Contacts of the strand formed by residues 223 - 228 (chain G) in PDB entry 1YYL
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 PHE 223 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G ALA* 3.5 9.7 - - - +
220G PRO* 3.1 32.9 + - + +
221G ALA 3.6 14.6 - - - -
222G GLY* 1.3 82.0 - - - +
224G ALA* 1.3 61.8 + - - +
488G VAL* 4.1 18.8 - - + -
489G VAL 3.3 10.3 - - - +
490G LYS* 3.8 33.9 - - + -
491G ILE* 3.6 11.1 - - - +
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Residues in contact with ALA 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G ALA* 4.1 4.5 - - - -
223G PHE* 1.3 75.6 - - - +
225G ILE* 1.3 62.8 + - - +
226G LEU* 4.1 7.2 - - + -
244G THR* 4.8 9.2 - - - +
245G VAL 5.5 0.2 - - - -
488G VAL* 3.3 4.2 - - - +
489G VAL* 2.7 45.7 + - + +
491G ILE* 4.2 14.6 - - + +
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Residues in contact with ILE 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G MET* 4.1 25.6 - - + -
217G TYR 3.5 25.1 - - - +
218G CYS* 3.8 4.7 - - - +
219G ALA* 3.8 26.4 - - + +
224G ALA* 1.3 77.0 - - - +
226G LEU* 1.3 73.1 + - - +
244G THR* 3.5 4.2 + - - -
245G VAL* 3.2 49.7 + - + +
246G GLN 4.2 3.8 - - - +
247G CYS* 4.7 1.3 - - - -
248G THR* 4.4 1.8 - - + -
486G TYR* 4.0 15.3 - - + -
487G LYS 3.6 6.1 - - - +
488G VAL* 4.7 10.1 - - + -
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Residues in contact with LEU 226 (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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89G VAL* 5.9 4.5 - - + +
91G GLU* 3.0 44.4 - - + +
93G PHE* 3.8 15.3 - - + -
224G ALA* 4.6 7.0 - - + -
225G ILE* 1.3 82.4 - - - +
227G LYS* 1.3 59.6 + - - +
242G VAL* 4.0 12.3 - - + -
243G SER 3.5 6.1 - - - +
244G THR* 4.9 7.2 - - - -
485G LYS 3.6 0.5 - - - +
486G TYR* 3.4 5.9 - - - -
487G LYS* 2.8 38.6 + - + +
489G VAL* 3.7 28.0 - - + -
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Residues in contact with LYS 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G LEU* 1.3 75.9 - - - +
228G CYS* 1.3 70.8 - - - +
229G ASN* 3.4 18.5 + - - +
242G VAL* 3.3 5.6 - - - +
243G SER* 2.9 48.4 + - - +
245G VAL* 4.2 21.3 - - + +
249G HIS* 6.0 2.8 - - - +
485G LYS* 3.2 40.1 - - + +
486G TYR* 3.8 27.4 + - + +
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Residues in contact with CYS 228 (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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93G PHE* 3.7 14.1 - - + -
227G LYS* 1.3 79.7 - - - +
229G ASN* 1.3 64.6 + - - +
230G ASP* 3.8 6.1 - - - -
233G PHE* 3.2 51.1 - - + -
239G CYS* 2.0 50.3 - - + -
242G VAL* 4.7 0.4 - - - -
485G LYS* 3.0 27.1 + - + +
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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