Contacts of the helix formed by residues 234 - 249 (chain C) in PDB entry 5V8Z
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 234 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C MET* 1.3 79.1 - - - +
235C ASP* 1.3 65.4 + - - +
236C GLY 3.6 3.5 + - - -
237C LYS* 3.0 19.4 + - - +
238C LYS* 3.1 19.4 + - - +
352D GLU* 2.9 38.7 + - - -
353D ALA 3.4 19.9 + - - -
354D PRO* 3.9 6.1 - - - -
355D ARG* 3.9 14.4 - - - +
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Residues in contact with ASP 235 (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 MET 4.9 1.7 - - - +
234C SER* 1.3 73.9 - - - +
236C GLY* 1.3 62.5 + - - +
238C LYS* 3.3 19.8 + - - +
239C GLU* 3.1 30.4 + - + +
355D ARG* 3.1 30.4 + - - +
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Residues in contact with GLY 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C SER* 3.2 5.4 + - - -
235C ASP* 1.3 79.8 - - - +
237C LYS* 1.3 61.9 + - - +
239C GLU* 3.3 15.2 + - - +
240C GLU* 3.2 27.6 + - - +
352D GLU* 5.1 3.1 - - - -
355D ARG* 5.1 2.6 - - - +
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Residues in contact with LYS 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C MET* 4.1 17.9 - - + -
234C SER* 3.0 24.1 + - - +
236C GLY* 1.3 73.2 - - - +
238C LYS* 1.3 66.3 + - - +
240C GLU* 2.5 39.1 + - - +
241C LEU* 2.9 26.5 + - - +
343D TRP* 3.7 14.1 - - + -
348D ASP 2.7 27.8 + - - -
349D GLY* 3.9 1.6 - - - -
350D GLU 3.2 26.4 + - - +
352D GLU* 3.7 36.3 + - + +
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Residues in contact with LYS 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LYS* 6.1 2.0 - - + -
239A GLU* 5.5 9.9 - - - -
242A GLN* 6.0 0.2 - - - -
228C ILE* 3.8 30.8 + - + +
231C ASN* 3.4 24.6 + - - +
233C MET* 3.7 28.0 + - - +
234C SER 3.1 11.2 + - - +
235C ASP* 3.3 23.0 + - - +
237C LYS* 1.3 76.7 - - - +
239C GLU* 1.3 57.6 + - + +
241C LEU* 3.3 4.6 + - - +
242C GLN* 2.9 50.6 + - - +
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Residues in contact with GLU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASN* 5.2 5.4 + - - -
238A LYS* 4.7 13.7 + - - +
235C ASP* 3.1 18.0 + - + +
236C GLY* 3.5 12.9 - - - +
237C LYS 3.2 0.2 - - - -
238C LYS* 1.3 77.7 - - + +
240C GLU* 1.3 57.9 + - + +
242C GLN* 3.2 14.9 + - - +
243C LYS* 2.9 34.2 + - + +
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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
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197C LYS* 5.0 12.1 + - - -
198C TRP* 3.6 28.2 - - + -
236C GLY 3.2 11.1 + - - +
237C LYS* 2.5 52.5 + - - +
239C GLU* 1.3 76.8 - - + +
241C LEU* 1.3 59.3 + - + +
243C LYS* 3.1 6.0 + - - +
244C SER* 2.8 30.5 + - - -
348D ASP 4.3 1.4 - - - +
352D GLU* 5.1 2.4 - - - +
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Residues in contact with LEU 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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224C ILE* 3.8 24.5 - - + +
227C LEU* 4.4 8.3 - - + -
228C ILE* 3.8 14.8 - - + -
233C MET* 3.6 34.8 - - + -
237C LYS* 2.9 14.7 + - - +
238C LYS 3.6 7.4 - - - +
240C GLU* 1.3 77.6 - - + +
242C GLN* 1.3 58.4 + - - +
244C SER* 3.0 10.4 + - - +
245C LEU* 2.8 30.5 + - - +
343D TRP* 4.0 15.0 - - + -
348D ASP* 3.9 40.2 - - + +
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Residues in contact with GLN 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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225A ALA* 5.0 3.6 - - - +
228A ILE* 3.5 32.2 - - + +
229A GLU* 4.6 4.0 - - - +
238A LYS* 4.2 20.1 + - - +
242A GLN* 2.9 42.1 + - - +
228C ILE* 4.0 8.5 - - + -
238C LYS* 2.9 40.7 + - - +
239C GLU* 3.6 15.9 - - - +
241C LEU* 1.3 71.9 - - - +
243C LYS* 1.3 66.4 + - - +
245C LEU* 3.2 10.2 + - + +
246C ASN* 3.0 22.9 + - - +
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Residues in contact with LYS 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLU* 3.1 45.9 + - - +
157C SER* 5.5 6.7 - - - +
195C GLN* 5.0 5.1 + - - -
198C TRP* 3.2 59.4 - - + +
239C GLU* 2.9 19.5 + - + +
240C GLU* 3.4 8.5 - - - +
242C GLN* 1.3 74.9 - - - +
244C SER* 1.3 57.9 + - - +
246C ASN* 3.3 7.1 + - - +
247C ILE* 3.1 33.9 + - - +
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Residues in contact with SER 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C TRP* 3.7 11.5 - - - -
201C GLN* 3.3 27.9 + - - -
205C ILE* 5.1 1.0 - - - +
224C ILE* 4.4 14.6 - - - -
240C GLU 2.8 14.2 + - - -
241C LEU* 3.0 16.2 + - - +
243C LYS* 1.3 75.4 - - - +
245C LEU* 1.3 60.1 + - - +
247C ILE* 3.4 10.0 + - - +
248C LEU* 3.0 34.1 + - - +
347D MET 4.4 3.0 + - - -
348D ASP* 5.9 0.2 - - - -
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Residues in contact with LEU 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ALA* 4.4 7.9 - - + -
242A GLN* 3.7 29.6 - - - +
245A LEU* 4.1 19.5 - - + -
221C MET* 3.7 47.1 - - + +
224C ILE* 3.8 14.8 - - + -
225C ALA 4.5 4.0 - - - +
228C ILE* 4.1 15.5 - - + -
241C LEU 2.8 12.7 + - - +
242C GLN* 3.5 9.6 - - - +
244C SER* 1.3 75.6 - - - +
246C ASN* 1.3 65.7 + - - +
248C LEU* 3.1 6.8 + - + +
249C THR* 3.1 28.9 + - + +
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Residues in contact with ASN 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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222A THR 4.9 0.5 - - - +
225A ALA* 3.9 13.4 - - - +
226A ARG* 3.4 30.4 + - - +
229A GLU* 3.5 38.8 - - + +
157C SER* 6.2 1.8 - - - +
162C ASP* 5.4 1.6 - - - +
202C TYR* 5.7 1.8 + - - -
242C GLN 3.0 12.7 + - - +
243C LYS* 3.5 11.6 + - - +
245C LEU* 1.3 76.9 - - - +
247C ILE* 1.3 64.8 + - - +
249C THR* 2.7 22.9 + - - -
250C ALA* 4.0 2.9 + - - +
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Residues in contact with ILE 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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198C TRP* 3.7 48.5 - - + +
201C GLN* 4.1 8.1 - - + -
202C TYR* 3.7 49.1 - - + +
205C ILE* 3.7 22.7 - - + -
243C LYS* 3.1 19.6 + - - +
244C SER* 3.7 7.2 - - - +
246C ASN* 1.3 83.1 - - - +
248C LEU* 1.3 63.1 + - - +
250C ALA* 3.1 21.0 + - - +
251C PHE* 3.6 5.1 - - + -
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C ILE* 3.6 34.8 - - + -
216C PHE* 4.8 1.6 - - + -
217C PRO* 4.1 28.3 - - + +
220C GLU* 3.7 29.4 - - + -
221C MET* 3.6 29.8 - - + +
224C ILE* 3.7 17.3 - - + -
244C SER* 3.0 23.2 + - - +
245C LEU* 3.1 4.9 + - - +
247C ILE* 1.3 76.9 - - - +
249C THR* 1.3 57.5 + - - +
251C PHE* 2.9 31.0 + - - +
252C GLN* 4.4 2.9 - - - +
347D MET* 5.6 0.9 - - + -
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Residues in contact with THR 249 (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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221A MET* 3.8 15.3 - - + +
222A THR* 3.5 23.3 + - - +
225A ALA* 3.8 19.9 - - + +
245A LEU* 5.9 0.9 - - + -
221C MET* 3.9 15.0 - - - -
245C LEU* 3.1 14.7 + - + +
246C ASN* 2.7 23.9 + - - -
248C LEU* 1.3 76.6 - - - +
250C ALA* 1.3 60.8 + - - +
251C PHE 3.1 1.5 + - - -
252C GLN* 3.0 38.1 + - - +
254C LYS* 4.8 2.4 + - - -
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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