Contacts of the helix formed by residues 269 - 276 (chain A) in PDB entry 4RG1
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 CYS 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A PHE* 4.4 5.4 - - - -
116A ASP 3.5 13.9 - - - +
118A GLU 6.2 0.4 - - - +
267A ALA* 3.2 3.3 - - - +
268A SER* 1.3 90.3 - - - +
270A LEU* 1.3 66.0 + - - +
271A SER* 3.4 12.3 - - - -
272A ALA* 3.2 19.6 + - - +
273A VAL* 3.4 12.3 + - - +
324A ASP* 3.2 29.8 - - + +
326A ASN* 5.1 4.5 - - - -
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Residues in contact with LEU 270 (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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115A PHE* 4.1 30.1 - - + -
116A ASP 4.4 1.0 + - - -
269A CYS* 1.3 73.6 - - - +
271A SER* 1.3 63.4 + - - +
273A VAL* 3.1 29.7 + - + +
274A PHE* 3.5 19.4 - - + -
310A VAL* 4.3 16.6 - - + -
317A LEU* 4.4 14.6 - - + +
320A GLY* 3.9 15.5 + - - +
321A ALA* 3.7 22.7 - - + +
324A ASP* 3.6 2.6 + - - +
327A LEU* 3.8 11.9 - - + -
335A LEU* 3.8 24.9 - - + -
336A PHE* 5.1 2.7 - - + -
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Residues in contact with SER 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A CYS* 3.4 7.3 - - - -
270A LEU* 1.3 71.6 - - - +
272A ALA* 1.3 56.8 + - - +
274A PHE* 3.1 11.4 + - - +
275A ALA* 2.8 29.9 + - - +
324A ASP* 2.5 32.5 + - - -
326A ASN* 3.4 25.0 + - - +
327A LEU* 3.5 27.6 - - - +
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ARG* 3.0 12.5 + - - -
267A ALA* 4.0 10.1 - - + -
268A SER* 4.0 10.1 - - - +
269A CYS* 3.2 24.4 + - - +
271A SER* 1.3 76.8 + - - +
273A VAL* 1.3 64.7 + - - +
275A ALA* 4.1 9.2 - - - +
276A GLU* 3.0 43.8 + - - +
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ALA* 3.8 22.2 - - + -
113A VAL* 4.1 9.6 - - + -
115A PHE* 3.6 42.4 - - + -
265A ARG* 2.8 29.4 + - - +
267A ALA* 3.9 5.4 - - + -
269A CYS 3.4 1.8 + - - +
270A LEU* 3.1 21.3 + - + +
272A ALA* 1.3 76.9 - - - +
274A PHE* 1.3 64.1 + - + +
283A TYR* 3.4 6.9 - - - -
308A LEU* 3.8 23.1 - - + -
310A VAL* 4.8 3.8 - - + -
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 3.5 33.0 - - + -
271A SER* 3.1 11.8 + - - +
273A VAL* 1.3 80.9 - - + +
275A ALA* 1.3 66.2 + - - +
276A GLU 3.4 0.2 + - - -
277A ALA* 3.6 15.1 + - - +
282A GLY* 5.4 2.8 - - - -
283A TYR* 4.5 8.3 + + - -
286A THR* 4.0 28.5 - - + -
308A LEU* 4.1 12.6 - - + -
310A VAL* 5.1 0.9 - - + -
327A LEU* 4.9 9.2 - - + -
335A LEU* 3.5 35.0 - - + -
336A PHE* 3.7 26.2 - + - -
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Residues in contact with ALA 275 (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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271A SER* 2.8 21.3 + - - +
272A ALA* 3.5 6.5 + - - -
274A PHE* 1.3 75.6 - - - +
276A GLU* 1.3 63.4 + - + +
277A ALA* 3.4 3.9 + - - +
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Residues in contact with GLU 276 (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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265A ARG* 3.2 29.6 + - - +
266A LEU 4.5 11.8 - - - +
267A ALA* 4.8 1.2 - - - -
268A SER* 5.2 2.9 + - - -
272A ALA* 3.0 36.6 + - + +
275A ALA* 1.3 81.0 - - + +
277A ALA* 1.3 65.3 + - - +
278A PRO* 3.5 0.5 - - - +
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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