Contacts of the helix formed by residues 223 - 228 (chain F) in PDB entry 5X6E
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 GLU 223 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E TYR* 5.2 14.4 + - + -
215F LYS* 4.4 7.8 + - - +
219F PRO 3.8 8.2 + - - +
220F LYS 4.6 1.1 - - - -
221F LEU 3.6 0.2 - - - -
222F ASP* 1.3 90.5 - - - +
224F TRP* 1.3 60.2 + - - +
225F PHE 3.1 0.4 - - - -
226F TYR* 3.3 45.8 - - + +
227F LEU* 3.3 18.5 - - - +
233F TRP* 4.5 10.4 - - + +
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Residues in contact with TRP 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E VAL 4.2 3.8 - - - -
122F LYS* 3.3 37.5 - - - -
125F SER* 3.0 51.8 + - - -
126F TYR* 3.5 30.1 - + + -
129F ALA* 4.0 8.3 - - + -
220F LYS 3.4 18.7 + - - +
221F LEU* 3.3 12.5 + - + +
222F ASP 3.0 0.2 - - - -
223F GLU* 1.3 78.3 - - - +
225F PHE* 1.3 100.6 + + - +
226F TYR 3.2 0.2 - - - -
227F LEU* 4.1 6.6 - - + +
228F ALA* 3.1 32.5 + - + +
229F CYS* 4.1 16.4 - - - -
301F GSH 4.3 12.1 - - + -
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Residues in contact with PHE 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F TYR* 5.3 1.6 - + - -
148F LEU* 4.4 11.0 - - + -
149F ILE* 4.3 29.6 - - + -
152F TYR* 3.2 49.4 - + + -
153F VAL* 4.6 10.1 - - + -
221F LEU* 3.1 27.6 - - + -
222F ASP* 2.9 9.7 + - - +
224F TRP* 1.3 104.0 - + - +
226F TYR* 1.3 59.0 + - - +
228F ALA 2.8 17.6 - - - +
229F CYS* 3.3 4.0 - - - +
230F PRO* 3.3 12.5 - - - +
232F THR* 3.1 27.1 - - + +
233F TRP* 3.2 13.6 - - + -
301F GSH 5.0 5.2 - - - -
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Residues in contact with TYR 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E THR* 6.3 0.4 - - + -
82E TYR* 4.2 12.6 - - - -
223F GLU* 3.3 35.9 + - + +
224F TRP 3.2 0.2 - - - -
225F PHE* 1.3 76.1 - - - +
227F LEU* 1.3 87.8 - - + +
230F PRO* 3.2 24.3 - - + +
233F TRP* 3.1 40.9 - + - +
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Residues in contact with LEU 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E PHE* 4.5 3.6 - - + -
76E THR* 5.6 2.4 - - - +
78E THR* 3.5 28.7 - - + +
79E SER* 3.1 32.1 - - - +
80E VAL 3.7 6.7 - - - +
81E GLY* 3.5 29.2 - - - +
82E TYR* 3.9 26.9 - - + +
220F LYS* 6.4 0.2 - - - +
223F GLU 3.3 17.6 + - - +
224F TRP* 3.6 6.9 + - + +
226F TYR* 1.3 100.9 - - + +
228F ALA* 1.3 58.8 + - + +
230F PRO* 3.8 8.5 - - - +
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Residues in contact with ALA 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E PHE* 3.5 30.3 - - + -
118F GLN* 6.2 0.4 - - - +
122F LYS* 4.2 20.0 - - + -
224F TRP* 3.1 21.9 + - + +
225F PHE 2.8 16.3 - - - +
227F LEU* 1.3 75.8 - - + +
229F CYS* 1.3 77.9 + - - +
230F PRO* 3.3 3.1 - - - -
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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