Contacts of the helix formed by residues 293 - 300 (chain A) in PDB entry 3R5J
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 LEU 293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LEU* 4.1 26.0 - - + -
281A GLY* 2.8 35.0 + - - +
282A ALA* 4.1 5.8 - - - +
283A ILE* 4.2 22.7 - - + -
291A LEU 3.5 0.6 + - - -
292A GLN* 1.3 69.6 - - - +
294A GLN* 1.3 66.0 + - - +
296A VAL* 3.1 11.8 + - + +
297A PHE* 2.9 43.3 + - + -
317A ILE* 4.2 20.4 - - + -
321A ARG* 6.3 1.1 - - + +
368B TYR* 4.1 27.6 - - + +
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Residues in contact with GLN 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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281A GLY 4.5 1.0 + - - +
292A GLN* 3.2 5.7 - - + +
293A LEU* 1.3 78.7 - - - +
295A GLU* 1.3 57.1 + - - +
297A PHE* 4.0 14.6 - - - -
298A GLN* 3.0 29.5 + - - +
361B ARG* 2.7 43.3 + - - +
368B TYR* 5.7 0.2 + - - -
372D LYS* 3.9 49.9 - - + +
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Residues in contact with GLU 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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252A GLN* 5.7 5.2 - - + +
291A LEU* 4.4 13.9 - - + -
292A GLN* 3.0 19.8 + - + +
294A GLN* 1.3 76.5 - - - +
296A VAL* 1.3 64.6 + - - +
298A GLN* 3.5 14.3 + - - +
299A LEU* 3.4 25.9 + - - +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 4.0 19.1 - - + -
272A VAL* 5.1 0.4 - - + -
274A LEU* 4.1 19.7 - - + -
291A LEU* 3.7 33.2 - - + -
292A GLN 3.8 9.2 - - - +
293A LEU* 3.1 21.0 + - + +
295A GLU* 1.3 73.8 - - - +
297A PHE* 1.3 71.0 + - + +
299A LEU* 3.0 20.1 + - + +
300A PHE* 3.2 23.7 - - + -
315A PHE* 4.4 17.9 - - + -
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Residues in contact with PHE 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 LEU* 2.9 44.2 + - + +
294A GLN* 4.0 12.1 - - - -
296A VAL* 1.3 78.4 - - + +
298A GLN* 1.3 64.0 + - - +
300A PHE 3.0 11.8 + - - -
301A ASP* 3.3 9.0 + - - +
315A PHE* 3.8 41.3 - + + -
317A ILE* 4.9 7.9 - - + -
361B ARG* 3.6 33.7 - - - +
364B MET* 3.5 18.2 - - - +
366B CYS* 3.6 26.9 - - + -
368B TYR* 3.6 26.5 - + - -
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Residues in contact with GLN 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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294A GLN 3.0 18.1 + - - +
295A GLU* 3.6 14.4 - - - +
296A VAL 3.2 0.2 - - - -
297A PHE* 1.3 78.2 - - - +
299A LEU* 1.3 63.4 + - + +
300A PHE 3.1 1.4 + - - -
301A ASP* 3.1 25.1 + - - +
304A ASN* 3.0 35.5 + - - +
360B THR* 6.2 1.0 - - - +
361B ARG* 3.8 9.2 - - - +
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Residues in contact with LEU 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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252A GLN* 4.0 23.6 - - + +
255A LEU* 3.8 17.0 - - + -
256A GLN* 3.7 51.6 - - + +
259A ALA* 3.6 15.5 - - + +
260A GLN* 4.5 1.6 + - - -
291A LEU* 6.5 0.2 - - + -
295A GLU 3.4 16.8 - - - +
296A VAL* 3.0 15.9 + - + +
298A GLN* 1.3 77.9 - - + +
300A PHE* 1.3 65.8 + - + +
304A ASN* 3.8 15.3 - - + +
305A CYS* 3.5 15.2 - - - +
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Residues in contact with PHE 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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255A LEU* 4.1 21.8 - - + -
258A PHE* 3.8 28.9 - + - -
259A ALA* 3.6 24.2 - - + -
270A CYS* 4.1 6.7 - - - -
272A VAL* 3.7 20.2 - - + -
296A VAL* 3.2 20.9 - - + -
297A PHE 3.0 5.7 + - - +
299A LEU* 1.3 84.6 - - + +
301A ASP* 1.3 66.8 + - - +
305A CYS* 3.7 11.4 - - - +
308A LEU* 4.2 19.0 - - + +
313A LYS* 3.2 27.6 + - + +
315A PHE* 3.8 34.5 - + + -
364B MET* 3.6 5.6 - - + -
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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