Contacts of the helix formed by residues 219 - 225 (chain B) in PDB entry 2W93
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 ASP 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B LEU* 5.0 3.8 - - + +
218B ALA* 1.3 73.2 - - - +
220B ALA* 1.3 81.6 + - - +
221B CYS 3.3 1.8 - - - -
222B CYS* 3.0 18.1 + - - +
223B SER 3.9 1.2 + - - -
245B THR* 2.6 36.1 + - + +
247B MET* 4.0 1.0 - - - +
248B GLY* 3.8 10.0 - - - -
251B SER* 4.6 0.3 + - - -
284B SER* 5.7 0.9 - - - +
285B VAL 2.9 8.7 + - - +
286B GLY 3.2 16.8 - - - +
287B ALA* 3.3 7.9 - - - +
288B LEU 2.9 26.7 + - - +
289B LEU* 4.2 5.9 - - - +
293B ASN* 2.9 21.0 + - - -
299B TYR* 4.4 0.3 + - - -
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Residues in contact with ALA 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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219B ASP* 1.3 83.6 + - - +
221B CYS* 1.3 59.0 + - - +
223B SER* 3.1 10.7 + - - -
224B ARG* 3.0 31.9 + - + +
247B MET* 3.8 52.7 - - + +
248B GLY* 4.0 1.9 - - - -
288B LEU* 4.2 16.2 - - + -
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Residues in contact with CYS 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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92B HIS* 4.4 6.1 - - - -
220B ALA* 1.3 74.4 - - - +
222B CYS* 1.3 62.7 + - - +
223B SER 3.1 1.8 - - - -
224B ARG* 3.7 6.5 - - - +
225B HIS* 2.9 37.6 + - + +
286B GLY* 3.0 14.6 + - - -
288B LEU* 4.7 6.7 - - - -
326B MET* 3.6 6.5 - - + +
603B PY0 1.8 90.0 - - - +
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Residues in contact with CYS 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 ALA* 4.1 10.5 - - + -
219B ASP 3.0 19.6 + - - +
221B CYS* 1.3 77.6 - - - +
223B SER* 1.3 55.6 + - - +
226B ASP* 3.5 0.5 - - - -
227B VAL* 2.9 40.4 + - - -
228B LYS* 3.6 8.4 + - - -
231B THR* 3.5 35.2 - - - -
251B SER* 4.1 20.2 - - - +
285B VAL* 3.6 18.4 - - + +
286B GLY* 3.9 4.2 - - - -
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Residues in contact with SER 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 ASP 4.9 0.4 - - - -
220B ALA* 3.1 10.6 + - - -
222B CYS* 1.3 78.7 - - - +
224B ARG* 1.3 76.5 + - - +
225B HIS 3.2 0.2 - - - -
226B ASP* 3.1 20.3 + - - +
228B LYS* 4.1 14.2 + - - +
247B MET 5.7 1.6 - - - -
248B GLY* 5.4 4.0 - - - -
251B SER* 4.2 16.6 - - - -
405B TYR* 3.2 29.8 + - - -
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Residues in contact with ARG 224 (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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62B ALA 4.5 1.6 + - - -
63B ARG* 3.5 41.7 + - - +
91B GLU* 3.1 26.0 - - - +
92B HIS* 2.9 35.5 + - + +
93B VAL* 3.8 15.9 - - - +
160B GLN* 3.2 47.3 + - - +
220B ALA* 3.0 27.1 + - + +
221B CYS* 4.3 6.3 - - - -
223B SER* 1.3 87.0 + - - +
225B HIS* 1.3 60.5 + - + +
226B ASP* 3.3 1.8 + - - +
247B MET* 6.1 0.9 - - + -
405B TYR* 3.1 26.1 + - - -
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Residues in contact with HIS 225 (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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92B HIS* 3.0 29.1 + - + +
158B VAL 4.6 5.5 + - - -
159B THR* 3.0 32.1 - - - -
160B GLN* 3.8 14.8 - - + +
161B ARG* 5.8 0.2 - - - -
221B CYS* 2.9 23.7 + - - +
224B ARG* 1.3 78.0 + - - +
226B ASP* 1.3 65.1 + - - +
227B VAL* 3.3 14.4 + - - +
311B SER* 3.5 27.8 + - - -
326B MET* 3.8 5.4 - - + +
327B LYS* 5.1 2.6 - - - +
603B PY0 3.4 24.1 + - - -
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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