Contacts of the helix formed by residues 269 - 276 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PHE* 4.3 4.5 - - - -
116B ASP 3.4 13.0 - - - -
119B GLY* 4.3 12.6 - - - -
267B ALA* 3.2 4.8 + - - +
268B SER* 1.3 90.2 - - - +
270B LEU* 1.3 67.4 + - - +
271B SER* 3.3 24.2 - - - -
272B ALA* 3.2 24.5 + - - +
273B VAL* 3.5 8.3 + - - +
324B ASP* 3.5 18.6 - - + +
325B PRO* 5.7 1.1 - - + -
326B ASN* 4.6 7.0 - - - -
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE* 4.1 28.7 - - + -
116B ASP 4.3 1.2 + - - -
269B CYS* 1.3 74.2 - - - +
271B SER* 1.3 62.2 + - - +
273B VAL* 3.0 30.7 + - + +
274B PHE* 3.5 23.7 - - + -
310B VAL* 4.2 18.4 - - + -
317B LEU* 4.3 15.3 - - + +
320B GLY* 4.0 16.9 + - - +
321B ALA* 3.6 30.3 - - + +
324B ASP* 3.7 2.4 + - - +
327B LEU* 4.2 6.7 - - + -
335B LEU* 3.9 18.6 - - + -
336B PHE* 5.2 2.0 - - + -
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Residues in contact with SER 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B CYS* 3.3 9.5 - - - -
270B LEU* 1.3 74.3 - - - +
272B ALA* 1.3 58.6 + - - +
274B PHE* 3.1 16.0 + - - +
275B ALA* 2.9 28.9 + - - +
324B ASP* 2.6 33.9 + - - -
326B ASN* 3.5 18.4 + - - +
327B LEU* 4.0 21.9 - - - +
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ARG* 3.0 11.8 + - - -
267B ALA* 4.0 9.2 - - + -
268B SER* 4.0 9.4 - - - +
269B CYS* 3.2 24.3 + - - +
271B SER* 1.3 76.6 + - - +
273B VAL* 1.3 65.6 + - - +
274B PHE 3.2 0.2 - - - -
275B ALA* 3.7 9.2 - - - +
276B GLU* 2.9 45.1 + - - +
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA* 3.7 22.9 - - + -
113B VAL* 4.1 9.2 - - + -
115B PHE* 3.6 42.8 - - + -
265B ARG* 2.7 30.8 + - - +
267B ALA* 4.0 4.7 - - + +
269B CYS 3.8 1.3 - - - +
270B LEU* 3.0 21.5 + - + +
272B ALA* 1.3 77.2 - - - +
274B PHE* 1.3 62.9 + - + +
283B TYR* 3.4 6.9 - - - -
308B LEU* 3.8 23.3 - - + -
310B VAL* 4.7 4.3 - - + -
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Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 3.5 35.7 - - + -
271B SER* 3.1 11.5 + - - +
273B VAL* 1.3 79.8 - - + +
275B ALA* 1.3 65.5 + - + +
276B GLU 3.4 0.7 + - - -
277B ALA* 3.5 16.5 + - - +
282B GLY* 5.3 2.9 - - - -
283B TYR* 4.5 7.8 + + - -
286B THR* 4.1 24.9 - - + -
308B LEU* 4.2 11.4 - - + -
310B VAL* 4.8 2.9 - - + -
327B LEU* 5.7 2.2 - - + -
335B LEU* 3.6 35.4 - - + -
336B PHE* 3.6 33.0 - + - -
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Residues in contact with ALA 275 (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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271B SER* 2.9 17.5 + - - +
272B ALA* 4.3 6.3 - - - -
274B PHE* 1.3 79.6 - - + +
276B GLU* 1.3 62.2 + - + +
277B ALA* 3.4 3.5 + - - +
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Residues in contact with GLU 276 (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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265B ARG* 3.2 29.6 + - - +
266B LEU 4.5 11.6 - - - +
267B ALA* 4.8 1.2 - - - -
268B SER* 5.1 3.3 + - - -
272B ALA* 2.9 34.1 + - + +
275B ALA* 1.3 81.4 - - + +
277B ALA* 1.3 67.7 + - - +
278B PRO* 3.4 1.0 - - - +
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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
------------------------------------------------------------
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