Contacts of the helix formed by residues 234 - 245 (chain A) in PDB entry 2YZ5
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 ALA 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A THR* 4.6 0.2 - - - -
195A LEU* 3.8 13.7 - - + -
232A GLY 3.2 2.2 + - - -
233A PHE* 1.3 98.2 - - + +
235A PHE* 1.3 59.2 + - - +
236A PRO* 3.3 7.8 - - - +
237A GLU* 3.2 25.7 + - - +
238A VAL* 2.9 29.5 + - + +
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Residues in contact with PHE 235 (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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1A MET 5.0 1.6 - - - -
2A VAL 3.6 10.1 - - - -
3A ASP* 3.5 48.7 - - + -
30A LEU* 4.0 18.6 - - + -
192A THR* 4.0 4.3 - - + -
221A LEU* 3.6 35.4 - - + -
222A GLY* 3.8 6.1 - - - -
223A SER* 3.8 15.0 - - - -
232A GLY* 3.2 26.2 + - - +
233A PHE 3.0 16.6 + - - -
234A ALA* 1.3 76.2 - - - +
236A PRO* 1.3 72.8 - - + +
238A VAL* 4.5 1.6 - - - +
239A GLN* 2.9 42.5 + - - +
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Residues in contact with PRO 236 (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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28A LYS* 6.2 2.9 - - + -
232A GLY 4.5 2.9 - - - +
234A ALA* 3.5 6.5 - - - +
235A PHE* 1.3 94.7 - - + +
237A GLU* 1.3 60.4 + - - +
239A GLN* 3.5 6.9 + - + +
240A ALA* 3.1 23.9 + - - +
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Residues in contact with GLU 237 (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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195A LEU* 3.6 29.7 - - - +
202A VAL* 5.7 0.3 - - - +
234A ALA* 3.2 23.3 + - + +
236A PRO* 1.3 79.4 - - - +
238A VAL* 1.3 58.3 + - - +
240A ALA* 3.2 8.6 + - - +
241A LEU* 3.0 26.4 + - + +
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Residues in contact with VAL 238 (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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190A VAL* 3.7 17.9 - - + -
192A THR* 3.5 20.9 - - + -
195A LEU* 4.2 9.2 - - + -
202A VAL* 3.6 26.0 - - + -
221A LEU* 3.6 28.7 - - + -
234A ALA 2.9 17.9 + - - +
235A PHE 4.0 2.2 - - - +
237A GLU* 1.3 75.1 - - + +
239A GLN* 1.3 60.6 + - - +
241A LEU* 3.1 8.9 + - + +
242A LEU* 2.8 39.4 + - + +
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Residues in contact with GLN 239 (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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1A MET 3.8 20.9 + - - +
30A LEU* 5.6 0.5 - - - +
221A LEU* 3.7 24.0 - - + +
235A PHE* 2.9 41.2 + - - +
236A PRO* 4.0 5.5 - - + +
238A VAL* 1.3 72.3 - - - +
240A ALA* 1.3 58.3 + - - +
242A LEU* 3.8 5.4 - - - +
243A ALA* 3.0 29.6 + - - +
261A TYR* 4.6 7.2 + - - -
262A PRO 5.3 1.0 + - - -
263A LEU* 3.9 40.0 - - + +
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A PRO 3.1 14.3 + - - +
237A GLU* 3.4 12.1 - - - +
239A GLN* 1.3 74.7 - - - +
241A LEU* 1.3 65.3 + - - +
243A ALA* 3.4 5.3 + - - +
244A GLY* 2.9 20.8 + - - -
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Residues in contact with LEU 241 (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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202A VAL* 4.0 32.3 - - + -
206A PRO* 4.4 22.4 - - + -
209A LEU* 4.8 6.3 - - + -
237A GLU* 3.0 13.7 + - + +
238A VAL* 3.4 13.7 - - + +
240A ALA* 1.3 75.9 - - - +
242A LEU* 1.3 58.9 + - + +
244A GLY* 3.0 3.9 + - - -
245A LEU* 2.9 48.6 + - + +
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Residues in contact with LEU 242 (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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190A VAL* 4.2 13.9 - - + -
209A LEU* 3.7 26.7 - - + -
219A LEU* 3.6 33.0 - - + -
221A LEU* 4.8 8.7 - - + -
238A VAL* 2.8 35.9 + - + +
239A GLN* 3.8 7.6 - - - +
241A LEU* 1.3 75.7 - - + +
243A ALA* 1.3 66.4 + - - +
245A LEU* 2.9 16.0 + - + +
247A PHE* 3.1 28.1 + - + +
250A ALA* 5.6 3.8 - - + -
263A LEU* 3.8 21.1 - - + -
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A GLN 3.0 18.5 + - - +
240A ALA* 4.0 4.7 - - - +
242A LEU* 1.3 76.9 - - - +
244A GLY* 1.3 61.5 + - - +
246A GLY 3.2 3.8 + - - -
247A PHE 3.2 17.5 - - - +
248A ARG* 2.9 27.5 + - - +
263A LEU* 4.1 18.3 - - + +
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Residues in contact with GLY 244 (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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210A ARG* 5.3 3.5 + - - -
240A ALA 2.9 15.5 + - - -
241A LEU* 3.4 6.3 - - - -
242A LEU 3.0 0.2 - - - -
243A ALA* 1.3 79.4 - - - +
245A LEU* 1.3 60.2 + - - +
246A GLY 3.1 1.2 + - - -
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Residues in contact with LEU 245 (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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206A PRO* 4.0 15.3 - - + +
209A LEU* 3.7 40.4 - - + -
210A ARG* 3.3 48.4 + - + +
213A ARG* 2.9 32.7 + - - +
241A LEU* 2.9 33.2 + - + +
242A LEU* 2.9 12.1 + - + +
244A GLY* 1.3 77.2 - - - +
246A GLY* 1.3 58.7 + - - +
247A PHE* 3.6 12.1 - - + -
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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