Contacts of the strand formed by residues 224 - 230 (chain A) in PDB entry 1GZK
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 ARG 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A MET* 6.4 0.7 - - - -
165A LYS* 3.6 30.7 - - - +
182A ILE* 3.4 27.0 - - + +
183A LEU 3.0 14.8 - - - +
184A ARG* 3.7 37.6 - - - +
185A LYS* 3.5 2.9 - - - -
220A GLN* 3.4 4.5 - - - +
221A THR* 2.6 44.6 + - + +
223A ASP* 1.3 102.8 + - + +
225A LEU* 1.3 65.4 + - - +
226A CYS* 4.8 2.7 - - - -
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Residues in contact with LEU 225 (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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181A LYS 3.3 3.5 - - - +
182A ILE* 3.5 2.4 - - - -
183A LEU* 2.7 46.9 + - + +
185A LYS* 3.7 22.4 - - + -
188A ILE* 4.2 33.4 - - + -
201A SER* 5.8 4.3 - - - -
219A PHE 4.0 2.0 - - - +
220A GLN* 3.5 29.2 - - + +
224A ARG* 1.3 72.7 - - - +
226A CYS* 1.3 61.5 + - - +
227A PHE* 3.6 27.0 - - + -
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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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149A MET* 4.3 13.0 - - - -
180A MET* 4.5 5.4 - - + -
181A LYS 3.4 2.5 - - - +
182A ILE* 4.2 25.6 - - - -
217A TYR 4.0 0.3 - - - +
218A ALA* 3.3 4.9 - - - -
219A PHE* 2.6 84.0 + - + +
221A THR* 4.5 8.7 - - - -
224A ARG 4.8 1.1 - - - -
225A LEU* 1.3 83.3 - - - +
227A PHE* 1.3 66.7 + - - +
228A VAL 4.1 0.7 - - - -
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Residues in contact with PHE 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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179A ALA 3.3 3.1 - - - +
180A MET* 3.2 3.2 - - - +
181A LYS* 2.9 56.8 + - + +
183A LEU* 4.0 20.4 - - + -
200A GLU 5.5 0.9 - - - -
201A SER* 4.1 32.5 - - - -
202A ARG 5.0 3.1 - - - -
205A GLN* 5.9 0.4 - - + -
215A LEU* 3.8 25.6 - - + -
217A TYR 3.6 2.7 - - - -
218A ALA* 4.2 13.7 - - + -
219A PHE 5.9 0.2 - - - -
225A LEU* 3.6 34.5 - - + -
226A CYS* 1.3 77.8 - - - +
228A VAL* 1.3 63.0 + - - +
229A MET* 3.6 10.1 + - + +
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A PHE* 3.9 21.8 - - + -
169A VAL* 4.9 2.2 - - + -
178A TYR* 3.4 36.8 - - + -
179A ALA 3.5 3.6 - - - +
180A MET* 3.8 30.1 - - + -
215A LEU 3.6 0.2 - - - -
216A LYS* 2.6 31.4 + - - +
217A TYR* 2.8 37.3 + - + +
219A PHE* 4.1 12.3 - - + -
227A PHE* 1.3 74.1 - - - +
229A MET* 1.3 53.6 + - - +
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Residues in contact with MET 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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166A VAL* 5.6 0.2 - - + -
178A TYR* 3.1 8.8 - - - +
179A ALA* 2.7 47.0 + - + +
181A LYS* 4.6 16.8 - - + -
204A LEU* 6.2 4.9 - - - -
213A THR* 3.8 16.8 - - + +
214A ALA 3.1 17.7 - - - +
215A LEU* 3.8 18.4 - - + -
216A LYS 3.9 0.4 - - - +
227A PHE* 4.0 15.9 - - - +
228A VAL* 1.3 80.6 - - - +
230A GLU* 1.3 62.4 + - - +
293A ASP* 5.0 11.2 - - + -
294A PHE* 3.8 33.7 - - + -
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Residues in contact with GLU 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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177A TYR 4.7 0.4 - - - -
178A TYR* 3.9 15.9 - - + -
179A ALA* 4.8 2.3 + - - +
212A LEU 3.2 4.5 - - - +
213A THR* 3.0 28.9 - - + +
214A ALA* 2.6 53.3 + - + +
216A LYS* 4.7 2.1 - - + +
229A MET* 1.3 73.5 - - - +
231A TYR* 1.3 62.1 + - - +
232A ALA* 4.2 2.4 + - - +
282A MET* 5.8 0.7 - - - +
290A LYS* 3.1 38.4 + - + +
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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