Contacts of the helix formed by residues 291 - 299 (chain A) in PDB entry 5XFR
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 GLU 291 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A LEU* 3.9 7.3 - - + +
283A LYS* 3.4 23.2 + - - -
285A TYR 4.5 0.3 - - - +
286A PHE* 3.2 26.1 - - + -
287A ASP* 2.5 43.1 + - + +
290A LEU* 1.3 83.5 - - + +
292A LEU* 1.3 67.0 + - - +
293A MET 3.5 0.2 - - - -
294A THR* 3.6 3.0 + - - -
295A TYR* 3.2 23.0 + - - +
343A LEU* 4.8 2.4 - - - +
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Residues in contact with LEU 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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270A ALA* 4.2 5.2 - - + +
273A CYS* 3.8 14.1 - - + -
274A LEU* 3.8 42.2 - - + +
277A LEU* 3.7 16.3 - - + +
286A PHE* 4.8 2.2 - - + +
287A ASP 2.9 14.2 + - - +
288A SER* 3.5 11.2 - - - +
291A GLU* 1.3 72.0 - - - +
293A MET* 1.3 63.7 + - - +
295A TYR* 3.1 5.7 + - - +
296A ILE* 3.0 34.1 + - + +
320A VAL* 4.1 11.9 - - + -
324A LEU* 3.7 39.7 - - + -
344A PHE* 5.7 1.3 - - + -
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Residues in contact with MET 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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288A SER 3.0 11.8 + - - +
289A GLU* 3.3 18.1 + - + +
291A GLU 3.5 0.2 - - - -
292A LEU* 1.3 79.4 - - - +
294A THR* 1.3 62.3 + - - +
296A ILE* 3.5 20.4 + - + -
297A ASN* 3.1 64.4 + - - +
313A LYS 5.0 0.9 - - - +
316A ARG* 3.6 24.7 - - + -
317A TYR* 3.5 42.4 - - + +
320A VAL* 3.9 17.0 - - + -
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Residues in contact with THR 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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289A GLU 3.7 5.0 + - - -
290A LEU* 2.6 31.0 + - - +
291A GLU* 3.6 4.2 + - - -
292A LEU 3.2 0.6 - - - -
293A MET* 1.3 77.2 - - - +
295A TYR* 1.3 64.3 + - - +
297A ASN* 3.5 4.9 + - - +
298A GLU* 3.1 52.6 + - + +
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Residues in contact with TYR 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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239A LEU* 3.3 16.0 - - + +
273A CYS* 3.7 37.0 - - + -
276A ASN* 3.2 36.5 + - + +
277A LEU* 3.6 28.7 - - + -
280A ILE* 4.5 17.9 - - + +
291A GLU 3.2 11.2 + - - +
292A LEU 3.1 8.6 + - - +
294A THR* 1.3 77.9 - - - +
296A ILE* 1.3 57.3 + - - +
298A GLU* 3.3 7.9 + - - -
299A ASN* 2.8 59.5 + - - +
302A ARG* 3.9 6.3 + - - -
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Residues in contact with ILE 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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269A ILE* 4.0 19.5 - - + +
270A ALA* 4.6 1.8 - - - -
273A CYS* 3.7 27.8 - - + -
292A LEU* 3.0 38.3 + - + +
293A MET* 3.7 20.4 - - + +
295A TYR* 1.3 77.0 - - - +
297A ASN* 1.3 57.8 + - - +
299A ASN 3.3 1.7 + - - -
300A TRP* 2.9 55.7 + - + +
303A LEU* 3.8 3.6 - - + +
320A VAL* 3.9 29.8 - - + -
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Residues in contact with ASN 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 MET* 3.1 50.8 + - - +
294A THR* 3.9 5.2 - - - +
296A ILE* 1.3 76.5 - - - +
298A GLU* 1.3 62.9 + - + +
299A ASN 3.4 0.2 + - - -
300A TRP* 3.5 13.5 + - - +
313A LYS* 3.6 38.6 + - - +
316A ARG* 3.1 29.6 + - - +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A THR* 3.1 40.2 + - + +
295A TYR* 3.8 8.7 - - - +
297A ASN* 1.3 77.4 - - + +
299A ASN* 1.3 68.2 + - - +
300A TRP 3.5 0.6 + - - -
301A ASP 5.4 0.3 + - - -
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Residues in contact with ASN 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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239A LEU* 4.6 6.3 - - + -
295A TYR* 2.8 57.0 + - + +
296A ILE 3.4 3.8 - - - +
298A GLU* 1.3 86.8 + - - +
300A TRP* 1.3 57.1 + - - +
301A ASP 3.4 2.5 - - - -
302A ARG* 3.0 48.3 + - + +
303A LEU* 2.8 34.9 + - + +
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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