Contacts of the helix formed by residues 235 - 245 (chain A) in PDB entry 1YZ3
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 SER 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A LEU* 3.7 4.9 - - - -
218A GLU* 3.5 18.4 - - - -
234A VAL* 1.3 74.3 - - - +
236A GLU* 1.3 58.9 + - - +
237A GLU* 3.6 9.3 + - - +
238A GLU* 3.0 39.6 + - - +
239A VAL* 3.0 30.5 + - - +
51B ASN* 5.4 4.9 + - - -
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Residues in contact with GLU 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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217A LEU* 3.7 14.0 - - + +
235A SER* 1.3 71.4 - - - +
237A GLU* 1.3 66.8 + - - +
239A VAL* 3.1 7.7 + - - +
240A ARG* 2.9 29.3 + - - +
253A LEU* 3.2 38.8 - - + +
254A ARG 4.1 0.2 - - - -
255A THR* 2.6 35.7 + - - +
273A PHE* 5.5 1.3 - - + -
56B TRP* 5.7 0.2 + - - -
236B GLU* 4.5 0.5 - - - +
253B LEU 4.8 2.6 - - - +
254B ARG* 3.3 16.1 - - - +
255B THR* 2.7 43.2 + - - +
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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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235A SER* 3.8 8.4 + - - +
236A GLU* 1.3 79.9 + - - +
238A GLU* 1.3 61.5 + - + +
240A ARG* 3.3 27.8 + - - +
241A GLU* 3.0 45.9 + - - +
51B ASN* 5.5 2.1 - - - +
56B TRP* 3.6 27.2 - - + +
59B ARG* 2.8 48.2 + - - +
60B CYS* 5.7 0.2 - - - -
63B GLN* 4.6 2.9 + - - -
254B ARG* 4.6 8.0 + - - +
255B THR 5.5 0.2 + - - -
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Residues in contact with GLU 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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191A LEU* 4.3 34.1 - - + +
194A PHE* 5.3 1.2 - - - -
218A GLU* 4.7 1.6 - - - +
233A PRO 3.9 5.6 - - - +
234A VAL* 3.5 10.9 - - + +
235A SER* 3.0 44.0 + - - +
237A GLU* 1.3 80.0 - - + +
239A VAL* 1.3 55.2 + - - +
241A GLU* 3.8 12.4 + - - +
242A ALA* 3.1 28.8 + - - +
51B ASN* 4.9 10.1 + - - +
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Residues in contact with VAL 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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194A PHE* 4.7 11.9 - - + -
198A LEU* 5.5 0.2 - - - +
213A LEU* 4.9 5.6 - - + -
234A VAL* 3.8 24.9 - - + -
235A SER 3.0 20.8 + - - +
236A GLU* 3.1 9.6 + - - +
238A GLU* 1.3 72.8 - - - +
240A ARG* 1.3 66.4 + - - +
242A ALA* 3.4 7.2 + - - +
243A LEU* 3.0 36.1 + - + +
253A LEU* 4.6 7.2 - - + -
273A PHE* 3.7 43.5 - - + -
275A ALA* 4.9 0.7 - - + -
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Residues in contact with ARG 240 (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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236A GLU* 2.9 17.0 + - - +
237A GLU* 3.6 33.1 - - - +
239A VAL* 1.3 76.9 - - - +
241A GLU* 1.3 59.2 + - - +
243A LEU* 2.7 32.7 + - - +
244A VAL* 3.0 19.0 + - + +
250A VAL* 3.8 29.2 - - + -
253A LEU* 5.2 11.2 - - + +
56B TRP* 5.4 0.6 - - - +
63B GLN* 4.4 3.0 + - - -
252B ASP* 4.8 4.9 + - - -
254B ARG* 2.9 68.2 - - - +
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Residues in contact with GLU 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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195A GLN* 4.8 0.4 - - - -
237A GLU* 3.0 37.6 + - + +
238A GLU* 3.9 12.8 - - - +
240A ARG* 1.3 81.5 - - + +
242A ALA* 1.3 61.2 - - - +
244A VAL* 3.5 9.3 + - - +
245A ARG* 3.1 24.9 + - - +
63B GLN* 5.3 6.8 + - - -
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Residues in contact with ALA 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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191A LEU* 5.8 4.5 - - + -
194A PHE* 4.1 25.8 - - + -
195A GLN* 3.1 38.7 - - + +
198A LEU* 3.3 13.0 - - + +
238A GLU 3.1 19.8 + - - +
239A VAL 3.5 6.3 - - - +
240A ARG 3.0 0.8 - - - -
241A GLU* 1.3 74.3 - - - +
243A LEU* 1.3 65.6 + - - +
245A ARG 3.6 0.3 + - - -
246A SER* 3.3 7.6 + - - -
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Residues in contact with LEU 243 (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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198A LEU* 3.9 13.5 - - + -
211A LEU* 3.8 28.3 - - + -
213A LEU* 4.6 7.9 - - + -
239A VAL* 3.0 24.0 + - + +
240A ARG* 2.7 17.6 + - - +
242A ALA* 1.3 68.1 - - - +
244A VAL* 1.3 66.1 + - - +
246A SER 3.1 6.9 + - - -
248A TYR* 3.1 39.1 + - + +
250A VAL* 3.7 26.9 - - + -
253A LEU* 4.7 2.2 - - + -
275A ALA* 3.8 27.6 - - + -
277A ALA* 4.1 11.2 - - + -
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Residues in contact with VAL 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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240A ARG* 3.0 17.9 + - + +
241A GLU* 3.7 9.6 - - - +
243A LEU* 1.3 71.0 - - - +
245A ARG* 1.3 55.4 + - - +
246A SER 2.5 4.5 + - - -
247A GLY* 2.5 31.2 + - - -
248A TYR 3.7 16.8 + - - +
250A VAL* 4.9 10.8 - - + +
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Residues in contact with ARG 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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195A GLN* 3.2 31.1 - - - +
199A ASP* 4.0 5.7 - - - +
241A GLU 3.1 10.4 + - - +
244A VAL* 1.3 77.8 - - - +
246A SER* 1.3 58.4 + - - +
247A GLY 3.4 0.2 - - - -
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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