Contacts of the strand formed by residues 220 - 227 (chain A) in PDB entry 4BDG
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A LEU* 2.9 35.1 + - + +
217A ARG* 3.3 24.1 - - - +
218A ASP 3.9 0.2 - - - -
219A GLU* 1.3 93.9 + - + +
221A ILE* 1.4 63.0 + - - +
222A MET* 3.8 5.9 + - - +
237A ALA* 4.3 4.9 - - + -
238A PHE 3.3 4.3 - - - +
239A GLU* 3.5 48.1 + - + -
240A ARG* 3.5 4.7 + - - +
246A VAL* 3.7 15.9 - - + -
248A ILE* 3.9 16.8 - - + -
289A LYS* 4.7 3.1 + - - +
290A ASN* 3.3 25.2 + - - +
292A PHE* 3.7 11.0 - + - -
300A VAL* 3.6 33.1 - - + +
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Residues in contact with ILE 221 (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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220A TYR* 1.4 67.7 - - - +
222A MET* 1.3 68.9 + - - +
223A SER* 6.2 0.2 - - - -
237A ALA* 3.3 2.5 - - - -
238A PHE* 2.9 57.4 + - + +
240A ARG* 3.4 44.9 - - + +
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Residues in contact with MET 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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212A TYR* 3.5 60.8 - - + +
216A LEU* 4.0 12.6 - - + -
217A ARG* 5.9 1.8 - - + -
220A TYR* 3.8 5.7 + - - +
221A ILE* 1.3 80.1 - - - +
223A SER* 1.4 59.4 + - - +
235A LYS* 3.6 30.3 - - + -
236A LEU 4.1 1.3 - - - -
237A ALA* 3.7 7.0 - - - -
248A ILE* 3.5 45.5 - - + -
250A ILE* 4.5 3.8 - - + -
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Residues in contact with SER 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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212A TYR* 4.8 1.2 + - - -
222A MET* 1.4 74.8 - - - +
224A LYS* 1.4 75.4 + - - +
235A LYS* 3.4 22.7 + - - +
236A LEU* 2.7 38.1 + - - +
238A PHE* 4.0 20.3 - - - -
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Residues in contact with LYS 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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223A SER* 1.4 80.9 + - - +
225A THR* 1.3 68.6 + - - +
226A LEU* 5.3 4.5 - - + -
235A LYS* 3.7 0.8 - - - +
236A LEU* 2.9 49.5 + - + +
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Residues in contact with THR 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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224A LYS* 1.3 78.1 - - - +
226A LEU* 1.3 64.5 + - - +
227A GLY 3.8 19.7 - - - +
228A SER* 4.0 13.0 - - - +
233A GLU* 4.7 8.1 - - + -
234A VAL 3.6 13.7 - - - +
235A LYS* 3.3 25.5 + - - +
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Residues in contact with LEU 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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224A LYS* 4.8 4.3 - - + +
225A THR* 1.3 76.5 - - - +
227A GLY* 1.3 54.9 + - - +
234A VAL* 2.7 25.6 + - + +
235A LYS 3.7 7.9 - - - +
236A LEU* 3.6 39.0 - - + +
247A ALA* 4.2 3.1 - - + -
303A LEU* 3.5 31.9 - - + -
304A MET 6.1 0.2 - - - +
1513A P3J 3.3 39.9 - - + -
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Residues in contact with GLY 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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225A THR* 3.7 3.7 - - - -
226A LEU* 1.3 80.6 - - - +
228A SER* 1.4 63.0 + - - +
233A GLU* 3.5 1.7 - - - -
234A VAL* 2.7 37.7 + - - +
308A GLU* 5.5 2.5 - - - -
1513A P3J 4.2 12.2 + - - -
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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