Contacts of the helix formed by residues 235 - 247 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C VAL* 3.6 4.1 - - - +
234C THR* 1.3 88.4 + - - +
236C GLU* 1.3 59.9 + - - +
237C SER* 3.4 11.2 + - - -
238C GLU* 3.2 23.8 + - - +
239C GLN* 3.0 27.4 + - - +
276C GLN* 3.9 10.6 + - - +
280C PHE* 4.2 6.0 - - - -
203D LYS 5.6 5.8 - - - -
204D GLY* 6.3 2.0 - - - -
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Residues in contact with GLU 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C SER* 1.3 71.0 - - - +
237C SER* 1.3 61.0 + - - +
239C GLN* 3.3 2.3 + - - +
240C GLU* 2.9 33.2 + - - +
276C GLN* 4.0 12.6 + - - +
279C ARG* 2.5 42.8 + - - -
280C PHE* 3.8 16.5 - - + -
303C LEU* 3.4 24.6 - - + +
323D TYR 4.7 4.1 - - - +
325D PRO* 3.4 23.9 - - + +
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Residues in contact with SER 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C PHE* 3.8 8.3 - - - -
203C LYS* 3.4 36.0 + - - +
235C SER* 3.4 11.9 + - - -
236C GLU* 1.3 78.0 - - - +
238C GLU* 1.3 59.1 + - - +
240C GLU* 3.3 8.7 + - - +
241C PHE* 2.9 28.6 + - - +
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Residues in contact with GLU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C PHE* 4.0 14.4 - - + -
205C ASN* 5.3 1.9 + - - -
207C TYR* 2.8 30.5 + - + +
232C SER 2.9 15.0 - - - +
233C VAL* 4.1 1.6 - - + -
234C THR* 2.9 31.8 + - - -
235C SER* 3.2 17.4 + - - +
237C SER* 1.3 79.1 + - - +
239C GLN* 1.3 64.9 + - - +
241C PHE* 3.2 2.0 + - + +
242C LEU* 2.9 38.3 + - + +
320C LYS* 2.5 30.2 + - - -
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Residues in contact with GLN 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C VAL* 3.6 19.7 - - + +
235C SER 3.0 15.1 + - - +
236C GLU 3.6 8.1 - - - +
238C GLU* 1.3 75.1 - - - +
240C GLU* 1.3 57.9 + - - +
242C LEU* 3.2 4.2 + - - +
243C TYR* 3.0 30.5 + - + +
280C PHE* 3.5 31.1 + - + +
298C ILE* 4.7 5.6 - - - +
303C LEU* 2.7 44.0 + - + +
305C ALA* 3.7 9.7 - - - +
306C TRP* 3.0 34.3 + - - +
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Residues in contact with GLU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C GLU* 2.9 21.9 + - - +
237C SER* 3.6 8.5 - - - +
239C GLN* 1.3 76.1 - - - +
241C PHE* 1.3 63.7 + - - +
243C TYR* 3.5 23.5 - - + -
244C LYS* 3.1 56.2 + - + +
303C LEU* 4.1 7.2 - - + +
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Residues in contact with PHE 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B SER 4.6 0.4 - - - -
197B GLN* 4.0 26.9 - - + -
200C LYS* 4.2 14.1 - - + -
201C TYR 4.3 2.7 - - - -
202C PHE* 3.6 47.1 - + + -
207C TYR* 3.4 45.5 - + + -
209C PHE* 4.4 5.2 - + - -
237C SER 2.9 17.1 + - - +
238C GLU 3.6 3.6 - - - +
240C GLU* 1.3 76.2 - - - +
242C LEU* 1.3 76.1 + - + +
244C LYS* 4.1 2.4 - - - +
245C THR* 2.8 57.6 + - + -
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Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C TYR* 3.8 29.2 - - + -
209C PHE* 4.3 8.1 - - + -
231C THR* 4.1 23.8 - - + +
233C VAL* 3.5 32.5 - - + -
238C GLU* 2.9 29.8 + - + +
239C GLN* 3.6 4.0 - - - +
241C PHE* 1.3 86.7 - - + +
243C TYR* 1.3 62.2 + - - +
245C THR* 3.8 2.0 - - - -
246C ALA* 2.8 31.5 + - - +
298C ILE* 3.7 19.1 - - + +
318C ILE* 4.3 10.9 - - + +
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Residues in contact with TYR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ARG* 4.4 8.4 + - - -
239C GLN* 3.0 25.8 + - + +
240C GLU* 3.5 25.9 - - + +
242C LEU* 1.3 76.1 - - - +
244C LYS* 1.3 92.5 + - + +
246C ALA* 3.6 8.2 - - - +
247C GLY 3.5 13.5 + - - -
248C GLY 4.8 2.3 + - - -
298C ILE* 4.2 7.1 - - + +
300C ALA 4.2 3.6 - - - +
301C PRO* 3.5 27.0 + - + +
302C SER* 3.3 34.6 - - - +
303C LEU* 3.6 24.6 + - + +
305C ALA* 4.0 15.5 - - + -
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Residues in contact with LYS 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B TYR* 4.7 4.3 + - - -
225B SER 3.7 18.0 + - - -
226B ARG* 2.8 56.5 + - - +
227B ASN* 5.1 7.7 - - - +
240C GLU* 3.1 44.5 + - + +
241C PHE* 4.1 3.1 - - - +
243C TYR* 1.3 107.7 - - + +
245C THR* 1.3 65.8 + - - +
247C GLY* 3.2 4.3 + - - -
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Residues in contact with THR 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B GLN* 4.0 18.8 + - - +
198B GLY* 5.4 0.2 - - - -
208B TYR* 4.4 8.7 + - - -
211B LEU* 5.5 5.5 - - - +
200C LYS* 4.1 23.6 - - + -
209C PHE* 3.4 37.0 - - + -
241C PHE* 2.8 44.9 + - + -
244C LYS* 1.3 74.6 - - - +
246C ALA* 1.3 64.4 + - - +
247C GLY* 3.1 3.1 + - - -
251C TYR* 5.2 0.7 + - - -
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Residues in contact with ALA 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 5.5 2.6 - - - +
209C PHE* 3.8 5.5 - - + -
242C LEU 2.8 19.7 + - - +
243C TYR* 3.6 11.0 - - - +
244C LYS 3.2 0.2 - - - -
245C THR* 1.3 76.7 - - - +
247C GLY* 1.3 64.1 + - - +
248C GLY 3.4 1.3 - - - +
249C LEU* 3.2 23.1 + - - +
251C TYR* 3.4 39.8 + - + -
298C ILE* 4.2 11.9 - - + -
318C ILE* 5.0 1.1 - - + -
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Residues in contact with GLY 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B TYR* 4.1 12.9 + - - -
211B LEU* 5.3 2.8 + - - +
212B ILE* 3.4 27.2 + - - +
222B PHE* 4.5 8.8 - - - -
226B ARG* 3.9 10.8 - - - -
243C TYR 3.5 3.6 + - - -
244C LYS 3.2 13.9 + - - -
245C THR 3.1 5.5 - - - -
246C ALA* 1.3 78.9 - - - +
248C GLY* 1.3 57.9 + - - +
249C LEU* 3.2 4.7 + - - +
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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