Contacts of the strand formed by residues 221 - 228 (chain A) in PDB entry 4K88
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 TYR 221 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A MET* 5.4 5.0 - - + +
183A ALA* 4.3 25.9 + - + +
186A VAL* 4.9 6.6 - - + +
187A LEU* 5.1 8.0 - - + +
209A ARG* 3.6 41.7 - - - +
215A LYS* 4.4 6.3 - - + -
219A GLY 4.0 3.0 - - - +
220A ASP* 1.3 84.4 - - + +
222A THR* 1.3 74.1 + - - +
223A THR* 4.4 20.9 - - + -
242A HIS* 3.7 2.6 - - - +
243A HIS* 3.2 64.9 + + + +
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Residues in contact with THR 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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209A ARG* 3.5 4.8 - - - +
210A LYS* 2.7 49.9 + - + +
215A LYS* 3.7 16.7 - - - +
216A PHE* 3.1 20.0 + - - +
221A TYR* 1.3 88.2 + - - +
223A THR* 1.3 67.3 + - - +
224A THR* 5.3 0.2 - - - -
240A THR* 4.7 5.4 - - + -
241A SER 4.0 3.6 - - - -
242A HIS* 2.9 36.4 + - + +
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Residues in contact with THR 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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186A VAL* 3.5 17.4 + - + +
187A LEU* 5.0 8.7 - - + -
190A LEU* 3.7 17.0 - - + +
208A GLY 3.3 6.3 - - - -
209A ARG* 4.4 2.2 - - + +
221A TYR* 4.4 18.2 - - + -
222A THR* 1.3 78.2 - - - +
224A THR* 1.3 62.3 + - - +
240A THR* 3.7 1.9 - - - -
241A SER* 2.6 55.0 + - - -
483A PHE* 3.9 22.4 - - + -
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Residues in contact with THR 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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190A LEU* 3.8 8.3 - - - +
206A VAL 3.5 2.8 - - - +
207A LYS* 3.6 3.6 - - - -
208A GLY 2.8 31.1 + - - +
210A LYS* 3.7 22.2 - - + -
223A THR* 1.3 78.6 - - - +
225A ILE* 1.3 70.5 + - - +
226A GLU* 3.3 27.4 + - + +
237A GLN* 3.3 12.2 + - - -
239A GLY 3.4 12.1 + - - -
240A THR* 3.9 3.0 - - - +
480A CYS* 3.6 26.5 - - + -
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Residues in contact with ILE 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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190A LEU* 3.3 33.9 - - + +
193A TYR* 4.0 3.8 - - + +
194A ALA* 3.5 27.6 - - + +
197A TYR* 4.5 10.5 - - + -
205A VAL* 3.5 30.1 - - + -
206A VAL 3.6 1.3 - - - +
207A LYS* 3.9 17.5 - - + -
224A THR* 1.3 79.1 + - - +
226A GLU* 1.3 56.9 + - - +
237A GLN* 3.6 2.8 - - - -
238A GLY* 2.6 41.0 + - - -
239A GLY* 3.2 30.0 + - - +
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Residues in contact with GLU 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 VAL* 3.2 3.6 - - - -
206A VAL* 2.7 48.7 + - + +
210A LYS* 3.5 7.4 - - - -
224A THR* 3.3 34.2 + - + +
225A ILE* 1.3 77.5 - - - +
227A ALA* 1.3 62.6 + - - +
235A ALA* 5.2 1.5 - - + -
236A ILE 3.4 16.1 + - - +
237A GLN* 3.5 18.1 + - - +
479A LEU* 3.7 37.5 - - + +
480A CYS* 4.1 13.5 - - + -
507A LEU* 5.0 4.0 - - + -
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Residues in contact with ALA 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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197A TYR* 4.8 4.5 - - + -
203A ILE* 3.9 19.5 - - + -
204A PRO 4.0 4.7 - - - +
205A VAL* 3.7 19.7 - - + -
206A VAL* 6.0 0.2 - - - -
225A ILE 4.3 0.6 + - - +
226A GLU* 1.3 75.6 - - - +
228A PHE* 1.3 60.2 + - - +
235A ALA* 3.2 4.9 - - - +
236A ILE* 2.6 53.5 + - + +
238A GLY 5.7 1.1 - - - +
282A VAL* 4.5 7.0 - - + -
420A LEU* 6.1 0.9 - - - -
442A ILE* 6.0 0.4 - - - -
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Residues in contact with PHE 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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203A ILE* 5.6 0.9 - - - +
204A PRO 4.7 4.0 + - - -
227A ALA* 1.3 76.7 - - - +
229A ILE* 1.3 60.7 + - - +
230A SER* 3.4 25.8 + - - -
233A GLY* 3.4 33.9 - - - -
234A ARG 2.9 31.2 - - - -
235A ALA* 4.0 0.9 - - + -
286A VAL* 4.0 15.6 - - - +
419A ASP* 4.6 4.4 - - - +
420A LEU* 3.4 30.8 - - + +
423A HIS* 3.2 35.9 - + + -
440A GLY 3.7 11.2 - - - -
441A LYS* 4.3 2.7 - - - -
442A ILE* 4.0 27.6 - - + -
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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