Contacts of the helix formed by residues 234 - 243 (chain J) in PDB entry 2BDI
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 PHE 234 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91J HIS* 3.7 27.4 - + - -
101J ASN* 3.3 31.2 - - - -
103J LEU* 3.5 42.8 - - + -
179J SER* 3.4 20.0 - - - -
229J THR* 3.9 13.0 - - + -
230J ASN 3.6 20.4 - - - -
231J LEU* 2.8 10.7 + - - +
233J LYS* 1.3 90.1 - - + +
235J THR* 1.3 58.0 + - - +
236J GLU 3.4 2.5 - - - -
237J TRP* 3.2 10.0 + - + +
238J ILE* 2.7 41.0 + - + +
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Residues in contact with THR 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123J ILE* 4.5 10.8 - - + +
124J ALA 3.9 22.7 - - - +
125J SER* 4.2 14.6 - - - +
231J LEU 3.7 8.9 + - - +
232J CYS* 4.3 10.4 + - - +
233J LYS 3.6 1.3 - - - -
234J PHE* 1.3 78.1 - - - +
236J GLU* 1.3 71.2 + - - +
238J ILE* 3.0 8.4 + - - +
239J GLU* 2.8 28.4 + - - +
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Residues in contact with GLU 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233J LYS 5.6 0.2 + - - -
234J PHE 3.4 0.4 - - - -
235J THR* 1.3 81.3 + - - +
237J TRP* 1.3 65.2 + - - +
239J GLU* 3.1 6.5 + - - +
240J LYS* 2.9 31.2 + - + +
92O PRO* 6.1 1.4 - - - +
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Residues in contact with TRP 237 (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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53J LEU* 5.4 0.2 - - + -
89J VAL* 3.4 34.4 - - + +
90J ARG 3.7 7.2 - - - -
91J HIS* 3.6 42.0 - + + +
92J PRO* 3.5 22.5 - - + +
103J LEU* 3.8 32.3 - - + -
104J MET* 4.8 0.4 - - - -
105J LEU* 3.8 28.3 - - + -
234J PHE* 3.2 15.2 + - + +
235J THR 3.2 0.6 - - - -
236J GLU* 1.3 79.1 - - - +
238J ILE* 1.3 81.0 + - + +
239J GLU 3.0 0.9 + - - -
240J LYS* 4.0 4.8 - - + +
241J THR* 3.1 37.8 + - - -
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Residues in contact with ILE 238 (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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47J VAL* 5.1 2.5 - - + -
53J LEU* 4.2 14.1 - - + -
103J LEU* 4.3 3.4 - - + -
105J LEU* 3.7 22.4 - - + +
123J ILE* 3.6 45.5 - - + -
231J LEU* 4.4 9.0 - - + +
234J PHE* 2.7 43.8 + - + +
235J THR* 3.5 5.4 - - - +
237J TRP* 1.3 92.0 - - + +
239J GLU* 1.3 61.9 + - - +
242J VAL* 3.0 34.2 + - + +
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Residues in contact with GLU 239 (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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235J THR* 2.8 19.0 + - - +
236J GLU* 3.5 6.7 - - - +
237J TRP 2.9 0.2 - - - -
238J ILE* 1.3 78.2 - - - +
240J LYS* 1.3 67.4 + - - +
241J THR 2.7 6.2 + - - -
242J VAL* 3.1 8.7 + - - +
243J GLN* 2.9 42.4 + - + +
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Residues in contact with LYS 240 (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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236J GLU* 2.9 20.7 + - + +
237J TRP* 4.1 5.6 - - + +
239J GLU* 1.3 78.8 - - - +
241J THR* 1.3 58.5 + - - +
243J GLN* 5.0 1.6 - - - -
244J ALA* 3.0 38.5 + - + +
240O LYS* 5.1 15.1 - - - +
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Residues in contact with THR 241 (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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51J TRP* 3.8 18.8 - - + -
89J VAL* 4.4 20.4 - - + +
105J LEU* 3.3 33.7 - - + -
237J TRP* 3.1 37.1 + - - -
239J GLU 2.7 2.0 + - - -
240J LYS* 1.3 78.4 - - - +
242J VAL* 1.3 65.6 + - - +
243J GLN 3.2 1.4 + - - -
244J ALA* 3.5 13.7 - - - +
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Residues in contact with VAL 242 (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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47J VAL* 5.0 2.9 - - + -
48J HIS* 3.7 25.9 + - + +
51J TRP* 3.1 62.0 + - + +
105J LEU* 4.0 16.8 - - + -
107J LYS* 5.5 1.0 + - - -
238J ILE* 3.0 23.6 + - + +
239J GLU* 4.0 9.6 - - - +
241J THR* 1.3 78.2 - - - +
243J GLN* 1.3 71.7 + - - +
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Residues in contact with GLN 243 (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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48J HIS* 5.5 5.7 + - - -
107J LYS* 5.9 0.7 + - - -
239J GLU* 2.9 30.2 + - + +
240J LYS* 4.7 1.8 - - - +
242J VAL* 1.3 90.2 - - - +
244J ALA* 1.3 75.6 + - + +
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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