Contacts of the helix formed by residues 240 - 245 (chain B) in PDB entry 4HOO
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 ALA 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B CYS* 3.0 15.8 - - - -
239B GLY* 1.3 79.6 - - - +
241B PHE* 1.3 63.9 + - - +
242B LEU* 3.3 4.0 - - - +
243B ARG* 3.2 21.2 + - + +
244B HIS* 4.5 0.2 - - - -
308B SER* 3.8 24.2 - - - +
309B GLN 3.6 25.1 - - - +
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Residues in contact with PHE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B THR* 5.9 0.4 - - + -
227B ALA* 4.4 11.7 - - + -
228B ARG* 5.5 2.7 - - + -
231B PHE* 3.8 45.1 - + + -
234B SER* 3.4 44.4 - - - +
235B SER* 4.4 7.6 - - - +
238B CYS* 3.8 13.8 - - - +
239B GLY 3.7 0.4 - - - -
240B ALA* 1.3 72.8 - - - +
242B LEU* 1.3 78.6 + - + +
243B ARG 2.9 11.0 + - - -
244B HIS* 3.0 32.2 + + - +
246B VAL* 3.8 30.2 + - + -
247B ALA* 4.4 4.9 - - + -
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B TRP* 3.6 22.7 - - + +
192B HIS* 4.4 5.0 - - - +
223B LEU* 4.5 11.9 - - + -
224B GLU* 4.1 17.7 - - + -
227B ALA* 3.6 33.0 - - + -
240B ALA* 3.3 2.2 - - - +
241B PHE* 1.3 88.3 - - + +
243B ARG* 1.3 59.9 + - + +
244B HIS 3.1 2.8 + - - -
245B LYS* 3.4 12.8 + - - +
247B ALA* 4.1 17.7 - - + -
249B ILE* 5.9 1.3 - - + -
279B TYR* 3.4 46.7 - - + +
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Residues in contact with ARG 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B HIS* 6.1 0.7 - - - -
193B THR* 2.9 29.0 + - - -
194B GLU 2.9 20.2 + - - -
195B ASP* 4.3 2.4 - - - +
196B MET 4.3 5.7 - - - +
197B ASP* 2.8 29.5 + - - +
240B ALA* 3.4 22.4 - - + +
241B PHE 2.9 1.0 + - - -
242B LEU* 1.3 77.8 - - - +
244B HIS* 1.3 61.9 + - + +
245B LYS* 3.2 17.6 + - - +
307B ALA* 3.8 11.9 - - - +
308B SER* 3.1 31.6 + - - +
309B GLN* 4.1 11.4 + - - -
310B CYS* 4.4 8.7 - - + +
315B ALA* 3.4 28.1 - - + +
317B VAL* 5.6 4.0 - - - -
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Residues in contact with HIS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B SER* 5.4 1.8 - - - -
238B CYS* 3.6 5.0 - - + +
240B ALA 4.5 1.8 - - - -
241B PHE* 3.0 35.9 + + - +
243B ARG* 1.3 77.3 - - - +
245B LYS* 1.3 73.6 + - - +
246B VAL* 3.2 26.8 + - + +
312B CYS* 4.1 5.8 - - - -
314B GLU* 3.4 28.7 - - + +
315B ALA* 4.4 9.2 - - + +
402B ZN 2.4 34.7 - - - -
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Residues in contact with LYS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLN* 4.9 0.9 + - - -
90B HIS* 4.7 14.8 - - + -
190B ALA* 3.4 24.6 - - + +
191B TRP 4.3 4.9 - - - -
192B HIS* 4.0 41.6 - - + +
193B THR 4.8 5.0 + - - -
194B GLU* 5.3 3.0 + - - +
195B ASP* 3.9 25.2 + - - +
241B PHE 4.5 0.2 + - - -
242B LEU 3.4 10.3 + - - -
243B ARG* 3.2 16.9 - - - +
244B HIS* 1.3 84.6 - - - +
246B VAL* 1.3 59.9 + - - +
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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