Contacts of the helix formed by residues 245 - 257 (chain H) in PDB entry 3EXG
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 245 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196H GLY 3.1 23.9 + - - +
197H LYS* 3.2 20.8 + - - +
198H ALA* 2.8 31.4 + - + +
238H MET* 5.5 3.9 + - - +
240H THR* 4.8 2.0 + - - -
243H PRO 3.6 1.2 + - - -
244H MET* 1.3 69.2 - - - +
246H MET* 1.3 61.7 + - - +
247H GLU* 3.6 10.6 + - - +
248H THR* 2.4 40.3 + - - -
249H ILE* 3.8 15.0 + - - +
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Residues in contact with MET 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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244H MET* 3.0 24.5 + - - +
245H ASP* 1.3 73.4 + - - +
247H GLU* 1.3 65.4 + - - +
249H ILE* 3.2 44.6 + - + +
250H GLU* 3.1 40.3 + - + +
275H ILE* 3.8 23.8 - - + +
278H ARG* 3.5 45.1 - - + +
279H ILE* 3.8 16.8 - - + +
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Residues in contact with GLU 247 (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 LYS* 5.8 5.9 - - - +
245H ASP* 3.3 9.5 + - - +
246H MET* 1.3 78.8 - - - +
248H THR* 1.3 56.4 + - - +
250H GLU* 4.4 10.7 + - - +
251H ALA* 2.8 36.7 + - - +
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Residues in contact with THR 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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197H LYS* 4.2 9.4 - - - +
198H ALA* 4.3 18.5 + - + -
199H LYS* 5.3 0.9 - - - -
200H ILE* 4.3 17.9 - - + +
236H ILE* 4.1 16.9 - - + +
245H ASP* 2.4 35.7 + - - -
246H MET 3.4 0.6 - - - -
247H GLU* 1.3 79.4 - - - +
249H ILE* 1.3 60.6 + - - +
251H ALA* 3.9 6.1 - - - +
252H SER* 3.3 21.0 + - - -
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Residues in contact with ILE 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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198H ALA* 5.8 0.9 - - + -
208H THR* 5.0 1.1 - - + -
210H VAL* 3.9 43.3 - - + -
236H ILE* 4.7 11.9 - - + -
238H MET* 5.1 5.8 - - + -
244H MET* 5.7 1.8 - - - -
245H ASP 3.8 16.2 - - - +
246H MET* 3.3 37.2 - - + +
248H THR* 1.3 76.9 - - - +
250H GLU* 1.3 55.4 + - - +
252H SER* 2.9 7.2 + - - -
253H VAL* 2.7 47.0 + - + +
259H LEU* 4.5 7.2 - - + -
275H ILE* 4.5 12.8 - - + -
279H ILE* 4.3 3.8 - - + -
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Residues in contact with GLU 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H MET* 3.1 41.4 + - + +
247H GLU* 3.9 9.0 - - - +
249H ILE* 1.3 70.7 - - - +
251H ALA* 1.3 66.9 + - - +
252H SER 3.1 0.3 + - - -
253H VAL* 3.2 3.1 + - - +
254H MET* 2.8 38.2 + - + +
278H ARG 3.7 10.9 - - - +
279H ILE* 4.2 5.2 - - + +
282H GLY* 3.7 10.4 - - - -
283H PRO* 3.4 35.5 - - + +
284H ALA* 3.7 25.3 - - + +
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Residues in contact with ALA 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 GLU* 2.8 18.4 + - + +
248H THR* 3.9 7.4 - - - +
250H GLU* 1.3 79.1 - - - +
252H SER* 1.3 61.2 + - - +
254H MET* 3.4 27.7 + - + +
255H LYS* 3.6 8.1 + - - +
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Residues in contact with SER 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 ILE* 5.2 0.7 - - - -
208H THR* 2.7 26.7 + - - +
234H GLU* 2.7 35.0 + - - +
236H ILE* 4.1 11.0 - - - -
248H THR 3.3 13.1 + - - -
249H ILE 2.9 9.6 + - - -
251H ALA* 1.3 75.2 - - - +
253H VAL* 1.3 57.8 + - - +
255H LYS* 2.7 28.2 + - - +
256H THR* 3.0 11.8 + - - +
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Residues in contact with VAL 253 (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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208H THR* 4.2 7.2 - - - +
249H ILE* 2.7 29.1 + - + +
250H GLU* 3.6 6.3 - - - +
252H SER* 1.3 67.6 + - - +
254H MET* 1.3 57.5 + - - +
255H LYS 2.8 5.8 - - - -
256H THR* 3.7 7.9 - - - -
257H ASN* 2.7 31.3 + - - +
258H HIS 4.9 0.2 - - - +
259H LEU* 4.0 36.1 - - + -
279H ILE* 4.3 4.3 - - + -
284H ALA* 4.2 21.3 - - + +
287H PHE* 4.0 4.3 - - + +
288H LEU* 3.6 27.8 - - + -
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Residues in contact with MET 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 GLU* 2.8 35.0 + - + +
251H ALA* 3.6 28.7 - - + +
253H VAL* 1.3 72.9 - - - +
255H LYS* 1.3 59.7 + - - +
257H ASN* 4.3 5.4 + - - -
283H PRO* 5.2 8.5 - - + +
284H ALA* 4.7 8.3 - - + -
287H PHE* 3.7 61.1 - - + -
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Residues in contact with LYS 255 (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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203H GLN* 5.0 5.7 + - - +
204H GLY 2.7 19.3 + - - +
205H THR* 3.6 27.7 - - + +
234H GLU* 2.6 36.4 + - - -
251H ALA 4.0 7.9 - - - +
252H SER* 2.7 11.6 + - - +
254H MET* 1.3 80.8 - - - +
256H THR* 1.3 61.7 + - + +
257H ASN* 4.3 5.7 - - - +
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Residues in contact with THR 256 (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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204H GLY 4.2 6.7 - - - +
205H THR* 3.2 35.3 - - - +
206H HIS* 3.2 15.1 - - - +
207H ILE* 3.8 10.8 - - - +
208H THR* 2.7 31.2 + - - +
234H GLU* 4.7 1.8 - - + -
252H SER* 3.3 12.6 + - - +
253H VAL* 3.7 2.4 - - - -
255H LYS* 1.3 83.6 - - + +
257H ASN* 1.3 68.2 + - - +
258H HIS* 2.7 26.0 + - - -
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Residues in contact with ASN 257 (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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253H VAL* 2.7 20.7 + - - -
254H MET 4.3 6.4 + - - -
255H LYS 4.3 4.7 - - - +
256H THR* 1.3 77.4 + - - +
258H HIS* 1.3 68.0 + - + +
287H PHE* 2.7 42.0 + - - +
288H LEU* 3.4 10.0 - - - -
289H ASP* 2.8 45.1 + - - +
290H 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