.0 + - - -
248E GLY 4.7 1.9 + - - -
298E ILE* 4.1 7.8 - - + +
300E ALA 4.1 10.3 - - - +
301E PRO* 3.5 23.1 + - + +
302E SER* 3.2 45.8 - - - +
303E LEU* 3.6 13.8 + - + +
305E ALA* 4.3 7.6 - - + -
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Residues in contact with LYS 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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208D TYR* 4.4 4.5 + - - -
225D SER 4.8 6.8 + - - -
226D ARG* 2.6 56.6 + - - +
240E GLU* 3.0 49.1 + - + +
241E PHE* 3.9 3.8 - - - +
243E TYR* 1.3 108.0 - - + +
245E THR* 1.3 61.9 + - - +
247E GLY* 3.1 10.7 + - - -
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Residues in contact with THR 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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197D GLN* 3.9 19.7 + - - +
198D GLY* 5.1 0.9 - - - -
208D TYR* 4.6 5.8 + - - -
211D LEU* 4.1 13.2 - - - +
200E LYS* 4.1 22.4 - - + -
209E PHE* 3.4 37.2 - - + -
241E PHE* 2.8 47.4 + - + -
244E LYS* 1.3 68.5 - - - +
246E ALA* 1.3 66.5 + - - +
247E GLY* 3.0 4.1 + - - -
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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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211D LEU* 4.1 4.8 - - - +
209E PHE* 3.9 4.9 - - + -
242E LEU 2.8 18.4 + - - +
243E TYR 3.5 8.1 - - - +
244E LYS 3.2 0.4 - - - -
245E THR* 1.3 76.5 - - - +
247E GLY* 1.3 64.0 + - - +
248E GLY 3.1 3.3 + - - +
249E LEU* 3.2 21.1 + - - +
251E TYR* 3.4 41.7 + - + -
298E ILE* 4.1 15.0 - - + -
318E ILE* 5.1 1.3 - - + -
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Residues in contact with GLY 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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208D TYR* 3.6 23.2 + - - -
211D LEU* 4.4 5.0 + - - +
212D ILE* 3.3 30.6 + - - +
222D PHE* 5.1 10.4 - - - -
226D ARG* 4.8 3.6 - - - -
243E TYR 3.4 3.7 + - - -
244E LYS 3.1 11.5 + - - -
245E THR 3.0 3.5 - - - -
246E ALA* 1.3 78.7 - - - +
248E GLY* 1.3 57.4 + - - +
249E LEU 3.6 0.5 + - - -
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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