Contacts of the helix formed by residues 234 - 243 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91E HIS* 3.7 27.6 - + - -
101E ASN* 3.3 32.8 - - - -
103E LEU* 3.5 40.2 - - + -
179E SER* 3.4 19.7 - - - -
229E THR* 3.9 12.6 - - + -
230E ASN 3.6 20.2 - - - -
231E LEU* 2.9 10.6 + - - +
233E LYS* 1.3 89.2 - - + +
235E THR* 1.3 51.4 + - - +
236E GLU 3.4 2.0 - - - -
237E TRP* 3.8 10.5 - - + +
238E ILE* 2.7 49.1 + - + +
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Residues in contact with THR 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E ILE* 4.5 10.3 - - + +
124E ALA 3.9 20.4 - - - +
125E SER* 4.3 13.7 - - - +
231E LEU 3.7 4.9 + - - +
232E CYS 3.8 18.1 + - - +
233E LYS 3.6 1.9 + - - -
234E PHE* 1.3 75.2 - - - +
236E GLU* 1.3 71.1 + - - +
238E ILE* 3.0 7.4 + - - +
239E GLU* 2.8 29.9 + - - +
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Residues in contact with GLU 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D PRO* 6.1 1.6 - - - +
233E LYS 5.5 0.4 + - - -
234E PHE 3.4 0.4 - - - -
235E THR* 1.3 81.1 + - - +
237E TRP* 1.3 63.3 + - - +
239E GLU* 3.5 6.1 - - - +
240E LYS* 2.9 33.8 + - + +
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Residues in contact with TRP 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E VAL* 3.4 34.2 - - + +
90E ARG 3.7 7.4 - - - -
91E HIS* 3.6 39.5 - + + +
92E PRO* 3.4 22.7 - - + +
103E LEU* 3.9 32.5 - - + -
104E MET* 4.8 0.4 - - - -
105E LEU* 3.7 28.9 - - + -
234E PHE* 3.3 14.7 + - + +
235E THR 3.2 1.0 - - - -
236E GLU* 1.3 79.1 - - - +
238E ILE* 1.3 80.7 + - + +
239E GLU 3.1 0.3 + - - -
240E LYS* 3.4 5.6 + - + +
241E THR* 3.1 38.9 + - - -
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Residues in contact with ILE 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E VAL* 5.1 2.5 - - + -
53E LEU* 4.2 14.4 - - + -
103E LEU* 4.4 6.3 - - + -
105E LEU* 3.7 22.2 - - + +
123E ILE* 3.7 44.6 - - + -
231E LEU* 4.5 6.1 - - + +
234E PHE* 2.7 45.3 + - + +
235E THR* 3.5 5.2 - - - +
237E TRP* 1.3 90.7 - - + +
239E GLU* 1.3 61.6 + - - +
242E VAL* 3.0 34.3 + - + +
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Residues in contact with GLU 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E THR* 2.8 22.5 + - - +
236E GLU* 3.5 7.4 - - - +
238E ILE* 1.3 73.7 - - - +
240E LYS* 1.3 55.7 - - - +
241E THR 2.7 16.0 + - - -
242E VAL* 3.0 8.8 + - - +
243E GLN* 2.9 41.2 + - + +
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Residues in contact with LYS 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D LYS* 5.8 5.9 - - - +
236E GLU* 2.9 23.5 + - + +
237E TRP* 4.1 5.6 - - + +
239E GLU* 1.3 76.4 - - - +
241E THR* 1.3 57.4 + - - +
243E GLN* 5.0 1.1 - - - -
244E ALA* 3.0 38.3 + - + +
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Residues in contact with THR 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E TRP* 3.9 18.4 - - + -
89E VAL* 4.4 20.8 - - + +
105E LEU* 3.4 31.0 - - + -
237E TRP* 3.1 37.1 + - - -
239E GLU 2.7 5.3 + - - -
240E LYS* 1.3 76.8 - - - +
242E VAL* 1.3 67.4 + - - +
243E GLN 3.2 1.0 + - - +
244E ALA* 3.5 13.2 - - - +
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Residues in contact with VAL 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E VAL* 5.0 3.1 - - + -
48E HIS* 3.7 25.7 + - + +
51E TRP* 3.1 64.1 + - + +
105E LEU* 4.0 16.4 - - + -
107E LYS* 5.5 1.0 + - - -
238E ILE* 3.0 23.2 + - + +
239E GLU* 3.9 9.6 - - - +
241E THR* 1.3 79.8 - - - +
243E GLN* 1.3 72.0 + - - +
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Residues in contact with GLN 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E HIS* 5.5 4.8 + - - -
51E TRP* 5.6 0.2 - - - -
107E LYS* 5.9 0.7 + - - -
239E GLU* 2.9 28.8 + - + +
240E LYS* 4.7 1.3 - - - +
242E VAL* 1.3 91.5 - - - +
244E ALA* 1.3 75.0 + - + +
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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