Contacts of the helix formed by residues 298 - 305 (chain B) in PDB entry 4XDO
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 TRP 298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B VAL* 6.0 0.2 - - + -
159B LEU* 4.6 3.1 - - + -
194B MET* 2.9 30.8 + - + -
195B ASP 3.3 20.4 + - - -
196B LEU* 3.3 33.6 - - + +
197B TYR* 4.0 18.1 - - + -
274B PRO* 4.1 4.7 - - + -
294B ALA* 3.5 15.3 - - + -
295B THR* 3.1 13.8 + - - +
296B VAL 3.1 1.4 - - - -
297B ARG* 1.3 77.0 - - - +
299B ILE* 1.3 75.5 + - + +
300B ASP 3.3 0.2 - - - -
301B TYR* 2.7 30.7 + - + -
302B GLY* 2.8 22.7 + - - +
317B ILE* 5.3 3.6 - - + -
319B MET* 3.5 31.9 - - + -
322B PHE* 3.9 35.0 - + - -
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Residues in contact with ILE 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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158B VAL* 5.2 2.2 - - + -
295B THR 4.3 2.9 - - - +
296B VAL* 3.1 29.0 + - + +
298B TRP* 1.3 96.3 - - + +
300B ASP* 1.3 63.7 - - - +
302B GLY* 3.1 1.9 + - - -
303B LYS* 3.0 31.2 + - + +
319B MET* 3.8 4.7 - - + +
322B PHE* 3.9 31.6 - - + +
323B VAL* 4.4 3.4 - - + -
326B PHE* 3.6 37.7 - - + -
327B GLN* 3.6 26.7 - - + +
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Residues in contact with ASP 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B VAL 4.6 0.6 + - - -
297B ARG 4.0 7.7 + - - +
298B TRP 3.3 0.6 - - - -
299B ILE* 1.3 76.0 - - - +
301B TYR* 1.3 60.5 + - + +
303B LYS* 2.6 31.6 + - - -
304B VAL* 3.6 12.3 + - - +
327B GLN* 2.9 14.3 + - - +
330B ARG* 3.0 27.1 + - - -
341B TYR* 2.8 38.5 + - + -
343B ILE* 3.8 11.2 - - + +
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Residues in contact with TYR 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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194B MET 4.7 0.9 - - - -
195B ASP* 4.3 9.9 - - + +
215B PRO* 4.8 1.7 - - - +
274B PRO* 3.5 33.1 + - + -
275B TYR* 3.8 20.2 - + + -
297B ARG* 3.0 54.7 + - + -
298B TRP* 2.7 22.8 + - + +
300B ASP* 1.3 71.4 - - + +
302B GLY* 1.3 65.7 + - - +
303B LYS 3.2 0.2 - - - -
304B VAL* 3.1 5.1 + - + +
305B ALA* 3.0 24.4 + - - +
343B ILE* 3.6 29.4 - - + +
344B ASP 4.6 0.2 + - - -
345B HIS* 2.9 47.1 + + - +
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Residues in contact with GLY 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B MET* 3.6 35.0 - - - +
298B TRP* 2.8 29.2 + - - +
299B ILE 3.1 3.3 + - - -
301B TYR* 1.3 79.8 - - - +
303B LYS* 1.3 59.5 + - - +
304B VAL 3.3 0.7 + - - -
305B ALA* 3.4 7.6 + - - +
319B MET* 3.7 11.5 - - - +
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Residues in contact with LYS 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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299B ILE* 3.0 20.0 + - + +
300B ASP* 2.6 29.7 + - - +
301B TYR 3.2 0.2 - - - -
302B GLY* 1.3 76.8 - - - +
304B VAL* 1.4 57.0 + - - +
305B ALA 3.6 0.4 - - - +
319B MET* 4.0 16.1 - - + +
323B VAL* 3.7 19.7 - - + +
327B GLN* 2.7 23.9 + - - +
330B ARG* 3.3 9.3 - - - +
334B TRP* 3.6 30.1 + - + +
339B ASP* 2.7 29.2 + - - -
341B TYR* 3.3 16.7 - - - +
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Residues in contact with VAL 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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195B ASP* 6.0 0.2 - - - +
300B ASP 3.6 13.2 + - - +
301B TYR* 3.1 9.0 + - - +
303B LYS* 1.4 79.2 - - - +
305B ALA* 1.3 68.8 + - - +
306B LYS* 3.3 4.2 + - - +
341B TYR* 3.5 28.0 - - + +
343B ILE* 3.9 19.5 - - + -
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Residues in contact with ALA 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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194B MET* 3.9 22.9 - - + -
195B ASP* 3.5 29.6 - - - +
241B ARG* 4.1 3.6 - - - +
301B TYR 3.0 12.4 + - - +
302B GLY 3.4 11.7 + - - +
303B LYS 3.6 0.6 - - - +
304B VAL* 1.3 79.3 - - - +
306B LYS* 1.3 61.1 + - - +
307B LEU* 3.8 15.7 + - + +
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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