Contacts of the helix formed by residues 241 - 249 (chain A) in PDB entry 1BX4
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 ILE 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A GLU* 4.3 19.3 - - + +
227A ALA* 3.6 30.5 - - + -
239A LYS 3.5 4.2 + - - +
240A ASP* 1.3 73.9 + - - +
242A LYS* 1.3 66.1 + - + +
244A ILE* 3.5 8.9 + - + +
245A ALA* 3.0 27.5 + - - +
264A PHE* 3.7 22.2 - - + -
266A GLN* 3.5 31.6 - - - +
272A ILE* 4.1 21.5 - - + -
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Residues in contact with LYS 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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240A ASP* 3.1 11.7 + - - +
241A ILE* 1.3 84.3 - - + +
243A GLU* 1.3 60.8 + - - +
245A ALA* 3.5 4.3 + - - +
246A LYS* 3.1 26.7 + - - +
272A ILE* 3.9 23.8 - - + -
279A VAL* 4.0 37.8 + - + +
280A THR* 5.9 0.2 - - - +
281A ALA* 4.5 15.4 - - - +
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Residues in contact with GLU 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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238A THR* 3.8 28.5 - - + +
240A ASP* 2.9 22.0 + - + +
242A LYS* 1.3 74.9 - - - +
244A ILE* 1.3 61.5 + - - +
246A LYS* 3.3 30.7 + - - +
247A LYS* 3.0 46.4 + - - +
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Residues in contact with ILE 244 (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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227A ALA* 3.8 24.7 - - + +
228A ALA* 4.4 9.0 - - + -
230A PHE* 5.0 1.8 - - + -
231A ALA* 3.7 29.8 - - + +
236A PHE* 4.1 10.3 - - + -
238A THR* 3.9 15.7 - - + +
239A LYS* 3.8 21.8 - - - +
240A ASP 2.9 21.9 + - - +
241A ILE* 3.8 9.2 - - + +
242A LYS 3.4 0.2 - - - -
243A GLU* 1.3 77.3 - - - +
245A ALA* 1.3 57.4 + - - +
247A LYS* 3.3 1.4 + - - +
248A THR* 2.8 45.1 + - - +
264A PHE* 4.0 13.2 - - + -
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Residues in contact with ALA 245 (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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241A ILE 3.0 18.5 + - - +
242A LYS 3.7 5.2 - - - +
244A ILE* 1.3 76.4 - - - +
246A LYS* 1.3 58.3 + - - +
248A THR* 3.9 1.3 - - - -
249A GLN* 3.0 30.8 + - - +
262A VAL* 4.1 7.8 - - + +
264A PHE* 3.7 24.4 - - + -
272A ILE* 4.1 16.2 - - + -
274A ALA* 3.5 22.3 - - + +
279A VAL* 4.8 0.4 - - + -
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Residues in contact with LYS 246 (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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242A LYS 3.1 15.0 + - - +
243A GLU* 3.4 33.0 + - - +
245A ALA* 1.3 77.5 - - - +
247A LYS* 1.3 63.6 + - + +
249A GLN* 3.3 8.2 + - - +
250A ALA* 3.2 22.1 + - + +
274A ALA* 4.2 1.5 - - - +
279A VAL* 4.3 15.7 - - + -
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Residues in contact with LYS 247 (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 PHE* 3.8 59.2 + - + +
238A THR* 4.0 12.6 - - + -
243A GLU* 3.0 40.1 + - - +
246A LYS* 1.3 77.4 - - + +
248A THR* 1.3 62.6 + - - +
250A ALA* 3.3 16.4 + - - +
251A LEU* 3.4 16.5 + - - +
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Residues in contact with THR 248 (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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214A MET* 5.1 3.6 - - - -
220A LEU* 3.6 31.0 - - + -
230A PHE* 3.7 18.8 - - + -
236A PHE* 3.5 14.4 - - - -
244A ILE* 2.8 30.8 + - - +
245A ALA 3.9 4.5 - - - -
247A LYS* 1.3 73.0 - - - +
249A GLN* 1.3 67.0 + - - +
251A LEU* 3.3 26.6 + - + +
260A ARG* 3.5 9.9 + - - -
262A VAL* 4.0 14.1 - - + -
264A PHE* 4.2 3.9 - - + -
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Residues in contact with GLN 249 (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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245A ALA 3.0 18.6 + - - +
246A LYS* 3.3 6.3 + - - +
248A THR* 1.3 76.9 - - - +
250A ALA* 1.3 64.1 + - - +
251A LEU 4.1 0.2 - - - +
259A GLN* 4.2 2.8 + - - +
260A ARG* 2.9 62.8 + - - +
262A VAL* 3.7 12.9 - - + +
274A ALA* 3.9 13.2 - - + +
275A THR 3.6 23.4 - - - +
276A GLU* 3.5 25.5 - - - +
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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