Contacts of the helix formed by residues 212 - 216 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ASP* 2.8 28.4 + - - +
177B LYS* 3.0 21.7 + - - +
199B GLU* 4.9 0.3 + - - -
209B PHE* 3.2 16.2 + - - +
210B CYS 3.3 1.4 + - - -
211B GLY* 1.3 77.4 - - - +
213B PRO* 1.3 70.1 - - - +
215B TYR* 3.3 15.4 + - - +
216B ALA* 3.7 6.2 + - - +
255C LEU* 3.8 26.4 - - - +
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Residues in contact with PRO 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE 3.6 9.4 - - - +
211B GLY 3.3 4.5 - - - -
212B SER* 1.3 95.2 - - - +
214B PRO* 1.3 68.3 - - + +
215B TYR 3.0 1.8 + - - -
216B ALA* 3.1 18.1 + - + +
221B PHE* 4.6 4.3 - - + -
255B LEU* 3.9 11.4 - - + -
258B LEU* 3.6 25.9 - - + +
262B VAL* 5.2 0.9 - - - +
208C GLU 4.1 6.1 - - - +
209C PHE* 3.9 13.7 - - + -
213C PRO* 3.7 27.6 - - + -
255C LEU* 3.9 13.5 - - + -
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Residues in contact with PRO 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLY 3.1 16.2 - - - +
213B PRO* 1.3 97.4 - - + +
215B TYR* 1.3 62.2 + - + +
216B ALA 3.4 2.2 + - - +
234B TRP* 5.1 0.2 + - - -
238B VAL* 3.7 16.7 - - - +
248B LEU* 3.6 35.4 - - + -
249B PRO* 5.4 0.7 - - - +
250B PHE* 4.4 16.9 - - - +
258B LEU* 3.9 13.2 - - + -
262B VAL* 4.9 2.5 - - - +
207C ASP 3.5 23.6 - - - +
209C PHE* 3.9 14.4 - - + -
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Residues in contact with TYR 215 (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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138B PHE* 5.6 1.6 - - - -
176B LEU 3.5 23.6 - - - +
177B LYS* 3.4 20.2 - - + -
178B ALA* 3.2 31.4 + - + +
179B GLU* 4.3 4.2 + - - -
211B GLY* 3.0 29.4 - - - -
212B SER* 3.8 7.0 - - - +
213B PRO 3.0 1.4 - - - -
214B PRO* 1.3 89.8 - - + +
216B ALA* 1.3 62.8 + - - +
217B ALA 3.5 0.7 + - - -
226B TYR* 4.2 0.4 + - - -
234B TRP* 3.5 7.5 - - - -
235B SER* 3.0 26.5 + - - +
238B VAL* 3.6 27.8 - - + -
239B ILE* 3.8 22.9 - - + -
242B THR* 4.3 10.2 + - + +
248B LEU* 4.3 10.6 - - + +
206C LEU* 5.1 3.1 - - - +
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Residues in contact with ALA 216 (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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212B SER 3.7 1.9 + - - +
213B PRO 3.1 15.0 + - - +
214B PRO 3.4 0.4 - - - -
215B TYR* 1.3 77.8 - - - +
217B ALA* 1.3 65.3 + - - +
220B LEU* 3.9 28.5 - - + -
221B PHE* 3.9 11.9 - - + -
226B TYR* 3.4 10.3 - - - +
234B TRP* 3.4 10.4 + - - -
262B VAL* 3.5 17.7 - - - +
255C LEU* 4.3 9.9 - - + -
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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