Contacts of the strand formed by residues 218 - 227 (chain A) in PDB entry 2A3K
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 PHE 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A SER 3.9 4.7 - - - -
180A TRP* 3.8 11.9 - - + -
181A GLU* 3.4 43.3 - - + -
184A TRP* 3.8 21.8 - + + -
185A GLN* 5.9 1.1 - - + -
214A THR* 3.1 6.1 - - - -
215A TYR* 2.7 46.2 + - - +
216A GLY 3.2 1.2 - - - -
217A PRO* 1.3 98.6 - - + +
219A GLN* 1.3 60.0 + - - +
220A ILE* 4.4 7.4 - - + -
238A ILE* 4.0 26.9 - - + -
239A GLN 3.2 6.3 - - - +
240A TYR* 3.5 36.3 - + + -
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Residues in contact with GLN 219 (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 GLU* 3.4 23.8 + - - +
213A GLU 3.8 2.7 - - - +
214A THR* 3.8 18.5 - - + +
217A PRO 4.1 0.6 + - - -
218A PHE* 1.3 73.2 - - - +
220A ILE* 1.3 65.0 + - - +
221A ARG* 3.4 34.4 + - + +
237A THR 3.8 0.7 - - - +
238A ILE* 3.4 5.9 - - - -
239A GLN* 3.0 54.5 + - + +
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Residues in contact with ILE 220 (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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180A TRP* 3.5 54.7 - - + +
208A TRP* 5.0 0.2 - - - -
209A PRO* 3.3 27.4 - - + -
212A GLU* 3.1 26.7 - - - +
213A GLU 2.9 17.9 + - - +
215A TYR* 3.9 13.5 - - + -
218A PHE* 4.4 4.7 - - + -
219A GLN* 1.3 76.8 - - - +
221A ARG* 1.3 69.1 + - - +
222A ILE* 5.5 0.4 - - + -
236A LEU* 4.2 19.7 - - + -
237A THR 3.5 11.9 - - - +
238A ILE* 4.0 13.5 - - + -
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Residues in contact with ARG 221 (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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211A GLU* 3.4 26.9 + - - +
212A GLU* 3.6 25.4 - - + +
219A GLN* 3.4 31.9 + - + +
220A ILE* 1.3 82.6 - - - +
222A ILE* 1.3 63.6 + - - +
223A GLN* 3.7 9.9 + - - +
236A LEU* 3.2 4.9 - - - +
237A THR* 2.9 45.7 + - - +
239A GLN* 5.9 2.0 - - + -
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Residues in contact with ILE 222 (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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208A TRP* 6.0 0.4 - - + -
209A PRO* 3.7 17.0 - - + +
210A THR 3.3 28.7 - - - +
211A GLU* 2.9 38.8 + - - +
221A ARG* 1.3 74.3 - - - +
223A GLN* 1.3 65.4 + - - +
224A ASP 3.7 7.6 - - - +
225A MET* 4.0 25.4 - - + +
234A ARG* 3.8 34.3 - - + +
235A GLN 3.6 10.5 - - - +
236A LEU* 4.0 8.3 - - + -
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Residues in contact with GLN 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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221A ARG* 3.7 15.9 + - - +
222A ILE* 1.3 77.4 - - - +
224A ASP* 1.3 62.1 + - + +
235A GLN* 2.5 28.9 + - + +
236A LEU* 4.0 7.0 - - - -
237A THR* 3.6 39.1 + - + +
244A ARG* 6.2 0.2 - - - +
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Residues in contact with ASP 224 (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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222A ILE* 3.6 7.3 - - - +
223A GLN* 1.3 84.3 - - + +
225A MET* 1.3 66.2 + - - +
226A LYS* 5.4 5.2 - - - +
233A VAL 3.6 1.2 - - - +
234A ARG* 3.4 3.6 - - - -
235A GLN* 2.7 51.4 + - + +
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Residues in contact with MET 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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210A THR* 5.8 6.1 - - + +
222A ILE* 4.0 13.2 - - + +
224A ASP* 1.3 77.5 + - - +
226A LYS* 1.3 62.1 + - - +
227A GLU* 4.2 8.6 + - - -
232A THR* 3.9 13.7 - - + -
233A VAL 3.5 1.6 - - - -
234A ARG* 3.6 46.9 - - + -
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Residues in contact with LYS 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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224A ASP* 5.4 5.6 + - - +
225A MET* 1.3 74.3 - - - +
227A GLU* 1.3 64.1 - - - +
228A CYS* 3.8 5.2 + - - -
232A THR* 3.6 1.7 - - - -
233A VAL* 2.9 47.4 + - + +
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Residues in contact with GLU 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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225A MET* 4.2 9.3 - - - -
226A LYS* 1.3 72.5 - - - +
228A CYS* 1.3 64.9 + - - +
231A TYR 4.3 1.6 - - - -
232A THR* 3.9 25.1 - - + +
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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