Contacts of the helix formed by residues 244 - 251 (chain A) in PDB entry 4JU5
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 THR 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A ILE* 3.6 22.2 - - + +
239A GLU 3.1 23.4 + - - +
240A PHE* 3.8 0.2 - - - -
241A THR* 3.3 23.4 + - - +
242A GLU 3.3 0.2 - - - -
243A GLN* 1.3 80.6 - - - +
245A ALA* 1.3 63.3 + - - +
246A PRO 3.5 0.2 - - - -
247A LYS* 3.1 21.8 + - - +
248A ILE* 3.2 33.2 + - + +
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Residues in contact with ALA 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A PHE* 3.9 23.7 - - + -
241A THR 2.8 21.9 + - - +
242A GLU 3.8 5.2 - - - +
244A THR* 1.3 72.9 - - - +
246A PRO* 1.4 69.7 - - + +
248A ILE* 3.4 12.6 + - - +
249A PHE* 3.5 10.7 + - - +
303B GLU* 3.6 36.8 - - + +
304B PHE 4.6 1.6 - - - +
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Residues in contact with PRO 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ASP* 5.8 2.0 - - - +
242A GLU 3.5 9.0 - - - +
243A GLN* 3.4 17.3 - - - +
245A ALA* 1.4 94.8 - - + +
247A LYS* 1.3 64.9 + - + +
249A PHE* 3.8 1.9 + - - +
250A GLY* 3.3 19.8 + - - -
303B GLU 5.0 0.2 - - - +
306B GLY* 4.8 15.5 - - - -
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Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ASP* 3.6 48.4 + - - +
182A ILE* 5.4 3.2 - - - +
233A GLN* 4.6 20.2 + - + +
234A LEU* 5.1 16.9 - - + +
238A ILE* 5.4 6.7 - - + -
243A GLN* 3.9 22.4 - - - +
244A THR* 3.1 12.6 + - - +
246A PRO* 1.3 78.8 - - + +
248A ILE* 1.3 63.7 + - - +
250A GLY* 4.0 1.7 - - - -
251A GLY* 3.5 17.3 + - - -
287A LEU* 5.3 1.6 - - - +
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Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LEU* 6.4 0.4 - - + -
238A ILE* 4.3 17.0 - - + -
240A PHE* 3.6 27.1 - - + -
244A THR* 3.2 35.2 + - + +
245A ALA 3.7 7.6 - - - +
246A PRO 3.3 0.4 - - - -
247A LYS* 1.3 76.4 - - - +
249A PHE* 1.3 65.2 + - - +
251A GLY* 3.5 8.1 + - - -
256A HIS* 3.1 43.3 + - + +
287A LEU* 4.0 11.0 - - + +
289A ILE* 3.7 30.5 - - + -
304B PHE* 5.1 12.3 - - + +
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Residues in contact with PHE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ALA 3.5 6.3 + - - +
246A PRO 3.8 1.8 + - - +
248A ILE* 1.3 81.2 - - - +
250A GLY* 1.3 61.4 + - - +
251A GLY 4.0 0.3 - - - +
254A LYS* 3.5 17.5 + - - -
320A LEU* 4.3 18.6 - - + +
304B PHE 3.8 10.1 - - - +
305B PHE* 3.7 32.1 - - - +
306B GLY* 3.7 9.9 - - - +
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Residues in contact with GLY 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PRO 3.3 14.3 + - - -
247A LYS* 4.3 2.2 - - - -
248A ILE 3.3 0.6 - - - -
249A PHE* 1.3 79.1 - - - +
251A GLY* 1.3 64.1 + - - +
252A GLU* 3.6 2.8 + - - +
254A LYS* 4.3 4.2 + - - -
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Residues in contact with GLY 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LYS* 6.0 4.3 - - - -
234A LEU* 5.9 5.8 - - - -
247A LYS 3.5 10.9 + - - -
248A ILE 3.5 10.8 + - - +
249A PHE 3.3 3.4 - - - +
250A GLY* 1.3 76.9 - - - +
252A GLU* 1.3 57.2 + - - -
253A ILE* 3.1 19.5 + - - -
254A LYS* 2.8 28.8 + - - +
256A HIS* 5.0 1.5 + - - -
287A LEU* 5.3 4.3 - - - -
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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