Contacts of the strand formed by residues 225 - 230 (chain A) in PDB entry 1ZGA
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLU 3.0 18.7 + - - +
202A SER* 3.1 15.0 - - - -
203A LEU 2.8 26.5 + - - +
223A HIS 3.3 3.0 + - - +
224A LEU* 1.3 69.6 - - - +
226A CYS* 1.3 63.2 + - - +
227A THR* 3.3 25.7 + - - -
242A GLU 4.5 8.3 - - - +
243A ASN* 3.7 25.1 - - - +
244A LEU 4.9 0.2 - - - +
245A ASN* 3.6 20.0 + - - +
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Residues in contact with CYS 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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203A LEU* 3.2 13.9 - - + +
214A THR* 3.5 20.6 - - + +
217A ILE* 4.0 13.9 - - - -
218A HIS* 3.4 32.1 - - - +
224A LEU* 3.2 31.1 + - - -
225A LYS* 1.3 73.4 - - - +
227A THR* 1.3 61.8 + - - +
228A VAL 4.1 0.2 - - - -
243A ASN 2.9 10.3 + - - -
244A LEU* 3.4 6.8 - - - +
245A ASN* 2.9 25.5 + - - +
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Residues in contact with THR 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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203A LEU 2.8 13.7 + - - -
204A VAL* 3.3 16.6 - - + +
205A ASP* 2.7 33.1 + - - -
225A LYS* 3.3 15.2 + - - -
226A CYS* 1.3 73.6 - - - +
228A VAL* 1.3 63.3 + - - +
229A PHE 3.4 0.7 + - - -
245A ASN* 2.7 25.3 + - - +
247A VAL* 3.7 31.6 - - + -
256A PRO* 4.5 10.6 - - + +
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Residues in contact with VAL 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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205A ASP* 3.9 4.0 - - - +
208A GLY* 3.8 20.4 - - - +
209A GLY 3.5 25.4 - - - +
211A GLY* 3.9 11.9 - - - +
214A THR* 3.3 33.4 - - - +
227A THR* 1.3 73.0 - - - +
229A PHE* 1.3 59.1 + - - +
230A ASP 4.0 0.3 + - - -
235A VAL* 4.1 4.7 - - + +
244A LEU* 3.9 15.9 - - + -
245A ASN 2.9 7.9 + - - +
246A PHE* 3.5 22.3 - - + -
247A VAL 3.0 24.4 + - - +
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Residues in contact with PHE 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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204A VAL* 3.7 20.6 - - + -
205A ASP 3.0 8.9 + - - +
206A VAL* 4.5 8.1 - - + -
207A GLY* 2.6 33.1 + - - -
208A GLY 3.4 1.1 + - - -
227A THR* 3.4 1.9 + - + -
228A VAL* 1.3 72.9 - - - +
230A ASP* 1.3 60.9 + - - +
247A VAL* 3.1 25.4 - - + +
248A GLY 3.8 2.0 - - - -
249A GLY* 3.4 43.7 - - - -
250A ASP 3.7 0.7 - - - -
251A MET* 3.7 23.1 - - + -
254A SER* 3.3 29.2 - - - -
255A ILE* 4.0 10.5 - - + -
256A PRO* 3.4 30.5 - - + -
3994A SAH 4.7 2.7 - + - -
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Residues in contact with ASP 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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207A GLY* 3.0 12.6 - - - -
209A GLY* 2.7 29.5 + - - +
229A PHE* 1.3 74.3 - - - +
231A GLN* 1.3 75.8 + - - +
234A VAL* 3.0 18.1 - - + +
235A VAL* 3.6 13.8 - - + +
247A VAL 3.2 6.0 + - - -
248A GLY* 3.3 3.6 - - - -
249A GLY 2.9 29.0 + - - +
3994A SAH 2.6 51.7 + - - -
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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