Contacts of the helix formed by residues 218 - 223 (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 ALA 218 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133F ASP* 3.1 24.2 - - + +
145F GLY* 3.9 28.7 - - - +
148F LEU* 4.0 6.7 - - + +
214F LEU 3.0 13.8 + - - +
215F LYS 3.1 6.3 - - - +
217F TYR* 1.3 80.3 - - - +
219F PRO* 1.3 64.6 - - - +
221F LEU* 4.2 6.5 - - + -
222F ASP* 3.4 17.8 + - - +
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Residues in contact with PRO 219 (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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52E SER* 5.4 11.0 - - - -
53E GLU* 6.5 0.9 - - + -
132F ASN* 4.8 3.4 - - - +
133F ASP* 3.5 12.3 - - - +
136F ILE* 4.6 15.3 - - + -
215F LYS 3.1 11.6 - - - +
216F ARG* 3.5 13.9 - - - +
217F TYR 3.7 3.4 - - - +
218F ALA* 1.3 90.0 - - - +
220F LYS* 1.3 68.5 + - + +
221F LEU 3.3 0.9 + - - -
222F ASP* 3.4 14.0 + - + +
223F GLU* 3.8 11.6 + - - +
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Residues in contact with LYS 220 (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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31E GLN* 5.9 1.5 - - - +
50E SER* 4.2 13.7 - - - +
51E ILE 5.2 7.9 - - - -
52E SER* 6.3 0.9 - - - +
81E GLY* 6.2 0.9 - - - -
82E TYR* 3.3 56.2 + - - +
83E TYR* 4.6 15.0 - - + +
129F ALA* 3.2 26.7 - - - +
132F ASN* 3.4 22.2 - - + +
133F ASP* 3.1 18.0 + - - +
219F PRO* 1.3 82.6 - - + +
221F LEU* 1.3 59.0 + - - +
223F GLU 4.6 1.0 - - - -
224F TRP* 3.4 13.4 + - - +
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Residues in contact with LEU 221 (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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126F TYR* 4.5 11.9 - - + +
129F ALA* 3.5 14.6 - - + +
130F LYS* 3.6 34.8 - - + +
133F ASP* 2.5 25.4 + - + +
134F PHE* 4.0 6.7 - - + -
145F GLY* 3.9 22.4 - - - +
148F LEU* 4.0 11.7 - - + -
149F ILE* 3.8 33.4 - - + -
218F ALA* 3.9 5.4 - - + +
220F LYS* 1.3 74.6 - - - +
222F ASP* 1.3 67.6 - - - +
224F TRP* 3.3 11.2 - - + +
225F PHE* 3.1 20.7 - - + -
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Residues in contact with ASP 222 (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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148F LEU* 3.8 15.7 - - + +
152F TYR* 2.2 37.2 + - - +
215F LYS* 2.7 43.1 + - + +
218F ALA 3.4 11.4 + - - +
219F PRO* 3.4 9.5 + - + +
221F LEU* 1.3 79.0 - - - +
223F GLU* 1.3 81.7 + - - +
225F PHE* 2.9 29.3 + - - +
226F TYR 3.9 0.3 + - - -
233F TRP* 4.6 4.2 + - - -
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Residues in contact with GLU 223 (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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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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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