Contacts of the helix formed by residues 255 - 259 (chain G) in PDB entry 1QYY
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 PRO 255 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244G ALA* 3.5 24.5 - - + +
246G VAL 3.3 9.6 - - - +
247G GLN* 4.0 4.0 - - + -
248G CYS* 4.8 0.2 - - - -
252G ASP 3.7 6.4 - - - +
253G LYS* 3.6 5.8 - - - +
254G PHE* 1.3 88.2 - - - +
256G VAL* 1.3 59.9 + - - +
257G TYR* 3.2 32.3 - - + +
258G LYS* 2.8 37.6 + - + +
259G TYR* 3.6 2.4 + - - -
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Residues in contact with VAL 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207G TRP* 4.1 12.8 - - + -
209G CYS* 3.7 22.4 - - - -
213G ILE* 3.8 26.2 - - + +
216G PHE* 4.8 1.3 - - + -
217G ARG* 3.5 14.5 - - + +
220G LEU* 3.7 22.7 - - + -
246G VAL* 2.9 22.6 + - + +
247G GLN 3.8 14.4 - - - -
248G CYS* 3.9 7.9 - - - -
254G PHE 3.4 1.6 + - - -
255G PRO* 1.3 69.9 - - - +
257G TYR* 1.3 54.8 + - - +
259G TYR* 2.6 35.1 + - + +
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Residues in contact with TYR 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLY* 3.6 13.5 - - - -
217G ARG* 3.8 14.8 - - - +
220G LEU* 4.1 25.5 - - + +
221G GLN* 3.7 31.4 + - + -
224G ALA* 6.0 1.1 - - + -
243G VAL* 4.1 25.0 + - + +
244G ALA* 3.8 25.8 - - + +
246G VAL 4.7 0.4 + - - -
255G PRO* 3.1 33.9 + - + +
256G VAL* 1.3 74.7 - - - +
258G LYS* 1.3 85.5 + - + +
259G TYR 3.4 1.1 - - - -
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Residues in contact with LYS 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLN* 2.5 75.2 + - + +
233A GLY* 3.6 3.4 - - - -
221G GLN* 5.9 1.4 - - - +
254G PHE 5.7 0.2 - - - -
255G PRO* 2.8 24.1 + - + +
257G TYR* 1.3 118.7 + - + +
259G TYR* 1.3 62.5 + - - +
260G PRO* 3.2 4.2 - - - +
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Residues in contact with TYR 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLY* 3.9 2.6 - - - -
209G CYS* 3.2 35.1 + - + -
210G ASN* 3.0 39.3 - - - -
211G CYS* 3.6 2.3 + - - -
213G ILE* 3.6 9.2 - - + -
214G LEU* 3.6 21.3 - - + -
217G ARG* 2.6 38.3 + - - -
248G CYS* 4.5 5.8 - - - -
255G PRO 3.6 1.7 + - - -
256G VAL* 2.6 33.7 + - + +
257G TYR 3.4 0.8 - - - -
258G LYS* 1.3 69.5 - - - +
260G PRO* 1.3 70.9 - - + +
261G GLY* 3.2 32.1 - - - -
262G LYS 4.9 1.7 + - - -
264G CYS* 4.4 3.5 - - - -
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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