Contacts of the helix formed by residues 271 - 275 (chain A) in PDB entry 2CXO
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 GLY 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A HIS* 5.5 1.6 + - - -
211A LYS* 4.1 5.6 - - - -
268A ASP 4.8 0.4 + - - -
269A TRP 3.8 4.8 + - - -
270A VAL* 1.3 75.0 - - - +
272A GLY* 1.3 67.2 + - - -
273A ARG* 3.2 5.4 - - - -
274A TYR* 2.9 30.9 + - - +
275A SER* 3.1 10.9 + - - -
510A PHE* 5.6 5.8 - - - -
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Residues in contact with GLY 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY* 3.1 17.9 - - - +
160A SER* 5.8 1.3 - - - -
211A LYS* 4.8 10.6 - - - +
266A PHE* 5.9 1.1 - - - -
270A VAL 3.7 2.0 + - - -
271A GLY* 1.3 71.0 - - - -
273A ARG* 1.3 58.7 + - - +
274A TYR 3.1 3.5 + - - -
275A SER* 2.5 30.2 + - - -
276A LEU 4.8 0.2 + - - -
512A GLN* 5.8 1.0 + - - -
1601A DER 4.0 21.6 + - - -
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Residues in contact with ARG 273 (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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159A GLY* 4.0 6.4 - - - -
271A GLY* 5.1 1.7 - - - -
272A GLY* 1.3 76.0 - - - +
274A TYR* 1.3 80.5 + - + +
275A SER 3.6 0.7 - - - -
351A TYR* 3.2 25.5 + - + -
354A GLN* 3.9 16.9 - - + +
355A GLY* 3.9 14.8 - - - -
358A GLU* 3.1 58.5 + - - +
359A SER* 2.9 23.5 + - - +
495A GLU* 4.6 0.3 - - - +
509A SER 2.8 23.2 + - - -
510A PHE* 3.4 13.1 - - - +
511A ASP 2.9 21.2 + - - -
512A GLN* 2.7 20.4 + - - +
1601A DER 4.4 3.4 + - - -
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Residues in contact with TYR 274 (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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100A HIS* 3.5 42.9 - + + +
103A LEU* 4.1 0.5 - - - +
270A VAL* 4.0 5.2 - - - +
271A GLY* 2.9 21.6 + - - +
273A ARG* 1.3 107.3 - - + +
275A SER* 1.3 56.0 + - - +
276A LEU 3.7 2.0 - - - -
277A TRP* 3.3 20.5 - - - -
351A TYR* 4.7 1.3 - - - -
355A GLY* 4.1 3.8 + - - -
359A SER* 2.7 23.0 + - - -
495A GLU* 3.6 49.1 + - + +
498A ILE* 3.6 18.8 - - + +
509A SER* 4.8 0.2 - - - -
510A PHE* 3.6 36.3 - + - -
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY 3.1 14.6 + - - -
160A SER* 5.2 0.2 + - - -
266A PHE* 4.6 3.6 - - - -
270A VAL* 3.6 17.9 - - - -
271A GLY 3.3 9.6 - - - -
272A GLY* 2.5 27.1 + - - -
273A ARG 3.6 1.2 - - - -
274A TYR* 1.3 75.5 - - - +
276A LEU* 1.3 62.1 + - - +
277A TRP 3.0 5.6 - - - -
278A SER* 2.7 25.7 + - - -
280A ILE* 3.3 24.6 - - - +
351A TYR* 5.2 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
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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