Contacts of the strand formed by residues 209 - 216 (chain B) in PDB entry 4BGG
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 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207B ASP 4.9 2.1 + - - -
208B ILE* 1.3 76.7 - - - +
210B LEU* 1.3 69.0 + - - +
211B LEU* 3.4 14.6 + - + +
225B GLY* 3.1 4.0 - - - -
226B SER* 2.9 46.5 + - - -
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B ILE* 4.0 6.2 + - + +
209B THR* 1.3 76.2 - - - +
211B LEU* 1.3 62.9 + - - +
223B TRP* 3.8 49.6 - - + -
224B ARG 4.1 2.9 - - - +
225B GLY* 4.4 0.2 - - - -
234B VAL* 4.1 24.5 - - + -
236B ILE* 4.4 11.4 - - + -
280B TRP* 4.2 30.7 - - + -
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B THR* 3.4 24.7 + - + +
210B LEU* 1.3 79.0 - - - +
212B GLU* 1.3 61.0 + - - +
223B TRP* 4.2 5.1 - - - -
224B ARG* 2.9 50.0 + - - +
225B GLY 4.3 2.7 - - - -
226B SER* 4.0 25.6 - - - +
231B ASN* 4.5 2.0 - - - +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 1.3 79.8 - - - +
213B CYS* 1.3 64.5 - - - +
214B VAL* 3.5 18.6 + - + +
223B TRP* 3.2 10.1 - - - -
224B ARG* 2.7 74.9 + - + +
285B TYR* 4.2 2.8 + - - -
1000B 844 5.8 1.6 - - - -
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Residues in contact with CYS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B GLU* 1.3 74.6 - - - +
214B VAL* 1.3 60.7 + - - +
215B GLY 3.5 28.5 - - - -
216B LYS* 4.5 9.6 - - - -
221B GLU* 4.5 10.3 - - - -
222B VAL 3.7 7.2 - - - -
223B TRP* 3.3 36.8 - - + -
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B GLU* 3.5 24.7 + - + +
213B CYS* 1.3 75.7 - - - +
215B GLY* 1.3 56.9 + - - +
222B VAL* 2.9 39.7 + - + +
223B TRP 4.2 2.0 - - - +
224B ARG 4.3 7.0 - - - +
285B TYR* 3.8 14.1 - - + +
1000B 844 3.5 71.3 - - + +
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Residues in contact with GLY 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B CYS* 3.5 11.1 - - - -
214B VAL* 1.3 79.8 - - - +
216B LYS* 1.3 59.5 + - - -
219B TYR* 3.4 15.7 - - - -
221B GLU* 3.3 3.3 - - - -
222B VAL* 2.9 32.3 + - - -
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Residues in contact with LYS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B CYS* 4.5 8.7 - - - -
215B GLY* 1.3 73.4 - - - +
217B GLY* 1.3 65.2 + - - +
219B TYR* 3.7 8.4 + - - -
220B GLY 3.6 5.7 + - - +
221B GLU* 2.6 40.6 + - + +
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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