Contacts of the helix formed by residues 218 - 225 (chain Y) in PDB entry 5MG3
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 LEU 218 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415D ASN* 5.4 6.5 - - - +
49Y LEU* 4.1 31.6 - - + -
73Y SER* 5.5 8.7 - - - +
206Y THR* 5.3 2.0 - - - +
210Y ALA* 4.3 22.7 - - + +
211Y ARG* 5.1 4.8 - - - +
217Y PHE* 1.4 73.4 - - - +
219Y VAL* 1.3 71.0 + - + +
220Y LEU* 3.2 27.7 + - + +
221Y LEU* 3.3 44.4 + - + +
222Y LEU 4.2 1.2 + - - -
400Y TYR* 5.8 0.4 - - - +
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Residues in contact with VAL 219 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217Y PHE* 4.1 24.7 - - + -
218Y LEU* 1.3 74.7 - - + +
220Y LEU* 1.3 70.3 + - + +
222Y LEU* 2.9 35.8 + - + +
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Residues in contact with LEU 220 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Y LEU* 4.2 17.5 - - + -
50Y ALA 6.0 1.6 - - - +
60Y ILE* 4.3 20.0 - - + -
72Y LEU 3.6 24.2 - - - +
73Y SER* 5.1 2.9 - - - -
203Y ILE* 5.1 0.2 - - - +
218Y LEU* 3.2 14.6 + - + -
219Y VAL* 1.3 85.3 - - + +
221Y LEU* 1.3 56.6 + - - +
222Y LEU 3.2 3.7 + - - -
223Y VAL* 3.4 27.2 + - - +
400Y TYR* 3.7 29.9 + - + +
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Residues in contact with LEU 221 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203Y ILE* 3.7 29.4 - - + -
206Y THR 4.3 7.6 - - - +
207Y ILE* 3.7 18.6 - - + -
210Y ALA* 4.5 13.7 - - + -
211Y ARG* 3.6 37.0 - - + -
218Y LEU* 3.5 29.6 - - + +
219Y VAL 3.2 0.6 + - - -
220Y LEU* 1.3 72.8 - - - +
222Y LEU* 1.4 62.7 + - - +
223Y VAL 3.3 1.2 + - - +
224Y ALA* 3.4 18.7 + - + +
225Y VAL* 4.8 4.3 + - - +
400Y TYR* 3.7 7.6 - - - +
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Residues in contact with LEU 222 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218Y LEU 4.2 1.0 + - - -
219Y VAL* 2.9 21.4 + - + +
221Y LEU* 1.4 78.1 - - - +
223Y VAL* 1.3 61.7 + - + +
224Y ALA 3.2 4.0 + - - -
225Y VAL* 4.0 16.6 - - - +
226Y LEU* 5.0 0.9 - - - +
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Residues in contact with VAL 223 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202Y ALA* 4.4 0.7 - - - +
203Y ILE* 3.8 20.2 - - + -
220Y LEU* 3.4 18.4 - - - +
222Y LEU* 1.3 78.8 - - + +
224Y ALA* 1.4 61.9 + - - +
225Y VAL 3.4 2.5 + - - -
226Y LEU* 3.6 23.1 + - + +
398Y PRO* 3.5 34.8 - - + +
400Y TYR* 4.1 11.9 - - + -
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Residues in contact with ALA 224 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201Y PRO* 2.9 31.2 - - + +
202Y ALA* 3.8 0.6 - - - +
203Y ILE* 4.2 19.5 - - + -
207Y ILE* 4.5 13.0 - - + -
221Y LEU* 3.5 22.0 - - + +
222Y LEU 3.2 1.8 - - - -
223Y VAL* 1.4 75.3 - - - +
225Y VAL* 1.4 57.8 + - + +
226Y LEU 3.0 10.4 + - - -
227Y VAL* 3.5 9.9 - - - +
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Residues in contact with VAL 225 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221Y LEU 5.2 4.3 - - - +
222Y LEU 4.0 14.1 - - - +
223Y VAL 3.4 0.2 - - - -
224Y ALA* 1.4 77.1 - - + +
226Y LEU* 1.3 73.4 + - + +
227Y VAL* 3.4 11.0 + - - +
228Y PHE* 3.5 14.4 - - - -
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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