Contacts of the strand formed by residues 223 - 229 (chain J) in PDB entry 4R2G
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 223 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J GLY* 4.1 6.7 - - - -
137J PRO* 4.2 34.5 - - + +
216J VAL 3.4 4.5 - - - +
217J ASN* 3.9 2.4 + - - -
218J HIS* 2.9 32.2 + - - +
221J SER* 3.6 11.7 - - - -
222J ASN* 1.3 83.5 + - - +
224J LYS* 1.3 59.3 - - - +
225J VAL* 3.8 24.2 - - + -
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Residues in contact with LYS 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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216J VAL 3.4 3.1 - - - +
217J ASN* 3.5 38.0 - - + +
222J ASN* 5.7 5.6 - - - +
223J THR* 1.3 75.1 - - - +
225J VAL* 1.3 69.5 + - - +
226J ASP* 6.0 0.4 - - - +
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Residues in contact with VAL 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J PRO* 5.6 3.8 - - + +
139J VAL* 3.6 33.9 - - + +
214J CYS 3.7 0.7 - - - +
216J VAL* 2.7 43.2 + - + +
223J THR* 3.8 19.7 - - + -
224J LYS* 1.3 83.8 - - - +
226J ASP* 1.3 72.8 + - - +
227J LYS* 5.3 2.7 - - + -
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Residues in contact with ASP 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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213J ILE* 4.4 20.4 - - + +
214J CYS 3.3 6.7 - - - +
215J ASN* 3.1 44.3 + - - +
216J VAL 4.1 0.2 + - - -
224J LYS* 6.0 0.3 - - - +
225J VAL* 1.3 83.2 + - - +
227J LYS* 1.3 64.1 + - - +
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Residues in contact with LYS 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I GLU* 3.6 39.8 - - - +
139J VAL* 3.7 47.0 + - + +
140J PHE* 4.5 2.6 - - - -
141J PRO* 4.3 15.9 - - + -
158J CYS* 4.8 0.9 - - - -
213J ILE* 3.2 8.0 - - - -
214J CYS* 3.0 37.0 + - - -
225J VAL* 4.3 2.4 + - + +
226J ASP* 1.3 77.2 - - - +
228J LYS* 1.3 72.5 + - - +
229J VAL* 3.8 3.1 + - + +
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Residues in contact with LYS 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I GLU* 5.5 0.7 - - - +
141J PRO* 3.9 13.5 - - - +
211J THR* 5.1 17.2 - - + +
212J TYR 3.7 6.1 - - - +
213J ILE* 3.7 17.9 - - + -
227J LYS* 1.3 80.0 - - - +
229J VAL* 1.3 65.2 + - - +
230J GLU* 3.1 35.7 + - + +
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Residues in contact with VAL 229 (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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141J PRO* 4.3 11.7 - - + -
142J LEU 3.5 20.2 - - - +
143J ALA* 4.2 3.6 - - + +
156J LEU* 3.4 29.4 - - + +
157J GLY 3.3 28.7 - - - +
172J TRP* 3.6 20.4 - - + -
212J TYR* 2.7 36.2 + - - +
214J CYS* 4.6 7.0 - - - -
227J LYS* 4.2 7.9 - - + +
228J LYS* 1.3 77.7 - - - +
230J GLU* 1.3 65.2 + - - +
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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