Contacts of the helix formed by residues 223 - 228 (chain J) in PDB entry 6O81
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 SER 223 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85J GLY* 5.5 0.4 - - - -
86J THR* 3.3 7.0 - - - +
87J ALA* 4.5 0.7 - - - -
222J THR* 1.3 76.1 - - - +
224J ILE* 1.3 61.9 + - - +
225J ARG* 3.3 2.7 - - - -
226J SER* 3.3 18.1 + - - -
227J GLU* 3.0 29.4 + - - +
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Residues in contact with ILE 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J THR* 2.5 28.7 + - - +
87J ALA* 3.8 16.8 - - + +
90J LEU* 4.6 11.2 - - + -
203J HIS* 6.3 0.7 - - - +
205J TYR* 5.6 6.0 - - + -
215J LEU* 5.0 7.0 - - + -
222J THR 3.8 1.8 + - - -
223J SER* 1.3 72.2 - - - +
225J ARG* 1.3 56.6 + - - +
227J GLU* 4.3 2.7 - - - +
228J LEU* 2.9 40.9 + - + +
229J ILE 3.9 1.0 + - - -
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Residues in contact with ARG 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J THR* 4.0 4.0 + - + +
170J MET* 5.1 3.6 - - - +
201J ASP* 4.6 4.5 - - - +
203J HIS* 4.8 10.5 + - + +
205J TYR* 3.7 29.7 + - + +
223J SER* 3.3 2.8 - - - -
224J ILE* 1.3 78.7 - - - +
226J SER* 1.3 57.7 + - - +
229J ILE* 3.5 21.1 - - - +
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Residues in contact with SER 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223J SER* 3.3 19.1 + - - -
224J ILE 3.2 0.4 - - - -
225J ARG* 1.3 76.5 - - - +
227J GLU* 1.3 59.6 + - - +
229J ILE* 5.2 0.4 - - - -
230J PRO* 3.5 23.4 - - - +
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Residues in contact with GLU 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215J LEU* 6.4 1.1 - - + -
221J ILE* 3.8 29.4 - - + -
222J THR 5.2 0.2 - - - +
223J SER 3.0 17.0 + - - +
224J ILE* 4.4 2.2 - - - +
226J SER* 1.3 78.7 - - - +
228J LEU* 1.3 60.3 + - - +
229J ILE 3.2 1.8 - - - -
230J PRO* 5.0 0.2 - - - -
231J TYR* 3.0 38.1 + - + +
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Residues in contact with LEU 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J LEU* 3.7 21.3 - - + +
207J LEU* 4.9 11.7 - - + -
211J ILE* 5.2 8.4 - - + +
215J LEU* 5.3 10.3 - - + -
224J ILE* 2.9 25.3 + - + +
227J GLU* 1.3 75.3 - - - +
229J ILE* 1.3 59.4 + - - +
231J TYR* 5.3 0.4 - - - -
232J LEU* 3.3 24.8 - - - +
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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