Contacts of the strand formed by residues 241 - 246 (chain D) in PDB entry 4UQJ
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 GLU 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D TYR* 5.2 3.6 - - - -
218D TYR 3.1 6.9 + - - +
219D HIS* 3.2 38.3 + - + +
220D TYR* 2.9 25.1 + - - +
239D GLY 3.5 6.0 + - - +
240D ALA* 1.3 72.0 - - - +
242D VAL* 1.3 59.8 + - - +
243D SER* 4.3 0.7 - - - +
362D GLU* 5.6 3.3 - - - +
363D LEU 5.1 5.6 - - - +
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Residues in contact with VAL 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D TYR* 3.4 26.5 - - + +
222D ILE* 4.2 12.8 - - + -
227D PHE* 3.7 22.9 - - + -
232D LEU* 5.2 1.3 - - + -
235D ILE* 3.8 34.8 - - + +
240D ALA* 3.5 11.8 + - + +
241D GLU* 1.3 78.2 - - - +
243D SER* 1.3 66.9 + - - +
362D GLU* 3.6 1.7 - - - +
363D LEU* 2.8 49.4 + - + +
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Residues in contact with SER 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU* 4.4 9.4 - - - -
128D TYR* 2.7 32.4 + - - -
219D HIS* 3.3 20.9 + - - -
220D TYR 2.8 8.7 + - - +
221D ILE* 3.3 5.0 - - - -
222D ILE* 2.9 24.3 + - - +
227D PHE* 3.4 11.5 - - - -
241D GLU* 4.3 0.7 - - - +
242D VAL* 1.3 72.9 - - - +
244D GLY* 1.3 60.4 + - - +
361D MET 3.2 11.9 - - - -
362D GLU* 3.6 6.2 - - - +
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Residues in contact with GLY 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D LEU* 4.8 1.5 - - - +
221D ILE* 4.9 0.7 - - - -
222D ILE 3.6 12.6 - - - -
227D PHE* 3.3 18.8 - - - -
243D SER* 1.3 76.8 - - - +
245D PHE* 1.3 77.1 + - - -
360D ILE* 3.9 3.3 - - - +
361D MET 3.0 29.1 + - - +
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Residues in contact with PHE 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 3.6 25.6 - - + -
120D ALA* 3.4 29.2 - - + -
121D LEU* 3.6 26.5 - - + -
124D LEU* 3.6 24.5 - - + -
221D ILE* 4.2 13.9 - - + -
222D ILE 3.5 17.2 + - - -
223D ALA* 4.4 7.2 - - - -
224D ASN 3.1 21.3 + - - +
225D LEU* 3.3 4.7 - - - -
227D PHE* 3.0 27.2 + - - +
244D GLY* 1.3 77.9 - - - -
246D GLN* 1.3 60.4 + - - +
358D ILE* 3.9 17.3 - - + -
359D ASN 3.6 3.4 - - - -
360D ILE* 4.3 15.5 - - + -
361D MET* 4.4 0.4 - - - -
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Residues in contact with GLN 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D LEU 3.7 4.8 + - - -
226D GLY 3.8 0.5 - - - -
227D PHE* 3.1 26.2 + - - +
228D THR* 3.1 33.0 + - + +
229D ASP* 4.1 8.7 + - - -
245D PHE* 1.3 73.6 - - - +
247D ILE* 1.3 60.7 + - - +
248D VAL* 3.3 41.2 + - - +
249D ASP* 4.8 2.4 + - - +
250D TYR* 3.5 11.2 - - + -
280D TYR* 5.9 0.2 - - - +
357D THR 5.0 0.3 - - - +
358D ILE* 4.1 3.7 - - - -
359D ASN* 3.0 39.5 + - + +
361D MET* 3.6 26.7 - - + -
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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