Contacts of the helix formed by residues 298 - 305 (chain B) 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 ASN 298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A ARG* 2.6 39.8 + - - +
240B PHE* 4.0 7.5 + - - -
291B ILE* 3.5 28.7 - - + +
292B ASP* 2.8 37.3 + - - +
295B HIS* 3.1 18.8 + - - +
297B ASP* 1.3 75.6 - - - +
299B GLN* 1.3 66.7 + - - +
300B ARG 3.3 2.7 - - - -
301B ILE* 3.1 10.0 + - - +
302B LEU* 3.1 25.1 + - + +
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Residues in contact with GLN 299 (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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293B SER 2.7 22.8 + - - -
294B ASP 4.1 2.4 + - - -
295B HIS 2.7 25.9 + - - -
296B THR* 3.2 24.9 - - - +
297B ASP 3.4 1.6 - - - -
298B ASN* 1.3 79.3 - - - +
300B ARG* 1.3 58.2 + - - +
302B LEU* 3.1 16.5 + - - +
303B GLU* 2.9 37.9 + - + +
309B LYS* 3.4 28.6 + - - +
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 3.4 29.9 + - - -
241A THR* 4.2 4.9 - - - +
242A GLU* 2.7 38.0 + - - +
297A ASP* 3.2 40.0 + - - +
298A ASN* 3.5 16.3 + - - +
300A ARG* 4.6 15.9 - - + -
301A ILE* 3.5 21.8 - - + +
296B THR 5.0 0.4 + - - -
297B ASP 4.7 1.6 + - - +
298B ASN 3.3 0.4 - - - -
299B GLN* 1.3 76.8 - - - +
301B ILE* 1.3 57.7 + - - +
303B GLU* 2.7 43.6 + - - +
304B PHE* 2.8 28.4 + - - +
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Residues in contact with ILE 301 (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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300A ARG* 3.4 32.3 - - + +
301A ILE* 5.0 4.3 - - + -
304A PHE* 4.0 20.4 - - + -
240B PHE* 3.4 39.9 - - + -
260B PHE* 3.7 21.3 - - + -
291B ILE* 4.9 6.5 - - + -
298B ASN* 3.1 14.0 + - + +
300B ARG* 1.3 75.3 - - - +
302B LEU* 1.3 63.9 - - - +
304B PHE* 3.3 5.9 + - + -
305B PHE* 3.1 43.3 + - + -
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Residues in contact with LEU 302 (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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260B PHE* 3.5 27.8 - - + -
293B SER* 3.9 26.0 - - - +
298B ASN* 3.1 29.0 + - + +
299B GLN* 3.1 28.0 + - - +
301B ILE* 1.3 77.1 - - - +
303B GLU* 1.3 57.3 + - + +
305B PHE 3.3 1.0 + - - -
306B GLY 3.1 4.9 + - - -
307B LEU* 2.7 49.4 + - + +
308B LYS 4.0 4.9 - - - -
309B LYS* 3.8 34.8 - - + +
312B CYS* 4.3 3.8 - - - -
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Residues in contact with GLU 303 (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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240A PHE* 5.0 1.3 - - + -
242A GLU* 4.2 13.9 - - - +
245A ALA* 3.6 29.1 - - + +
246A PRO* 5.0 0.2 - - - +
299B GLN* 2.9 23.3 + - + +
300B ARG* 2.7 48.6 + - - +
301B ILE 3.3 0.2 - - - -
302B LEU* 1.3 73.2 - - + +
304B PHE* 1.3 66.3 + - - +
306B GLY* 3.0 14.0 + - - +
307B LEU 4.1 6.3 + - - +
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Residues in contact with PHE 304 (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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240A PHE* 3.6 37.6 - + + -
245A ALA 4.6 2.8 - - - +
248A ILE* 5.1 11.9 - - + +
249A PHE* 3.8 12.5 + - - +
256A HIS* 6.0 2.7 - - - -
258A LEU* 3.6 41.5 - - + -
289A ILE* 6.1 2.2 - - + -
291A ILE* 4.7 1.8 - - + -
301A ILE* 3.8 22.4 - - + -
304A PHE* 5.9 0.2 - + - -
305A PHE* 3.9 17.5 - + - -
318A ILE* 4.5 7.6 - - + -
320A LEU* 6.0 2.1 - - + +
300B ARG 2.8 19.7 + - - +
301B ILE* 3.3 11.4 + - - +
303B GLU* 1.3 73.7 - - - +
305B PHE* 1.3 91.2 + + + +
306B GLY 3.6 1.2 + - - -
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Residues in contact with PHE 305 (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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249A PHE* 3.7 12.3 - - - +
304A PHE* 3.8 26.7 - + - -
318A ILE* 4.3 5.4 - - + -
320A LEU* 3.7 22.0 - - + -
258B LEU* 3.8 13.0 - - + -
260B PHE* 3.8 17.9 - + + -
301B ILE* 3.1 42.2 + - + +
302B LEU 4.2 1.8 - - - +
303B GLU 3.2 0.2 - - - -
304B PHE* 1.3 104.1 - + - +
306B GLY* 1.3 64.5 + - - +
307B LEU* 3.4 3.7 - - + +
316B ARG* 3.4 40.6 + - + +
318B ILE* 3.8 24.5 - - + -
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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