Contacts of the helix formed by residues 292 - 297 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A TYR* 3.4 46.1 - - - +
200A PRO* 5.0 0.3 - - - +
204A ASN* 2.9 25.4 + - - +
205A ALA 4.5 4.5 - - - +
206A LEU* 3.4 19.6 - - + +
282B GLU* 4.6 1.4 + - - -
288B GLN 5.1 0.2 + - - -
290B TYR* 3.5 17.6 + - + +
291B PRO* 1.3 80.0 - - - +
293B ALA* 1.3 67.5 + - - +
294B ILE* 4.1 9.2 - - - +
295B ASN* 3.0 37.4 + - - +
296B ALA* 3.2 11.4 + - - +
303B PHE* 5.7 0.4 - - - +
322B VAL* 3.9 6.0 - - - +
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Residues in contact with ALA 293 (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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203A PHE 4.4 2.2 - - - +
204A ASN* 3.2 11.6 + - - +
205A ALA* 4.4 8.3 + - + +
248B VAL* 4.1 17.5 - - + -
250B SER 4.5 0.4 - - - -
251B ALA* 3.4 38.2 - - + +
253B SER* 4.1 14.1 + - - +
292B GLN* 1.3 69.2 - - - +
294B ILE* 1.3 64.2 + - - +
296B ALA 3.1 11.4 + - - -
297B VAL* 3.4 12.2 + - - +
322B VAL* 3.8 9.4 - - - +
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Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PRO* 3.8 28.3 - - + +
183A CYS* 4.0 20.1 - - - +
200A PRO* 3.8 33.7 - - + -
202A ALA 3.8 5.8 - - - +
203A PHE* 3.1 27.1 - - + +
204A ASN* 3.1 33.5 + - + +
250B SER 5.5 0.2 - - - -
292B GLN* 4.1 6.3 - - - +
293B ALA* 1.3 76.4 - - - +
295B ASN* 1.3 72.2 + - - +
296B ALA 3.6 0.3 + - - -
297B VAL* 3.9 17.6 + - - +
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Residues in contact with ASN 295 (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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183A CYS* 4.2 11.8 - - - +
199A TYR* 6.0 1.2 - - - -
282B GLU* 5.6 6.5 - - - +
290B TYR 5.5 1.6 + - - -
292B GLN* 3.0 39.9 + - + +
294B ILE* 1.3 87.8 - - - +
296B ALA* 1.3 62.1 + - - +
297B VAL 3.4 5.2 + - - +
299B SER* 5.2 2.8 - - - -
303B PHE* 5.1 4.1 - - - -
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ALA* 4.3 5.4 - - + -
292B GLN 3.2 4.0 + - - +
293B ALA 3.1 9.5 + - - +
295B ASN* 1.3 75.1 - - - +
297B VAL* 1.3 66.5 + - - +
298B GLY 3.3 0.3 + - - -
299B SER* 3.0 26.0 + - - +
303B PHE* 3.9 26.4 - - + -
322B VAL* 3.6 26.7 - - + -
323B SER* 4.4 0.4 - - - -
324B ASP* 3.9 12.1 - - - +
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Residues in contact with VAL 297 (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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250B SER* 3.5 37.9 - - - +
251B ALA* 4.1 1.3 - - + -
293B ALA 3.5 16.4 - - - +
294B ILE* 4.1 13.4 - - - +
295B ASN 3.4 6.4 - - - +
296B ALA* 1.3 77.9 - - - +
298B GLY* 1.3 63.0 + - - +
299B SER* 3.6 0.7 + - - -
324B ASP* 3.5 11.9 - - - +
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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