Contacts of the strand formed by residues 226 - 231 (chain L) in PDB entry 1VYH
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 CYS 226 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189L HIS 5.4 0.9 - - - +
190L GLY* 6.0 0.4 - - - -
217L LYS* 3.7 37.7 - - + -
218L MET 3.8 4.0 - - - -
219L TRP* 3.7 25.4 - - + -
224L GLY 3.8 1.8 + - - -
225L TYR* 1.3 76.3 - - - +
227L VAL* 1.3 63.8 + - - +
228L LYS 4.0 7.0 - - - -
229L THR* 3.9 9.2 - - - -
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Residues in contact with VAL 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206L HIS* 5.1 6.7 - - + +
218L MET* 2.8 21.9 + - + +
219L TRP 4.1 0.4 - - - -
220L GLU* 3.5 33.4 - - + +
225L TYR* 3.4 20.2 - - + +
226L CYS* 1.3 76.1 - - - +
228L LYS* 1.3 74.1 + - + +
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Residues in contact with LYS 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L ILE 4.6 0.2 - - - -
217L LYS* 3.4 2.4 - - - +
218L MET* 2.9 55.4 + - + +
226L CYS* 4.0 2.4 - - - -
227L VAL* 1.3 88.5 - - + +
229L THR* 1.3 65.7 + - - +
230L PHE* 4.3 13.2 - - + -
263L VAL* 3.0 26.8 + - - +
264L ALA* 3.0 24.7 + - - +
266L LYS* 4.6 25.1 - - + +
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Residues in contact with THR 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L THR* 3.4 26.2 - - + -
216L ILE 3.4 3.4 - - - -
217L LYS* 2.9 35.4 + - - +
226L CYS* 3.9 4.3 - - - -
228L LYS* 1.3 74.0 + - - +
230L PHE* 1.3 66.0 + - - +
231L THR* 3.6 15.7 + - - +
266L LYS* 5.5 6.6 - - - +
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Residues in contact with PHE 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214L LYS 4.2 1.0 - - - +
215L THR* 4.1 5.4 - - - -
216L ILE* 2.8 59.6 + - + +
218L MET* 3.8 28.0 - - + -
228L LYS* 4.3 12.8 - - + -
229L THR* 1.3 73.8 - - - +
231L THR* 1.3 62.9 + - - +
232L GLY 3.8 1.4 + - - -
233L HIS* 5.9 0.2 + - - -
249L ILE* 4.7 8.5 - - + -
261L TRP* 3.7 45.6 - + + -
262L VAL 4.0 7.0 - - - -
263L VAL* 4.1 24.5 - - + -
266L LYS* 3.4 37.0 - - + -
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Residues in contact with THR 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214L LYS* 4.9 6.3 - - + +
215L THR* 5.4 2.8 - - + +
229L THR* 3.6 16.4 + - - +
230L PHE* 1.3 72.1 - - - +
232L GLY* 1.3 61.5 + - - +
233L HIS 6.0 0.2 - - - +
259L ARG* 5.1 0.5 + - - -
261L TRP* 3.3 14.7 - - - -
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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