Contacts of the strand formed by residues 222 - 229 (chain A) in PDB entry 2O3B
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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A TYR* 3.0 34.8 + - - -
169A LEU* 4.1 14.8 - - - +
206A VAL* 3.0 53.7 + - + +
220A ASN 3.3 4.4 + - - +
221A THR* 1.3 74.6 - - - +
223A VAL* 1.3 66.4 + - - +
224A ILE* 3.6 18.0 - - + +
238A TRP* 4.9 3.0 - - - -
273A ASP* 2.9 41.8 + - - +
274A ASN* 5.1 2.2 + - - -
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Residues in contact with VAL 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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203A ILE* 4.0 13.5 - - + -
204A VAL 3.4 8.1 - - - +
205A VAL* 4.2 17.3 - - + -
221A THR* 3.5 15.5 + - + +
222A ARG* 1.3 82.8 - - - +
224A ILE* 1.3 66.9 + - - +
225A ALA* 4.1 1.1 + - + -
245A VAL* 3.7 30.3 - - + -
257A LEU* 4.7 2.9 - - + -
268A ILE* 4.1 35.2 - - + +
271A LYS 5.7 0.7 - - - +
273A ASP* 3.6 20.5 + - - +
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Residues in contact with ILE 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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162A LEU* 4.6 9.9 - - + -
165A TYR* 3.8 21.1 - - + -
166A CYS* 6.1 0.4 - - - -
169A LEU* 4.5 8.5 - - + -
202A LYS 3.8 0.9 - - - +
203A ILE* 3.3 4.0 - - - +
204A VAL* 2.7 54.8 + - + +
206A VAL* 4.6 5.2 - - + -
222A ARG* 3.6 43.1 - - + +
223A VAL* 1.3 74.1 - - - +
225A ALA* 1.3 64.8 + - - +
226A VAL* 4.6 7.2 - - + -
238A TRP* 3.7 27.1 - - + -
242A LYS* 5.1 1.3 - - + -
273A ASP* 3.8 14.4 - - + +
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Residues in contact with ALA 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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202A LYS 3.3 8.5 - - - +
203A ILE* 4.3 2.2 - - + -
223A VAL* 4.1 2.3 + - + +
224A ILE* 1.3 77.8 - - - +
226A VAL* 1.3 59.3 + - - +
242A LYS* 3.3 8.7 - - - +
243A VAL* 2.8 47.4 + - + +
244A SER 4.3 0.9 - - - -
245A VAL* 4.2 22.0 - - + +
248A LEU* 4.1 16.8 - - + -
273A ASP* 5.1 3.0 - - - +
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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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159A TRP* 5.1 0.4 - - + -
162A LEU* 3.6 27.1 - - + -
200A THR 4.8 0.7 - - - +
201A TRP* 3.2 7.9 - - - +
202A LYS* 3.0 44.6 + - + +
224A ILE* 4.6 2.5 - - + -
225A ALA* 1.3 80.6 - - - +
227A ASN* 1.3 61.2 + - - +
228A ILE* 4.0 21.1 - - + -
238A TRP* 3.9 38.6 - - + +
241A TYR 3.3 9.4 - - - +
242A LYS* 4.1 8.1 - - + -
243A VAL* 4.0 4.9 - - - -
248A LEU* 3.9 2.9 - - - +
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Residues in contact with ASN 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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199A SER* 2.8 36.7 + - - -
200A THR 3.9 1.1 - - - -
201A TRP* 3.8 16.0 - - - +
226A VAL* 1.3 75.1 - - - +
228A ILE* 1.3 59.1 - - - +
229A PRO* 3.5 10.8 - - - +
241A TYR* 3.0 19.0 + - - +
243A VAL* 4.1 14.9 - - + +
248A LEU* 4.0 10.5 - - + -
251A LEU* 3.7 23.8 - - - +
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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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154A ASN* 3.5 17.9 - - - +
158A THR* 3.5 33.0 - - + +
159A TRP* 3.9 31.9 - - + +
162A LEU* 5.1 2.0 - - + -
199A SER* 4.2 1.3 - - - -
200A THR* 2.8 44.4 + - - +
226A VAL* 4.0 18.4 - - + -
227A ASN* 1.3 71.9 - - - +
229A PRO* 1.3 78.2 - - + +
234A LEU* 4.0 7.2 - - + -
238A TRP* 4.6 6.7 - - + -
241A TYR* 3.9 19.5 - - + -
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Residues in contact with PRO 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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198A LYS* 3.7 8.7 - - + +
199A SER* 4.0 6.5 - - - -
227A ASN 3.5 8.9 - - - +
228A ILE* 1.3 84.7 - - + +
230A ASN* 1.3 58.1 + - - +
231A ASP* 2.9 35.7 + - - +
234A LEU* 3.2 32.6 - - + +
241A TYR* 3.6 23.8 - - + -
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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