Contacts of the helix formed by residues 212 - 216 (chain A) in PDB entry 2WZJ
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 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ASP* 2.6 29.9 + - - -
177A LYS* 3.1 18.7 + - - -
209A PHE* 3.6 19.6 + - - +
210A CYS 3.1 1.8 + - - -
211A GLY* 1.3 77.2 - - - +
213A PRO* 1.3 75.5 - - - +
215A TYR* 3.1 16.1 + - - +
216A ALA* 3.5 8.3 + - - +
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Residues in contact with PRO 213 (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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209A PHE* 3.8 11.9 - - + +
211A GLY 3.6 2.9 - - - +
212A SER* 1.3 93.2 - - - +
214A PRO* 1.3 65.9 - - + +
215A TYR 3.0 5.7 + - - -
216A ALA* 3.0 23.9 + - + +
220A LEU* 6.0 1.3 - - + -
221A PHE* 4.5 7.3 - - + -
255A LEU* 3.7 23.6 - - + -
258A LEU* 3.6 25.2 - - + +
262A VAL* 5.3 0.9 - - - +
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Residues in contact with PRO 214 (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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211A GLY* 3.2 20.4 - - - +
213A PRO* 1.3 99.0 - - + +
215A TYR* 1.3 62.1 + - + +
216A ALA 3.5 1.9 - - - +
234A TRP* 5.2 0.3 + - - -
238A VAL* 3.3 18.2 - - - +
248A LEU* 3.5 41.5 - - + -
249A PRO* 5.5 0.3 - - - +
250A PHE* 4.3 17.9 - - - +
258A LEU* 3.9 17.9 - - + -
262A VAL* 5.4 2.2 - - - +
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Residues in contact with TYR 215 (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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138A PHE* 5.6 0.9 - - - -
176A LEU 3.3 20.4 - - - +
177A LYS* 3.6 14.1 - - + -
178A ALA* 3.2 30.0 - - - +
179A GLU* 4.5 3.1 + - - -
211A GLY* 2.9 31.9 - - - -
212A SER 3.1 5.5 + - - +
213A PRO 3.1 0.8 - - - -
214A PRO* 1.3 86.1 - - + +
216A ALA* 1.3 62.3 + - - +
234A TRP* 3.4 11.0 - - - -
235A SER* 2.5 30.3 + - - +
238A VAL* 3.4 31.0 - - + -
239A ILE* 3.7 34.1 - - + -
242A THR* 4.0 15.7 + - + +
248A LEU* 4.3 8.3 - - + +
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Residues in contact with ALA 216 (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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212A SER 3.5 7.3 + - - +
213A PRO* 3.0 18.1 + - + +
214A PRO 3.5 0.9 - - - +
215A TYR* 1.3 77.0 - - - +
217A ALA* 1.3 64.6 + - - +
218A PRO 3.8 0.2 - - - -
220A LEU* 3.6 31.4 - - + -
221A PHE* 4.1 9.9 - - + -
226A TYR* 3.5 10.3 - - - +
234A TRP* 3.3 10.2 + - - -
262A VAL* 4.0 13.7 - - - +
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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