Contacts of the strand formed by residues 222 - 227 (chain Q) in PDB entry 5A0Q
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 LYS 222 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218Q ARG 4.6 0.2 - - - -
219Q GLU* 2.6 33.7 + - - +
220Q ASN 4.7 4.3 - - - +
221Q GLY* 1.4 82.5 - - - +
223Q THR* 1.3 66.8 + - - +
224Q VAL* 3.5 6.2 - - + +
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Residues in contact with THR 223 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Q GLU* 3.2 21.2 - - - +
71Q ASP* 3.3 32.5 + - - +
139Q TRP* 3.5 19.2 - - + -
145Q PHE* 4.4 9.0 - - + -
216Q LEU* 3.7 22.7 - - + -
217Q THR 3.3 21.8 - - - +
218Q ARG* 3.7 13.9 - - - +
219Q GLU 3.8 3.1 - - - +
221Q GLY 4.1 0.6 - - - -
222Q LYS* 1.3 73.3 - - - +
224Q VAL* 1.4 62.1 + - - +
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Residues in contact with VAL 224 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Q GLU* 4.0 13.0 - - + +
216Q LEU* 3.6 5.0 - - - +
217Q THR* 2.7 37.0 + - - +
219Q GLU* 3.6 35.4 - - + +
222Q LYS* 3.5 15.2 + - + +
223Q THR* 1.4 79.2 - - - +
225Q ILE* 1.4 75.5 + - - +
226Q ARG* 4.4 11.7 - - + +
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Residues in contact with ILE 225 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65Q ILE* 5.4 2.0 - - + -
66Q TYR 5.7 0.4 - - - +
67Q LYS* 3.2 39.0 + - + +
69Q ASN 3.3 26.7 - - - +
70Q GLU* 3.8 18.2 + - - +
72Q MET 3.3 17.3 - - - +
73Q ALA* 3.9 19.5 - - + -
137Q ILE* 5.3 2.0 - - + -
214Q ALA* 4.3 21.1 - - + -
215Q THR 3.7 6.3 - - - +
216Q LEU* 3.4 21.3 - - + -
224Q VAL* 1.4 83.6 - - - +
226Q ARG* 1.3 66.0 + - - +
227Q VAL 4.9 0.7 - - - +
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Residues in contact with ARG 226 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67Q LYS* 4.7 2.5 - - - +
214Q ALA* 4.2 2.9 - - - -
215Q THR* 3.0 48.3 + - - +
217Q THR* 3.0 34.5 + - - +
219Q GLU* 3.1 42.6 + - - +
224Q VAL* 4.4 6.5 - - + +
225Q ILE* 1.3 77.6 - - - +
227Q VAL* 1.4 69.4 + - - +
228Q LEU* 3.6 8.6 + - + -
232Q GLU* 6.0 0.9 - - - -
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Residues in contact with VAL 227 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Q ARG* 5.5 3.1 - - - +
65Q ILE* 5.4 7.6 - - + -
67Q LYS* 5.3 2.0 - - - +
212Q GLU* 4.3 26.0 - - + +
213Q ILE 3.7 11.0 - - - +
214Q ALA* 4.1 9.7 - - + +
225Q ILE* 4.9 1.2 - - - +
226Q ARG* 1.4 78.9 - - - +
228Q LEU* 1.3 77.7 + - - +
229Q LYS* 3.5 1.9 + - - -
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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