Contacts of the strand formed by residues 222 - 227 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118J ASN* 4.4 7.1 + - - +
121J LEU* 5.4 2.6 - - - +
144J LYS* 5.1 1.6 - - - -
145J SER* 2.9 30.0 + - - +
147J LEU 3.6 5.4 + - - -
148J MET* 3.8 16.4 + - + -
213J ALA 4.8 0.4 - - - +
216J ALA* 3.4 9.2 + - + -
217J PHE* 3.6 43.1 - - + +
220J GLY 3.3 6.1 - - - -
221J GLU* 1.3 80.8 - - - +
223J ALA* 1.3 70.6 + - - +
224J MET 3.6 20.5 + - - +
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Residues in contact with ALA 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J TYR* 3.5 0.7 - - - +
118J ASN* 2.9 29.8 + - - +
121J LEU* 4.2 23.6 - - + -
122J LEU* 4.9 8.6 - - + +
135J LEU* 6.4 0.2 - - + -
139J LEU* 3.8 23.1 - - + -
144J LYS* 5.6 0.4 - - - +
145J SER 2.8 13.8 + - - +
146J ALA 3.5 10.5 - - - +
217J PHE* 3.6 1.3 - - - -
222J THR* 1.3 74.0 + - - +
224J MET* 1.3 68.4 + - + +
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Residues in contact with MET 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J LEU* 3.9 22.4 - - + -
116J ILE 3.4 8.3 - - - +
117J TYR* 3.9 14.4 - - + -
126J PRO* 3.6 40.8 - - + -
132J ILE* 4.2 23.1 - - + -
135J LEU* 4.8 9.2 - - + -
146J ALA* 3.0 24.0 + - + +
147J LEU* 3.6 13.0 - - + -
148J MET 3.2 22.7 + - - +
217J PHE* 3.7 4.9 - - - -
222J THR* 3.5 8.8 + - - +
223J ALA* 1.3 90.3 - - + +
225J THR* 1.3 63.0 + - - +
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Residues in contact with THR 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115J LEU* 3.5 4.3 - - - +
116J ILE* 2.9 51.7 + - + +
147J LEU* 3.9 4.0 - - - -
148J MET 2.6 24.8 + - - -
149J PHE* 3.9 3.6 - - - -
213J ALA* 4.2 9.3 + - - +
214J GLU* 5.1 2.0 + - - -
217J PHE* 3.9 31.8 - - + -
224J MET* 1.3 71.7 - - - +
226J ILE* 1.3 76.9 + - - +
227J ASN* 4.7 10.0 + - + +
235J ILE* 5.6 2.9 - - + -
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Residues in contact with ILE 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J LEU* 4.1 22.9 - - + -
114J SER 3.7 10.5 - - - +
115J LEU* 4.6 10.1 - - + -
129J TRP* 3.7 35.2 - - + -
147J LEU* 4.4 7.6 - - + -
149J PHE* 3.7 39.8 - - + +
150J ASN 5.2 0.5 + - - -
156J PHE* 3.7 21.4 - - + +
159J PRO* 6.2 0.2 - - + -
225J THR* 1.3 82.4 + - - +
227J ASN* 1.3 72.3 + - - +
247J LEU* 4.0 24.0 - - + -
248J PRO* 5.7 1.3 - - + -
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Residues in contact with ASN 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J LEU* 3.5 12.8 - - - -
114J SER* 3.3 28.6 + - - +
116J ILE* 3.9 18.4 - - + +
156J PHE* 4.0 3.6 - - - -
210J TYR* 3.3 28.6 + - - -
214J GLU* 5.2 10.7 - - - +
225J THR* 4.2 12.2 + - + +
226J ILE* 1.3 80.8 + - - +
228J GLY* 1.3 74.1 + - - +
230J TRP* 3.0 22.0 + - - -
231J ALA* 3.5 25.0 - - + +
232J 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