Contacts of the helix formed by residues 217 - 223 (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 ALA 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B TYR 3.5 3.2 + - - -
216B ALA* 1.3 76.5 - - - +
218B PRO* 1.3 74.1 - - + +
219B GLU* 3.0 26.5 + - - +
220B LEU* 3.1 17.8 + - - +
221B PHE* 4.2 1.4 - - - -
226B TYR* 3.1 19.8 + - + +
231B VAL* 4.6 4.7 - - - +
234B TRP* 3.4 26.0 - - + -
262B VAL* 4.2 0.4 - - - -
292B ARG* 3.8 3.4 - - - +
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Residues in contact with PRO 218 (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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216B ALA 3.7 0.4 - - - -
217B ALA* 1.3 88.1 - - + +
219B GLU* 1.3 60.0 + - + +
221B PHE* 2.7 32.4 + - + +
222B GLN* 3.4 15.3 + - - +
234B TRP* 3.6 28.3 - - + -
262B VAL* 3.7 14.8 - - + -
263B LEU* 3.8 19.4 - - + +
287B LEU* 3.9 41.5 - - + +
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Residues in contact with GLU 219 (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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217B ALA* 3.0 14.0 + - - +
218B PRO* 1.3 81.2 - - + +
220B LEU* 1.3 63.9 + - - +
222B GLN* 3.0 16.6 + - - +
224B LYS* 3.4 23.3 + - + -
225B LYS 3.5 24.2 - - - +
226B TYR* 4.1 5.4 - - + -
230B GLU* 4.4 1.9 - - - +
231B VAL* 3.9 15.3 - - - +
289B PRO* 3.4 30.2 - - + +
292B ARG* 2.6 42.0 + - - -
259C ARG* 3.2 12.4 + - - -
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Residues in contact with LEU 220 (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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216B ALA* 3.9 13.7 - - + -
217B ALA 3.1 14.2 + - - +
219B GLU* 1.3 77.1 - - - +
221B PHE* 1.3 71.5 + - + +
222B GLN 3.5 0.2 + - - -
226B TYR* 3.5 23.0 - - + -
221C PHE* 3.6 22.7 - - + +
255C LEU* 3.6 56.5 - - + +
256C LYS* 4.5 2.9 - - - -
259C ARG* 3.1 49.8 + - + +
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Residues in contact with PHE 221 (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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213B PRO* 4.6 4.0 - - + -
216B ALA* 3.9 28.3 - - + -
217B ALA 4.2 4.7 - - - -
218B PRO 2.7 19.4 + - - +
220B LEU* 1.3 86.3 - - + +
222B GLN* 1.3 59.3 + - - +
223B GLY 3.6 0.7 - - - -
255B LEU* 5.1 6.5 - - + -
258B LEU* 4.6 17.7 - - + -
259B ARG* 3.7 41.2 - - + -
262B VAL* 4.2 28.9 - - + -
263B LEU* 4.1 7.2 - - + +
220C LEU* 3.5 35.3 - - + +
221C PHE* 4.0 3.8 - + - -
223C GLY* 2.9 27.5 + - - -
255C LEU* 5.8 0.2 - - + -
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Residues in contact with GLN 222 (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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218B PRO* 3.4 15.1 + - - +
219B GLU* 3.0 8.1 + - - +
221B PHE* 1.3 83.3 - - - +
223B GLY* 1.3 57.7 + - - +
224B LYS* 3.1 33.1 + - + +
263B LEU* 3.6 36.1 + - + +
221C PHE 3.8 1.3 - - - -
222C GLN 4.3 9.5 - - - +
223C GLY* 4.2 8.5 - - - +
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Residues in contact with GLY 223 (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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219B GLU 3.5 2.6 + - - -
222B GLN* 1.3 76.4 - - - +
224B LYS* 1.3 68.1 + - - +
221C PHE 2.9 21.8 + - - -
222C GLN* 4.6 4.9 - - - -
259C ARG* 3.5 11.0 + - - +
263C LEU* 5.4 5.8 - - - +
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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