Contacts of the helix formed by residues 217 - 223 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215C TYR 3.5 1.8 + - - -
216C ALA* 1.3 74.2 - - - +
218C PRO* 1.3 75.2 - - + +
219C GLU* 3.1 24.7 - - - +
220C LEU* 2.8 22.2 + - - +
221C PHE* 4.2 1.6 - - - -
226C TYR* 3.0 19.5 + - + +
231C VAL* 4.4 6.7 - - - +
234C TRP* 3.5 24.9 - - + -
262C VAL* 4.7 0.7 - - - -
292C ARG* 4.0 0.7 - - - +
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Residues in contact with PRO 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ALA 3.9 0.2 - - - -
217C ALA* 1.3 89.1 - - + +
219C GLU* 1.3 70.9 + - - +
221C PHE* 2.8 19.2 + - + +
222C GLN* 3.4 21.6 + - - +
234C TRP* 3.6 41.1 - - + -
262C VAL* 4.1 15.5 - - + -
263C LEU* 4.0 17.7 - - + -
287C LEU* 4.0 28.5 - - + +
289C PRO* 6.1 0.2 - - + -
292C ARG* 4.5 0.2 - - - +
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Residues in contact with GLU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B ARG* 3.2 3.6 + - - -
217C ALA* 2.9 5.3 + - - +
218C PRO* 1.3 88.4 - - - +
220C LEU* 1.3 62.2 + - - +
222C GLN* 3.2 10.2 + - - +
224C LYS* 3.1 38.4 + - + -
225C LYS 3.5 24.5 - - - +
226C TYR* 4.1 6.5 - - + -
230C GLU* 4.5 1.7 - - - +
231C VAL* 3.5 19.8 + - - +
289C PRO* 3.5 29.0 - - + +
292C ARG* 2.7 35.4 + - - -
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Residues in contact with LEU 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B PHE* 3.5 26.6 - - + +
255B LEU* 3.9 44.0 - - + +
256B LYS* 4.4 3.4 - - - +
259B ARG* 3.1 42.6 + - + +
216C ALA* 3.5 24.9 - - + -
217C ALA 2.8 14.7 + - - +
218C PRO 2.8 0.4 + - - -
219C GLU* 1.3 78.8 - - - +
221C PHE* 1.3 74.0 + - + +
222C GLN 3.5 0.3 + - - -
226C TYR* 3.5 23.4 - - + -
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Residues in contact with PHE 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B LEU* 3.6 34.4 - - + +
221B PHE* 3.9 4.7 - + - -
223B GLY* 2.9 28.5 + - - -
255B LEU* 6.0 0.2 - - + -
213C PRO* 4.7 10.8 - - + -
216C ALA* 4.0 24.0 - - + -
217C ALA 4.2 3.4 - - - -
218C PRO 2.8 11.5 + - - +
220C LEU* 1.3 95.1 - - + +
222C GLN* 1.3 61.9 + - - +
223C GLY 3.5 1.3 - - - -
255C LEU* 4.8 3.8 - - + -
258C LEU* 4.9 10.1 - - + -
259C ARG* 3.4 48.3 - - + -
262C VAL* 4.3 27.4 - - + -
263C LEU* 4.3 7.1 - - + +
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Residues in contact with GLN 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B PHE 3.8 2.0 - - - -
222B GLN* 4.3 10.3 - - - +
223B GLY* 4.2 6.1 - - - +
218C PRO* 3.8 21.4 - - - +
219C GLU* 3.2 12.1 + - - +
221C PHE* 1.3 82.4 - - - +
223C GLY* 1.3 64.7 + - - +
224C LYS* 3.1 26.9 + - + +
263C LEU* 3.2 33.1 + - + +
287C LEU* 5.7 2.1 - - - +
289C PRO* 5.8 3.1 - - - +
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Residues in contact with GLY 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B PHE 2.9 21.2 + - - -
222B GLN* 4.5 8.1 - - - -
259B ARG* 3.9 12.3 - - - -
263B LEU* 5.2 5.4 - - - -
219C GLU 3.4 1.6 + - - -
220C LEU 3.7 1.0 + - - -
222C GLN* 1.3 80.7 - - - +
224C LYS* 1.3 67.8 + - - +
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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