Contacts of the helix formed by residues 234 - 243 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M HIS* 3.7 26.9 - + - -
101M ASN* 3.3 31.2 - - - -
103M LEU* 3.6 44.4 - - + -
179M SER* 3.4 19.3 - - - -
229M THR* 3.9 13.5 - - + -
230M ASN 3.6 20.2 - - - -
231M LEU* 2.9 10.9 + - - +
233M LYS* 1.3 88.6 - - + +
235M THR* 1.3 59.3 + - - +
236M GLU 3.4 2.0 - - - -
237M TRP* 3.2 10.4 + - + +
238M ILE* 2.7 36.8 + - + +
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Residues in contact with THR 235 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123M ILE* 4.5 10.3 - - + +
124M ALA 3.9 20.4 - - - +
125M SER* 4.3 13.5 - - - +
231M LEU 3.7 5.3 + - - +
232M CYS 3.7 18.4 + - - +
233M LYS 3.6 1.3 + - - -
234M PHE* 1.3 76.4 - - - +
236M GLU* 1.3 72.1 + - - +
238M ILE* 3.0 7.8 + - - +
239M GLU* 2.9 27.1 + - - +
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Residues in contact with GLU 236 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92L PRO* 5.4 9.4 - - - +
93L GLU* 5.8 0.3 - - - +
234M PHE 3.4 0.8 - - - -
235M THR* 1.3 81.0 + - - +
237M TRP* 1.3 62.1 + - - +
239M GLU* 3.5 4.9 - - - +
240M LYS* 2.9 32.9 + - + +
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Residues in contact with TRP 237 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M LEU* 5.4 0.2 - - + -
89M VAL* 3.4 34.0 - - + +
90M ARG 3.8 7.2 - - - -
91M HIS* 3.7 40.2 - + + +
92M PRO* 3.5 21.7 - - + +
103M LEU* 3.9 33.7 - - + -
105M LEU* 3.8 28.5 - - + -
234M PHE* 3.2 14.7 + - + +
235M THR 3.2 0.6 - - - -
236M GLU* 1.3 78.6 - - - +
238M ILE* 1.3 79.9 + - + +
239M GLU 3.0 0.7 + - - -
240M LYS* 4.0 4.4 - - + -
241M THR* 3.1 37.5 + - - -
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Residues in contact with ILE 238 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M VAL* 5.1 2.5 - - + -
53M LEU* 4.2 13.0 - - + -
103M LEU* 4.3 3.6 - - + -
105M LEU* 3.8 22.2 - - + +
123M ILE* 3.6 44.9 - - + -
231M LEU* 4.5 9.4 - - + +
234M PHE* 2.7 43.1 + - + +
235M THR* 3.6 5.6 - - - +
237M TRP* 1.3 90.7 - - + +
239M GLU* 1.3 64.7 + - - +
242M VAL* 3.1 29.9 + - + +
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Residues in contact with GLU 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M THR* 2.9 18.3 + - - +
236M GLU* 3.5 6.5 - - - +
238M ILE* 1.3 76.7 - - - +
240M LYS* 1.3 56.3 - - - +
241M THR 2.8 15.4 + - - -
242M VAL* 3.1 9.4 + - - +
243M GLN* 2.9 41.9 + - + +
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Residues in contact with LYS 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240L LYS* 5.0 16.7 - - - +
236M GLU* 2.9 22.8 + - + +
237M TRP* 4.1 5.4 - - + +
239M GLU* 1.3 78.4 - - - +
241M THR* 1.3 57.9 + - - +
243M GLN* 5.0 1.3 - - - -
244M ALA* 3.0 37.8 + - + +
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Residues in contact with THR 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51M TRP* 3.9 18.4 - - + -
89M VAL* 4.4 20.1 - - + +
105M LEU* 3.4 31.2 - - + -
237M TRP* 3.1 37.4 + - + -
239M GLU 2.8 4.9 + - - -
240M LYS* 1.3 76.6 - - - +
242M VAL* 1.3 67.4 + - - +
243M GLN 3.3 0.5 + - - -
244M ALA* 3.5 13.9 - - - +
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Residues in contact with VAL 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M VAL* 5.0 3.1 - - + -
48M HIS* 3.7 26.0 + - + +
51M TRP* 3.1 60.1 + - + +
105M LEU* 4.0 16.6 - - + -
107M LYS* 5.5 1.0 + - - -
238M ILE* 3.1 24.2 + - + +
239M GLU* 4.0 9.0 - - - +
241M THR* 1.3 79.1 - - - +
243M GLN* 1.3 72.2 + - - +
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Residues in contact with GLN 243 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H SER* 4.9 6.4 + - - +
87H LEU* 3.8 34.8 + - + +
48M HIS* 5.5 5.1 + - - -
107M LYS* 5.9 0.7 + - - -
239M GLU* 2.9 28.7 + - + +
240M LYS* 4.9 1.3 - - - -
242M VAL* 1.3 91.5 - - - +
244M ALA* 1.3 75.4 + - + +
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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