Contacts of the helix formed by residues 227 - 231 (chain B) in PDB entry 1J5O
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 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B LYS 2.9 21.3 - - - +
224B GLU* 2.7 60.3 - - - -
225B PRO 2.9 7.9 + - - -
226B PRO* 1.3 66.8 - - - +
228B LEU* 1.3 63.5 + - - +
229B TRP* 3.5 10.5 - - - +
230B MET* 3.6 11.2 - - + +
102H ILE* 3.2 19.3 - - + -
104H SER 3.6 9.9 - - - -
105H VAL* 3.2 48.5 + - - +
106H THR* 4.0 2.9 - - - -
107H ASP 4.0 12.8 - - - -
108H SER* 3.3 22.0 - - - -
32L TYR* 6.5 0.2 - + - -
91L TYR* 4.2 8.1 - + - -
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Residues in contact with LEU 228 (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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66B LYS* 3.7 32.1 - - + +
226B PRO 2.9 13.6 + - - +
227B PHE* 1.3 72.8 - - - +
229B TRP* 1.3 59.6 + - - +
231B GLY* 2.8 20.4 + - - -
232B TYR* 3.2 39.1 + - + +
105H VAL* 4.8 3.9 - - + +
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Residues in contact with TRP 229 (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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199B ARG* 3.1 26.5 - - - -
221B HIS 3.5 2.7 - - - +
222B GLN* 3.2 38.1 - - + -
223B LYS 3.1 42.5 + - - +
227B PHE* 4.0 5.2 - - - +
228B LEU* 1.3 80.5 - - - +
230B MET* 1.3 79.8 + - + +
231B GLY 2.9 6.6 + - - -
232B TYR* 3.2 35.7 + - + +
233B GLU* 2.6 28.9 - - - +
32H SER* 3.7 34.8 - - - -
55H TRP* 4.9 5.2 - + - -
102H ILE* 4.0 24.0 - - + -
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Residues in contact with MET 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ARG* 2.9 37.7 + - - +
227B PHE* 3.6 8.5 + - + +
228B LEU 3.1 0.6 - - - -
229B TRP* 1.3 108.4 - - + +
231B GLY* 1.3 56.7 + - - +
233B GLU* 3.2 6.3 - - - +
235B HIS* 5.5 0.7 + - - -
32H SER* 6.0 0.7 - - - -
33H GLY* 5.7 1.8 - - - -
102H ILE* 3.6 33.2 - - + +
103H THR 3.1 27.1 - - - +
104H SER* 3.2 16.2 - - - -
105H VAL* 3.5 26.0 - - + +
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Residues in contact with GLY 231 (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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228B LEU 2.8 10.1 + - - -
230B MET* 1.3 79.9 - - - +
232B TYR* 1.3 53.1 + - - +
233B GLU* 2.6 33.0 + - - +
235B HIS* 4.6 5.9 - - - -
105H VAL* 3.6 13.9 - - - +
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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