Contacts of the helix formed by residues 234 - 245 (chain B) in PDB entry 4I5L
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 PHE 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B PHE* 4.1 9.0 - + - -
221B LEU* 4.3 10.3 - - + -
229B LEU* 3.7 38.6 - - + -
230B VAL 3.6 12.3 - - - -
231B GLN 3.2 8.3 + - - +
232B GLU 3.1 1.2 + - - -
233B ASP* 1.3 76.9 - - - +
235B VAL* 1.3 64.6 + - - +
236B PRO* 3.5 0.9 - - - -
237B PHE* 3.3 13.3 + + - +
238B LEU* 3.0 23.4 + - + +
266B ILE* 3.8 17.3 - - + -
269B ILE* 3.9 32.3 - - + -
270B PHE* 3.8 24.2 - + - -
281B ILE* 4.1 9.4 - - + -
286B LEU* 5.9 2.9 - - + -
291B PHE* 4.0 28.0 - + - -
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B GLN 5.1 0.2 - - - -
232B GLU* 3.1 24.6 + - + +
234B PHE* 1.3 73.1 - - - +
236B PRO* 1.4 73.6 - - + +
238B LEU* 3.2 4.5 + - - +
239B GLN* 2.9 48.3 + - + +
262B ILE* 4.5 11.6 - - + +
266B ILE* 4.0 20.6 - - + -
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Residues in contact with PRO 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B GLY* 5.0 6.3 - - - +
181B PRO* 5.7 1.3 - - + -
184B TYR* 3.6 59.0 - - + +
189B GLU* 5.0 4.0 - - - +
221B LEU* 6.3 1.1 - - + -
232B GLU 3.9 4.9 - - - +
233B ASP* 3.4 17.9 - - - +
234B PHE 3.6 0.4 - - - -
235B VAL* 1.4 93.6 - - + +
237B PHE* 1.3 61.3 + - - +
239B GLN* 3.3 9.4 + - + +
240B ASP* 3.1 21.3 + - - +
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Residues in contact with PHE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 3.2 28.3 - - + -
181B PRO* 3.8 31.6 - - + +
217B PHE* 4.6 7.2 - + - -
221B LEU* 4.4 10.7 - - + +
233B ASP 5.0 0.2 + - - -
234B PHE* 3.3 15.4 + + - +
235B VAL 3.2 0.8 - - - -
236B PRO* 1.3 79.4 - - - +
238B LEU* 1.3 73.0 + - + +
240B ASP* 3.1 7.9 + - + +
241B VAL* 3.0 47.2 + - + +
291B PHE* 3.9 16.6 - + - -
295B VAL* 4.0 27.4 - - + -
298B LEU* 4.2 3.6 - - + -
311B PHE* 3.9 28.0 - + - -
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B PHE* 3.0 19.5 + - + +
235B VAL 3.9 2.5 - - - +
237B PHE* 1.3 93.7 - - + +
239B GLN* 1.3 52.5 + - - +
241B VAL* 3.2 8.4 + - + +
242B VAL* 2.8 39.7 + - - +
261B TYR* 4.1 20.0 - - + -
262B ILE* 4.0 24.5 - - + -
265B VAL* 3.6 38.6 - - + -
266B ILE* 3.6 28.5 - - + -
269B ILE* 4.1 8.7 - - + -
311B PHE* 4.7 6.7 - - + -
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Residues in contact with GLN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B VAL* 2.9 38.5 + - + +
236B PRO* 3.5 8.1 - - + +
238B LEU* 1.3 76.0 - - - +
240B ASP* 1.3 57.8 + - - +
242B VAL* 3.2 2.2 + - - +
243B ASN* 2.9 43.4 + - - +
258B HIS* 2.8 31.4 + - - -
262B ILE* 3.6 17.7 - - + +
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Residues in contact with ASP 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B MET* 3.2 26.0 - - + +
177B TYR* 4.2 10.4 - - - +
179B LYS* 2.7 43.0 + - - +
180B GLY* 3.7 17.3 + - - -
181B PRO* 5.5 0.4 - - + -
236B PRO 3.1 11.0 + - - +
237B PHE* 3.1 10.0 + - + +
239B GLN* 1.3 74.4 - - - +
241B VAL* 1.3 64.0 + - - +
243B ASN* 3.0 8.8 + - - +
244B THR* 2.9 33.8 + - - -
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B TYR* 4.2 13.9 - - + -
237B PHE* 3.0 52.5 + - + +
238B LEU* 3.2 14.8 + - + +
240B ASP* 1.3 75.0 - - + +
242B VAL* 1.3 62.9 + - + +
245B HIS* 3.0 29.0 + - + +
248B LEU* 3.9 18.2 - - + +
261B TYR* 4.9 1.6 - - - +
298B LEU* 4.2 27.8 - - + -
304B ILE* 4.9 0.2 - - + -
311B PHE* 4.6 12.6 - - + -
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B LEU* 2.8 23.8 + - + +
239B GLN* 3.8 4.7 - - - +
241B VAL* 1.3 73.7 - - - +
243B ASN* 1.3 60.6 + - - +
244B THR 3.5 0.2 + - - -
245B HIS 4.5 1.0 + - - +
248B LEU* 3.6 25.9 - - + +
251B LEU* 3.6 28.0 - - + +
252B LYS* 4.0 5.5 - - - +
258B HIS* 3.5 32.8 - - + +
261B TYR* 3.6 35.9 - - + -
262B ILE* 4.1 13.0 - - + -
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Residues in contact with ASN 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B GLN* 2.9 30.4 + - - +
240B ASP* 3.0 9.1 + - - +
242B VAL* 1.3 78.0 - - - +
244B THR* 1.3 59.7 - - - +
252B LYS* 3.1 49.5 + - + +
258B HIS* 4.0 9.2 - - - -
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Residues in contact with THR 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 5.2 2.7 - - + -
177B TYR* 3.3 27.1 - - + +
179B LYS* 2.6 39.2 + - - +
240B ASP* 2.9 21.5 + - - -
242B VAL 3.3 0.2 - - - -
243B ASN* 1.3 80.5 - - - +
245B HIS* 1.3 69.1 + - - +
246B PRO* 3.3 7.6 - - - +
252B LYS* 4.6 4.9 + - - +
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Residues in contact with HIS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 3.5 18.6 - + + +
241B VAL* 3.0 19.3 + - + +
242B VAL 4.6 1.2 - - - +
244B THR* 1.3 79.0 - - - +
246B PRO* 1.3 67.0 - - + +
247B GLY* 3.0 21.8 + - - -
248B LEU* 3.0 30.3 + - + +
249B SER* 3.5 10.2 + - - -
252B LYS* 4.6 1.3 + - - -
298B LEU* 3.0 40.0 + - + +
301B GLU* 2.8 30.3 + - - +
302B ALA* 3.4 21.8 - - - -
304B ILE* 4.0 21.6 - - + +
307B LEU* 5.6 0.4 - - - +
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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