Contacts of the strand formed by residues 225 - 230 (chain A) in PDB entry 1WZN
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 LYS 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A GLU* 6.2 0.2 - - - -
223A PHE* 3.8 0.5 - - - +
224A GLU* 1.3 88.6 - - + +
226A VAL* 1.3 76.2 + - - +
227A LYS* 2.8 36.7 - - - +
246A VAL 3.8 0.7 - - - +
247A GLY* 3.6 1.7 - - - -
248A ILE* 2.8 52.9 + - + +
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Residues in contact with VAL 226 (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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216A ARG* 4.0 32.7 - - + -
219A ALA* 3.7 11.2 - - + +
220A GLU* 3.6 48.4 + - + +
223A PHE* 4.1 10.5 - - + -
225A LYS* 1.3 88.2 + - - +
227A LYS* 1.3 72.9 + - - +
245A ILE* 3.8 23.8 - - + -
246A VAL 3.2 8.7 - - - +
247A GLY* 4.5 1.1 - - - -
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Residues in contact with LYS 227 (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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37A ASP* 3.2 18.8 - - - +
225A LYS* 2.8 43.4 - - + +
226A VAL* 1.3 82.1 - - - +
228A ILE* 1.3 65.6 + - - +
229A TYR* 2.8 41.1 - - + +
234A ARG* 4.8 4.0 - - - +
244A TRP 3.6 0.2 - - - +
245A ILE* 3.4 4.9 - - - -
246A VAL* 2.8 39.0 + - + +
248A ILE* 4.4 10.8 - - + -
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Residues in contact with ILE 228 (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 PRO* 3.4 47.1 - - + +
213A ARG* 4.4 1.6 - - - +
216A ARG* 3.5 35.7 - - + +
226A VAL* 5.0 0.2 - - + -
227A LYS* 1.3 75.5 - - - +
229A TYR* 1.3 74.7 + - - +
235A GLU 4.6 0.2 - - - -
236A LEU* 3.7 35.8 + - + +
243A TYR* 4.7 4.7 - - + -
244A TRP 3.3 7.0 - - - +
245A ILE* 3.5 18.2 - - + -
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Residues in contact with TYR 229 (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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29A PHE* 4.0 22.7 - + + -
33A ILE* 4.5 1.8 - - + -
37A ASP* 2.8 41.5 + - - -
227A LYS* 2.8 27.3 - - + +
228A ILE* 1.3 84.3 - - - +
230A GLY* 1.3 59.4 + - - +
233A LYS 3.2 11.9 - - - +
234A ARG* 3.3 48.4 + - + -
235A GLU* 3.3 7.2 - - - -
236A LEU* 3.9 7.1 - - - +
243A TYR* 3.4 7.4 - - - +
244A TRP* 2.8 34.6 + - + +
246A VAL* 3.9 27.4 - - + -
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Residues in contact with GLY 230 (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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229A TYR* 1.3 77.2 - - - +
231A ASN* 1.3 72.5 + - - +
232A LEU 3.4 2.9 - - - -
233A LYS* 3.2 17.3 + - - +
235A GLU 2.9 12.9 + - - +
236A LEU* 4.0 3.1 - - - +
240A ASP* 3.5 21.2 - - - +
242A ARG 3.4 11.0 - - - -
243A TYR* 4.6 0.2 - - - -
244A TRP* 4.6 2.2 - - - -
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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