Contacts of the strand formed by residues 222 - 230 (chain A) in PDB entry 2Z9O
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 MET 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A TYR* 4.0 10.3 - - + +
169A LEU* 3.8 7.4 - - + -
170A CYS* 3.7 38.6 - - - +
173A ARG* 5.7 6.3 - - - +
216A ILE* 2.9 41.0 - - + +
217A ASN* 3.6 3.5 - - - +
220A THR* 2.7 13.6 + - - +
221A PRO* 1.3 78.1 - - + +
223A ARG* 1.3 75.9 + - - +
224A LEU* 3.8 10.1 - - - -
242A PHE* 3.3 51.1 - - + -
243A ARG 3.7 7.2 - - - +
244A ASP* 5.1 0.7 - - - +
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Residues in contact with ARG 223 (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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217A ASN* 3.1 32.2 + - - +
220A THR 2.9 28.7 + - - -
221A PRO 3.9 2.6 - - - -
222A MET* 1.3 81.5 + - - +
224A LEU* 1.3 61.4 + - - +
242A PHE* 2.8 29.3 - - - +
243A ARG* 2.8 42.5 + - + +
245A ILE* 3.0 36.9 - - + +
248A MET* 4.0 18.6 - - + -
251A GLY* 4.9 6.6 + - - +
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Residues in contact with LEU 224 (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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165A LEU* 4.6 2.9 - - + -
169A LEU* 3.2 37.5 - - + -
213A VAL* 3.2 54.6 - - + +
216A ILE* 4.2 16.4 - - + -
217A ASN* 2.8 18.7 + - - +
222A MET* 3.8 4.9 - - - -
223A ARG* 1.3 73.1 - - - +
225A SER* 1.3 62.5 + - - +
240A PHE* 3.8 16.8 - - + -
241A SER 4.3 0.4 - - - +
242A PHE* 3.3 31.6 - - + +
243A ARG* 4.0 1.8 - - - +
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Residues in contact with SER 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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224A LEU* 1.3 75.6 - - - +
226A TYR* 1.3 65.3 + - - +
239A VAL 3.9 0.2 - - - +
240A PHE* 3.3 5.7 - - - +
241A SER* 2.9 51.7 + - - -
243A ARG* 3.1 12.3 + - - -
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Residues in contact with TYR 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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205A ARG* 4.8 4.0 + - - -
209A LEU* 3.3 41.3 - - + +
210A GLN* 3.7 32.0 + - + +
213A VAL* 3.8 27.8 - - + -
214A ASN* 5.6 2.5 - - - -
225A SER* 1.3 78.8 - - - +
227A ILE* 1.3 74.6 + - - +
228A GLU* 4.6 15.7 + - + -
238A ILE* 3.9 9.0 - - + -
239A VAL 3.3 8.1 - - - +
240A PHE* 3.8 19.5 - - + -
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Residues in contact with ILE 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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226A TYR* 1.3 84.4 - - - +
228A GLU* 1.3 65.6 + - - +
229A LYS* 3.5 7.5 + - + +
238A ILE* 3.7 1.6 - - - -
239A VAL* 3.0 53.0 + - + +
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Residues in contact with GLU 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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201A MET* 5.1 1.3 - - - +
205A ARG* 2.6 53.4 + - - -
209A LEU* 5.5 1.1 - - - -
226A TYR* 4.6 14.4 + - + -
227A ILE* 1.3 75.5 - - - +
229A LYS* 1.3 58.5 + - - +
230A LYS* 3.8 2.5 + - - +
235A THR* 3.4 22.0 + - + +
237A HIS 3.8 6.1 - - - -
238A ILE* 3.9 17.5 - - + -
39D G 4.9 1.0 + - - -
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Residues in contact with LYS 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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182A SER* 5.3 1.6 - - - +
227A ILE* 3.5 7.1 + - + +
228A GLU* 1.3 70.1 - - - +
230A LYS* 1.3 56.0 + - - +
235A THR* 4.0 2.4 - - - +
236A THR* 2.6 38.3 - - + +
237A HIS* 2.9 35.2 + - + +
239A VAL* 4.6 21.1 - - + -
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Residues in contact with LYS 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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228A GLU 3.8 3.6 + - - +
229A LYS* 1.3 78.5 - - - +
231A LYS* 1.3 60.2 + - - +
232A GLY 3.6 13.2 + - - +
233A ARG* 4.6 3.6 - - - +
234A GLN 3.4 6.1 - - - +
235A THR* 3.4 33.7 - - + +
236A THR* 4.0 1.1 - - - -
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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