Contacts of the helix formed by residues 234 - 243 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A HIS* 3.7 28.3 - + - -
101A ASN* 3.3 32.1 - - - -
103A LEU* 3.5 41.7 - - + -
179A SER* 3.4 19.3 - - - -
229A THR* 3.9 13.2 - - + -
230A ASN 3.6 20.0 - - - -
231A LEU* 2.8 10.9 + - - +
233A LYS* 1.3 88.5 - - + +
235A THR* 1.3 60.4 + - - +
236A GLU 3.4 2.0 - - - -
237A TRP* 3.2 11.0 + - + +
238A ILE* 2.7 40.4 + - + +
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Residues in contact with THR 235 (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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123A ILE* 4.5 11.7 - - + +
124A ALA 3.9 17.9 - - - +
125A SER* 4.2 14.1 - - - +
231A LEU 3.7 5.3 + - - +
232A CYS 3.9 18.8 + - - +
233A LYS 3.6 1.5 - - - -
234A PHE* 1.3 77.6 - - - +
236A GLU* 1.3 70.9 + - - +
238A ILE* 3.5 8.1 - - - +
239A GLU* 2.8 28.6 + - - +
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Residues in contact with GLU 236 (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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234A PHE 3.4 0.2 - - - -
235A THR* 1.3 81.7 + - - +
237A TRP* 1.3 64.3 + - - +
239A GLU* 3.5 5.8 - - - +
240A LYS* 2.9 32.7 + - + +
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Residues in contact with TRP 237 (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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53A LEU* 5.4 0.4 - - + -
89A VAL* 3.3 36.7 - - + +
90A ARG 3.7 7.0 - - - -
91A HIS* 3.6 39.9 - + + +
92A PRO* 3.5 22.8 - - + +
103A LEU* 3.9 33.0 - - + -
104A MET 5.0 0.2 - - - -
105A LEU* 3.7 28.3 - - + -
234A PHE* 3.2 15.0 + - + +
235A THR 3.2 1.0 - - - -
236A GLU* 1.3 78.2 - - - +
238A ILE* 1.3 80.8 + - - +
239A GLU 3.1 0.7 + - - -
240A LYS* 3.9 5.0 - - + +
241A THR* 3.1 38.6 + - - -
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Residues in contact with ILE 238 (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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47A VAL* 5.1 2.0 - - + -
53A LEU* 4.2 13.5 - - + -
103A LEU* 4.4 3.1 - - + -
105A LEU* 3.7 23.3 - - + +
123A ILE* 3.6 44.4 - - + -
231A LEU* 4.4 9.4 - - + +
234A PHE* 2.7 44.1 + - + +
235A THR* 3.5 5.4 - - - +
237A TRP* 1.3 89.1 - - + +
239A GLU* 1.3 60.7 + - - +
242A VAL* 3.0 34.3 + - + +
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Residues in contact with GLU 239 (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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235A THR* 2.8 19.3 + - - +
236A GLU* 3.5 6.7 - - - +
238A ILE* 1.3 77.4 - - - +
240A LYS* 1.3 57.6 + - - +
241A THR 2.7 15.9 + - - -
242A VAL* 3.0 8.5 + - - +
243A GLN* 2.9 42.2 + - + +
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Residues in contact with LYS 240 (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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236A GLU* 2.9 27.9 + - + +
237A TRP* 4.1 6.1 - - + +
239A GLU* 1.3 71.8 - - - +
241A THR* 1.3 58.0 + - - +
243A GLN* 5.0 1.1 - - - -
244A ALA* 3.0 38.8 + - + +
240H LYS* 4.7 14.7 - - - +
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Residues in contact with THR 241 (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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51A TRP* 3.8 19.1 - - + -
89A VAL* 4.4 20.1 - - + +
105A LEU* 3.4 34.1 - - + -
237A TRP* 3.1 36.5 + - - -
239A GLU 2.7 5.7 + - - -
240A LYS* 1.3 72.1 - - - +
242A VAL* 1.3 66.4 + - - +
243A GLN 3.2 1.6 + - - -
244A ALA* 3.5 16.2 - - - +
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Residues in contact with VAL 242 (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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47A VAL* 5.0 2.7 - - + -
48A HIS* 3.7 26.4 + - + +
51A TRP* 3.0 65.7 + - + +
105A LEU* 4.0 16.2 - - + -
107A LYS* 5.5 0.9 + - - -
238A ILE* 3.0 24.2 + - + +
239A GLU* 4.0 9.4 - - - +
241A THR* 1.3 80.2 - - - +
243A GLN* 1.3 72.2 + - - +
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Residues in contact with GLN 243 (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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48A HIS* 5.5 4.9 + - - -
51A TRP* 5.6 0.2 - - - -
107A LYS* 5.9 0.7 + - - -
239A GLU* 2.9 29.1 + - + +
240A LYS* 4.9 0.9 - - - -
242A VAL* 1.3 90.1 - - - +
244A ALA* 1.3 75.7 + - + +
61L ASN* 5.1 17.3 + - - +
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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