Contacts of the helix formed by residues 301 - 305 (chain B) in PDB entry 4ACR
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 THR 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE* 3.8 19.3 - - + -
297B MET 3.3 19.3 - - - +
298B VAL* 2.6 21.7 + - - +
300B ILE* 1.3 75.8 - - - +
302B ASP* 1.3 67.3 + - - +
303B LYS 3.1 0.4 - - - -
304B PHE* 3.1 35.6 + - + +
305B TRP* 3.1 17.4 + - - -
379B VAL* 4.4 18.8 - - + -
382B ALA* 6.3 1.6 - - + -
383B LYS* 3.5 20.3 + - + -
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Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ARG* 2.7 38.4 + - - -
387A ARG 5.2 1.0 - - - +
390A GLN* 2.8 28.8 + - - +
391A ASP* 4.1 27.3 - - + +
298B VAL 4.5 1.2 - - - +
299B LEU* 3.3 26.5 - - - +
300B ILE 3.1 0.6 - - - -
301B THR* 1.3 83.7 + - - +
303B LYS* 1.3 63.7 + - + +
304B PHE 3.2 1.4 + - - -
305B TRP* 3.6 17.7 + - - +
383B LYS* 4.6 0.9 + - - -
471B TYR* 4.3 8.3 + - + +
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ASP* 4.9 10.7 + - - -
395A SER* 6.0 3.0 - - - -
215B ARG 5.8 0.4 - - - +
216B ALA* 5.6 0.9 - - - -
219B ALA* 4.3 14.9 - - + +
300B ILE* 3.1 27.8 + - + +
301B THR 3.1 1.0 - - - -
302B ASP* 1.3 78.6 - - - +
304B PHE* 1.3 65.1 + - - +
305B TRP 3.3 4.0 - - - +
308B SER 4.4 1.7 - - - +
309B GLY* 3.2 16.5 - - - -
310B VAL* 3.4 7.3 + - - +
470B ALA 5.4 1.1 - - - +
471B TYR* 3.6 51.2 + - + +
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Residues in contact with PHE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 4.1 16.2 - + - -
111B PHE* 3.9 14.8 - + - -
219B ALA* 4.5 5.2 - - + -
220B ALA* 4.5 9.2 - - - -
223B PHE* 3.9 27.8 - + + -
300B ILE 3.8 14.4 - - - -
301B THR* 3.1 26.3 + - + +
303B LYS* 1.3 80.0 - - - +
305B TRP* 1.3 68.3 + - + +
306B GLY 4.6 0.3 - - - +
309B GLY* 3.3 4.0 - - - -
310B VAL* 3.2 41.9 + - + +
311B GLU* 3.9 9.4 + - - +
312B SER* 5.1 0.7 + - - -
375B LEU* 3.7 28.2 - - + +
379B VAL* 3.8 28.7 - - + -
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Residues in contact with TRP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ALA 5.9 0.2 - - - +
387A ARG* 3.7 57.1 - - + +
388A ASP* 5.4 1.1 - - - -
390A GLN* 3.5 27.7 + - - +
301B THR* 3.1 24.5 + - - -
302B ASP 3.6 11.8 + - - +
303B LYS* 3.3 5.2 - - - +
304B PHE* 1.3 85.2 - - + +
306B GLY* 1.3 65.7 + - - +
308B SER* 4.3 3.6 + - - -
309B GLY* 3.2 15.1 + - - -
311B GLU* 4.8 6.5 - - - -
375B LEU* 3.5 31.2 - - + -
376B GLU* 3.5 35.2 - - + -
379B VAL* 3.7 31.3 - - + +
383B LYS* 5.7 0.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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