Contacts of the helix formed by residues 292 - 297 (chain A) in PDB entry 4R54
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 GLN 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A GLU* 4.5 2.0 + - - -
288A GLN 5.0 0.6 + - - -
290A TYR* 3.4 19.9 + - + +
291A PRO* 1.3 79.0 - - - +
293A ALA* 1.3 65.9 + - - +
294A ILE* 4.2 5.7 - - - +
295A ASN* 2.9 44.9 + - - +
296A ALA* 3.1 11.8 + - - +
303A PHE* 5.7 0.4 - - - +
322A VAL* 3.9 4.9 - - - +
199B TYR* 3.4 46.3 - - - +
200B PRO* 5.1 0.2 - - - +
204B ASN* 3.1 25.1 + - - +
205B ALA 4.6 4.7 - - - +
206B LEU* 3.4 18.4 - - + +
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Residues in contact with ALA 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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248A VAL* 4.2 12.8 - - + -
250A SER 4.1 4.3 - - - +
251A ALA* 3.4 38.4 - - + +
253A SER* 4.1 12.4 + - - +
292A GLN* 1.3 69.2 - - - +
294A ILE* 1.3 64.0 + - - +
296A ALA 3.1 11.1 + - - -
297A VAL* 3.3 12.4 + - - +
322A VAL* 3.7 11.2 - - - +
203B PHE 4.4 2.2 - - - +
204B ASN* 3.2 11.8 + - - +
205B ALA* 4.5 7.8 + - + +
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Residues in contact with ILE 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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250A SER 5.5 0.2 - - - -
292A GLN* 4.2 7.2 - - - +
293A ALA* 1.3 77.1 - - - +
295A ASN* 1.3 71.4 + - - +
297A VAL* 4.0 18.3 + - - +
182B PRO* 3.6 35.9 - - + +
183B CYS* 3.6 23.3 + - - +
200B PRO* 3.8 33.2 - - + +
202B ALA 3.7 1.6 - - - +
203B PHE 3.3 24.0 - - - +
204B ASN* 3.2 32.2 + - + +
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Residues in contact with ASN 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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282A GLU* 5.7 7.2 - - - +
290A TYR 5.5 1.4 + - - -
292A GLN* 2.9 37.6 + - + +
294A ILE* 1.3 87.1 - - - +
296A ALA* 1.3 62.6 + - - +
297A VAL 3.4 4.1 - - - +
299A SER* 5.2 2.6 - - - -
303A PHE* 4.9 5.2 - - - -
183B CYS* 3.9 17.5 - - - +
199B TYR* 5.9 1.6 - - - -
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Residues in contact with ALA 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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251A ALA* 4.3 5.6 - - + -
292A GLN 3.1 4.2 + - - +
293A ALA 3.1 9.5 + - - +
295A ASN* 1.3 76.6 - - - +
297A VAL* 1.3 66.8 - - - +
298A GLY 3.2 0.3 + - - -
299A SER* 3.0 24.7 + - - +
301A ASP 5.4 0.2 - - - +
303A PHE* 3.9 27.0 - - + -
322A VAL* 3.6 27.6 - - + -
323A SER* 4.5 0.2 - - - -
324A ASP* 3.9 11.6 - - - +
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Residues in contact with VAL 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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250A SER* 3.4 43.7 - - - +
251A ALA* 4.0 1.8 - - + -
293A ALA 3.5 10.5 - - - +
294A ILE* 4.1 13.4 - - - +
295A ASN 3.4 6.0 - - - +
296A ALA* 1.3 78.1 - - - +
298A GLY* 1.3 61.9 + - - +
299A SER* 3.6 0.5 + - - -
324A ASP* 3.6 11.0 - - - +
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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