Contacts of the helix formed by residues 291 - 301 (chain A) in PDB entry 4QBT
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 ALA 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A PHE* 3.7 11.5 - - - -
289A TYR* 3.4 1.8 - - - +
290A THR* 1.3 84.7 + - - +
292A TYR* 1.3 68.0 + - - +
293A VAL* 4.2 14.1 - - + -
294A ASP* 3.1 28.7 + - - +
295A LEU 3.5 6.6 + - - -
503A GOL 6.5 0.4 - - - -
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Residues in contact with TYR 292 (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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255A VAL 5.1 2.1 + - - -
261A LEU* 3.4 56.0 + - + +
262A SER* 5.3 0.5 - - - -
264A ILE* 4.4 0.4 - - + -
265A LYS* 3.7 53.5 - - + +
269A PHE* 3.7 32.1 - + + -
291A ALA* 1.3 73.4 - - - +
293A VAL* 1.3 67.6 + - - +
295A LEU* 2.9 11.9 + - + -
296A GLU* 2.9 55.0 + - + +
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Residues in contact with VAL 293 (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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291A ALA* 4.2 13.7 - - + -
292A TYR* 1.3 81.8 - - + +
294A ASP* 1.3 71.8 + - - +
296A GLU* 3.3 17.4 + - - +
297A LYS* 3.0 31.0 + - + +
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Residues in contact with ASP 294 (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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287A LYS* 6.1 1.1 - - - +
289A TYR* 3.7 22.4 - - + -
290A THR* 4.6 6.1 + - - -
291A ALA* 3.1 24.7 + - - +
292A TYR 3.1 1.0 - - - -
293A VAL* 1.3 87.0 - - - +
295A LEU* 1.3 64.3 + - - +
297A LYS* 3.4 10.0 + - - +
298A ASP* 3.1 20.1 + - - +
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Residues in contact with LEU 295 (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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261A LEU* 4.3 14.4 - - + -
264A ILE* 3.8 38.1 - - + -
269A PHE* 4.3 4.5 - - + -
275A PHE* 3.9 15.7 - - + -
277A ILE* 4.0 16.8 - - + -
289A TYR* 3.5 41.1 - - + -
291A ALA 3.5 2.1 + - - +
292A TYR* 2.9 13.0 + - + +
294A ASP* 1.3 78.6 - - - +
296A GLU* 1.3 59.5 + - - +
298A ASP* 3.3 1.0 + - - +
299A PHE* 2.8 27.4 + - + +
304A VAL* 4.2 10.1 - - + -
309A LEU* 4.1 7.9 - - + -
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Residues in contact with GLU 296 (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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255A VAL* 3.7 35.6 - - + +
261A LEU* 5.3 1.8 - - - -
265A LYS* 5.8 0.5 + - - -
292A TYR* 2.9 45.7 + - + +
293A VAL* 3.4 21.4 - - - +
295A LEU* 1.3 79.6 - - - +
297A LYS* 1.3 63.7 + - - +
299A PHE* 3.1 8.5 + - - +
300A ALA* 2.9 23.5 + - + +
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Residues in contact with LYS 297 (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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293A VAL* 3.0 18.8 + - + +
294A ASP* 3.7 10.5 - - - +
296A GLU* 1.3 77.3 - - - +
298A ASP* 1.3 67.1 + - - +
300A ALA* 3.2 6.6 + - - +
301A ALA* 2.9 27.4 + - + +
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Residues in contact with ASP 298 (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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279A ARG* 4.9 1.7 + - - -
287A LYS* 2.9 27.2 + - - +
289A TYR* 2.5 34.5 + - - +
294A ASP 3.1 10.4 + - - +
295A LEU 3.7 6.5 - - - +
297A LYS* 1.3 80.8 - - - +
299A PHE* 1.3 63.3 + - - +
301A ALA* 3.4 4.3 + - - +
302A GLU 3.1 3.8 + - - -
303A VAL* 3.1 48.5 + - + +
304A VAL* 3.6 6.4 + - + -
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Residues in contact with PHE 299 (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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250A CYS* 4.0 8.1 - - - -
251A GLU 3.5 27.4 - - - -
253A GLY* 3.3 24.2 + - - -
254A ASN 3.6 20.0 - - - -
255A VAL* 4.0 7.6 - - + -
258A ASN* 3.7 12.6 - - - -
261A LEU* 3.9 18.4 - - + -
295A LEU* 2.8 20.8 + - + +
296A GLU* 3.6 6.7 - - - +
298A ASP* 1.3 74.5 - - - +
300A ALA* 1.3 58.6 + - - +
302A GLU* 3.0 16.6 + - - -
304A VAL* 3.3 42.4 - - + +
306A PRO* 4.3 15.3 - - + -
309A LEU* 3.8 24.2 - - + -
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Residues in contact with ALA 300 (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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253A GLY* 3.8 18.5 - - - +
255A VAL* 4.1 15.2 - - + +
296A GLU* 2.9 19.7 + - + +
297A LYS* 3.6 7.2 - - - +
299A PHE* 1.3 74.4 - - - +
301A ALA* 1.3 59.0 + - - +
302A GLU* 3.1 11.8 + - - +
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Residues in contact with ALA 301 (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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297A LYS* 2.9 19.4 + - + +
298A ASP* 3.6 10.3 - - - +
300A ALA* 1.3 74.4 - - - +
302A GLU* 1.3 70.4 + - - +
303A VAL* 3.4 15.3 + - + +
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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