Contacts of the strand formed by residues 222 - 227 (chain G) in PDB entry 5TJ4
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 THR 222 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G ASN* 4.4 4.9 + - - +
121G LEU* 4.1 9.8 - - - +
145G SER* 2.9 30.0 + - - +
147G LEU 3.6 5.5 + - - -
148G MET* 3.8 16.0 + - + +
213G ALA 4.8 0.4 - - - +
216G ALA* 3.4 9.2 + - + -
217G PHE* 3.6 44.0 - - + +
220G GLY 3.3 3.4 - - - -
221G GLU* 1.3 80.5 - - - +
223G ALA* 1.3 70.0 + - - +
224G MET 3.6 20.3 + - - +
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Residues in contact with ALA 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G TYR* 4.0 0.5 - - - +
118G ASN* 2.9 29.4 + - - +
121G LEU* 4.2 14.7 - - + +
122G LEU* 3.6 23.7 - - + +
139G LEU* 4.1 18.6 - - + -
145G SER 2.7 13.9 + - - +
146G ALA* 3.5 14.6 - - - +
217G PHE* 4.0 1.8 - - - -
222G THR* 1.3 75.7 + - - +
224G MET* 1.3 64.2 + - - +
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Residues in contact with MET 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G LEU* 3.9 22.2 - - + -
116G ILE 3.4 7.9 - - - +
117G TYR* 3.9 13.7 - - + -
122G LEU* 4.0 14.1 - - + -
126G PRO* 3.6 30.3 - - + -
132G ILE* 3.6 31.9 - - + -
135G LEU* 4.4 6.7 - - + -
146G ALA* 3.0 26.9 + - + +
147G LEU* 3.6 13.5 - - + -
148G MET 3.1 23.2 + - - +
217G PHE* 3.7 6.3 - - - -
222G THR* 3.5 8.0 + - - +
223G ALA* 1.3 85.1 - - - +
225G THR* 1.3 62.5 + - - +
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Residues in contact with THR 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G LEU* 3.5 4.5 - - - +
116G ILE* 2.9 52.2 + - + +
147G LEU* 3.9 3.8 - - - -
148G MET 2.6 23.4 + - - -
149G PHE* 3.9 4.0 - - - -
213G ALA* 4.2 9.8 + - - +
214G GLU* 5.1 2.4 + - - -
217G PHE* 3.9 30.7 - - + -
224G MET* 1.3 73.1 - - - +
226G ILE* 1.3 75.5 + - - +
227G ASN* 4.7 10.5 + - + +
235G ILE* 5.6 3.6 - - + -
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Residues in contact with ILE 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G LEU* 4.1 25.8 - - + -
114G SER 3.7 5.2 - - - +
115G LEU* 4.6 5.6 - - + -
129G TRP* 3.7 34.1 - - + -
147G LEU* 4.4 7.4 - - + -
149G PHE* 3.7 40.2 - - + +
150G ASN 5.2 0.5 + - - -
156G PHE* 3.7 23.1 - - + +
159G PRO* 5.7 2.5 - - + -
225G THR* 1.3 82.3 + - - +
227G ASN* 1.3 71.4 + - - +
247G LEU* 3.9 29.4 - - + -
248G PRO* 5.7 0.9 - - + -
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Residues in contact with ASN 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G LEU* 3.6 13.2 - - - -
114G SER* 3.3 29.2 + - - +
116G ILE* 3.9 18.2 - - + +
156G PHE* 4.0 4.0 - - - -
210G TYR* 3.3 29.1 + - - -
214G GLU* 5.1 10.5 - - - +
225G THR* 4.2 12.6 + - + +
226G ILE* 1.3 78.6 + - - +
228G GLY* 1.3 74.8 + - - +
230G TRP* 3.0 21.5 + - - -
231G ALA* 3.5 26.0 - - + +
232G TRP* 4.9 0.3 + - - -
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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