Contacts of the helix formed by residues 241 - 249 (chain B) in PDB entry 2JAJ
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 TYR 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B ASP* 2.9 41.3 - - + +
216B ASP 5.3 0.4 - - - -
217B ILE* 3.4 25.8 - - + +
218B ALA* 3.7 25.1 - - + -
236B ARG* 4.1 21.2 - - + +
237B THR 3.3 11.8 + - - +
240B GLU* 1.3 97.2 - - + +
242B PRO* 1.4 60.6 - - - +
243B GLU 3.5 1.6 - - - -
244B SER* 3.1 4.3 + - - -
245B ALA* 3.0 22.2 + - - +
265B GLU* 2.6 40.4 + - - -
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Residues in contact with PRO 242 (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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215B ASP* 4.6 2.9 - - - +
238B PRO* 3.0 34.3 - - + +
239B GLU 3.2 12.3 - - - +
240B GLU 3.7 3.1 - - - +
241B TYR* 1.4 80.7 - - - +
243B GLU* 1.3 65.2 + - + +
244B SER 2.9 6.2 + - - -
245B ALA* 3.2 10.7 + - - +
246B LYS* 3.4 11.4 + - - +
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Residues in contact with GLU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PRO* 3.2 36.0 - - + +
215B ASP* 4.4 6.3 - - - +
241B TYR 3.5 0.4 - - - -
242B PRO* 1.3 81.0 - - + +
244B SER* 1.3 57.5 + - - +
246B LYS* 4.0 13.4 - - - +
247B VAL* 3.8 8.3 - - - +
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Residues in contact with SER 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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213B VAL* 3.4 11.5 - - - +
214B PRO* 3.2 10.5 - - - +
215B ASP* 3.2 36.7 + - - +
218B ALA* 3.7 21.6 - - - +
236B ARG 5.8 0.2 - - - -
241B TYR 3.1 10.9 + - - -
242B PRO 2.9 1.0 - - - -
243B GLU* 1.3 77.9 - - - +
245B ALA* 1.3 56.2 + - - +
246B LYS 3.1 5.4 - - - -
247B VAL* 3.2 22.2 + - - +
248B TYR* 3.3 15.6 - - - -
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Residues in contact with ALA 245 (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 HIS* 4.6 11.4 - - + -
236B ARG 4.0 10.7 + - - +
238B PRO* 3.7 42.2 - - + -
241B TYR 3.0 8.4 + - - +
242B PRO 3.2 3.5 + - - +
244B SER* 1.3 72.9 - - - +
246B LYS* 1.3 61.0 + - - +
248B TYR* 4.0 10.8 - - - +
249B GLU* 3.6 19.2 + - - +
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Residues in contact with LYS 246 (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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242B PRO 3.4 9.0 + - - +
243B GLU* 4.0 15.9 - - - +
244B SER 3.1 0.6 - - - -
245B ALA* 1.3 77.5 - - - +
247B VAL* 1.3 63.5 + - + +
248B TYR 3.3 0.8 + - - -
249B GLU* 3.6 13.5 + - - +
250B LYS* 3.6 10.4 + - - +
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Residues in contact with VAL 247 (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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211B LEU* 3.8 32.5 - - + +
212B THR 4.0 14.1 - - - +
213B VAL* 3.7 16.6 - - + -
214B PRO* 3.8 28.3 - - + -
243B GLU 3.8 5.4 - - - +
244B SER 3.2 8.5 + - - +
246B LYS* 1.3 76.4 - - + +
248B TYR* 1.3 63.3 + - - +
250B LYS* 3.3 22.2 + - - +
251B LEU* 4.9 0.2 - - - +
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Residues in contact with TYR 248 (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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186B ALA* 3.8 17.9 - - + +
211B LEU* 3.4 30.1 - - + -
213B VAL* 3.7 17.0 - - + +
218B ALA* 2.6 33.9 + - + -
219B ALA* 3.8 1.6 - - - -
221B CYS* 3.8 10.1 - - + +
233B LEU* 3.6 28.5 - - + -
235B HIS* 3.3 48.7 - + + +
236B ARG 5.3 1.1 - - - -
244B SER 3.3 20.3 + - - +
245B ALA* 4.5 1.8 - - - +
246B LYS 3.3 1.0 - - - -
247B VAL* 1.3 75.5 - - + +
249B GLU* 1.3 53.7 + - - +
250B LYS 2.9 4.5 - - - -
251B LEU* 2.7 29.5 + - + +
256B LEU* 3.2 20.8 - - + +
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Residues in contact with GLU 249 (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 HIS* 5.3 0.4 - - - -
245B ALA 3.6 13.5 + - - +
246B LYS* 3.6 12.0 + - - +
247B VAL 3.4 0.2 - - - -
248B TYR* 1.3 75.1 - - - +
250B LYS* 1.3 55.6 + - - +
251B LEU 3.1 10.2 + - - +
252B LYS* 4.7 1.7 + - - -
256B LEU* 3.6 14.5 - - + +
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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