Contacts of the helix formed by residues 242 - 254 (chain H) in PDB entry 3DV0
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 242 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353G PHE* 6.0 0.9 - - - -
193H GLY 3.1 24.4 + - - +
194H LYS* 3.3 12.4 + - - +
195H ALA* 2.7 37.0 + - + +
235H LEU* 5.3 1.8 - - + +
237H THR 5.0 2.0 + - - -
240H PRO 4.0 0.8 + - - -
241H LEU* 1.3 69.6 - - - +
243H ILE* 1.3 61.6 + - - +
244H GLU* 3.7 10.4 - - - +
245H THR* 2.7 33.6 + - - -
246H ILE* 3.1 25.0 + - + +
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Residues in contact with ILE 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353G PHE* 3.4 37.6 - - + -
241H LEU* 3.1 20.5 + - + +
242H ASP* 1.3 71.1 - - - +
244H GLU* 1.3 55.7 + - - +
246H ILE* 3.2 7.0 + - + -
247H ILE* 2.7 41.2 + - + +
275H GLU* 3.8 39.3 - - + +
279H ARG* 3.5 36.3 - - - +
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Residues in contact with GLU 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353G PHE* 5.2 10.0 - - + -
194H LYS* 3.8 14.0 + - - +
242H ASP* 3.4 9.4 + - - +
243H ILE* 1.3 79.1 - - - +
245H THR* 1.3 82.4 + - - +
247H ILE* 4.7 3.6 - - - -
248H GLY* 2.7 28.8 + - - -
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Residues in contact with THR 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H LYS* 3.6 10.2 + - - -
195H ALA* 4.1 21.5 - - + +
196H ASP* 5.2 0.4 - - - -
197H ILE* 4.1 24.9 - - + +
233H VAL* 4.2 5.8 - - + +
242H ASP* 2.7 31.5 + - - +
244H GLU* 1.3 97.5 + - - +
246H ILE* 1.3 65.2 + - - +
248H GLY* 3.9 0.8 - - - -
249H SER* 3.2 20.4 + - - -
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Residues in contact with ILE 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195H ALA* 5.5 0.4 - - + -
205H THR* 5.2 0.6 - - - +
207H ILE* 3.5 28.7 - - + -
233H VAL* 5.0 10.3 - - + -
235H LEU* 3.4 33.2 - - + -
241H LEU* 4.2 21.8 - - + -
242H ASP* 3.1 22.6 + - + +
243H ILE* 3.5 10.3 - - + +
245H THR* 1.3 76.7 - - - +
247H ILE* 1.3 70.0 + - + +
248H GLY 3.1 0.3 + - - -
249H SER* 3.2 3.8 + - - -
250H VAL* 3.1 23.9 + - + +
272H VAL* 4.5 7.4 - - + -
275H GLU* 6.3 2.9 - - + -
276H ILE* 4.1 20.4 - - + -
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Residues in contact with ILE 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H ILE* 2.7 40.7 + - + +
244H GLU* 4.2 3.1 - - - +
246H ILE* 1.3 74.9 - - + +
248H GLY* 1.3 66.6 + - - +
250H VAL* 3.2 5.4 + - + +
251H GLU* 2.9 45.1 + - + +
275H GLU* 4.1 2.7 - - + +
276H ILE* 3.8 30.7 - - + +
279H ARG* 3.7 30.1 - - + +
280H ALA* 4.1 13.2 - - + -
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Residues in contact with GLY 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244H GLU 2.7 23.8 + - - -
245H THR 3.9 0.9 - - - -
247H ILE* 1.3 77.3 - - - +
249H SER* 1.3 61.9 + - - +
251H GLU* 2.9 19.8 + - - +
252H LYS* 3.1 11.9 + - - +
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Residues in contact with SER 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197H ILE* 5.1 6.7 - - - -
205H THR* 2.7 40.2 + - - +
231H GLU* 2.8 33.1 + - - +
233H VAL* 5.3 2.9 - - - -
245H THR 3.2 11.5 + - - -
246H ILE* 3.2 9.3 + - - -
248H GLY* 1.3 73.7 - - - +
250H VAL* 1.3 58.3 + - - +
252H LYS* 3.2 8.0 + - - +
253H THR* 3.0 25.5 + - - +
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Residues in contact with VAL 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H THR* 3.9 11.7 - - + +
207H ILE* 4.8 0.2 - - + -
246H ILE* 3.1 23.4 + - + +
247H ILE* 3.7 7.9 - - - +
249H SER* 1.3 76.8 - - - +
251H GLU* 1.3 57.6 + - - +
253H THR* 3.9 0.9 - - - -
254H GLY* 2.8 30.0 + - - -
255H ARG 4.7 2.9 - - - +
256H ALA* 4.2 23.8 - - + -
276H ILE* 4.0 27.8 - - + -
280H ALA* 4.9 9.0 - - + +
283H SER* 4.6 3.5 - - - -
284H LEU* 3.8 29.8 - - + -
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Residues in contact with GLU 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247H ILE* 2.9 39.5 + - + +
248H GLY* 2.9 12.6 + - - +
250H VAL* 1.3 76.5 - - - +
252H LYS* 1.3 61.2 + - - +
254H GLY* 4.5 1.8 + - - -
279H ARG 4.5 4.7 - - - +
280H ALA* 4.1 16.3 - - + +
283H SER* 4.3 21.2 + - - +
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Residues in contact with LYS 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H GLU* 4.0 18.4 + - - +
201H GLY 3.0 23.6 + - - +
202H LYS* 4.1 12.7 - - + +
231H GLU* 2.9 32.8 + - - +
248H GLY 3.1 9.9 + - - +
249H SER* 3.5 7.9 - - - +
250H VAL 3.1 0.2 - - - -
251H GLU* 1.3 80.8 - - - +
253H THR* 1.3 67.1 + - + +
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Residues in contact with THR 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201H GLY 4.1 7.2 - - - +
202H LYS* 3.4 33.9 - - - +
203H ASP* 3.3 26.1 - - - +
204H ILE 3.8 11.4 - - - +
205H THR* 2.7 29.0 + - - +
231H GLU* 4.6 1.6 - - + -
249H SER* 3.0 10.4 + - - +
250H VAL 3.8 1.6 + - - -
252H LYS* 1.3 81.1 - - + +
254H GLY* 1.3 59.2 + - - +
255H ARG* 2.8 19.7 + - - +
285H GLU* 5.1 2.3 - - - +
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Residues in contact with GLY 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H VAL 2.8 22.3 + - - -
251H GLU 4.5 1.5 - - - -
252H LYS 3.6 1.0 - - - -
253H THR* 1.3 71.1 + - - +
255H ARG* 1.3 62.5 + - - +
283H SER* 3.3 19.3 - - - -
284H LEU* 3.3 10.4 - - - +
285H GLU* 2.7 34.7 + - - -
286H ALA 4.1 0.3 + - - -
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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