Contacts of the strand formed by residues 154 - 158 (chain F) in PDB entry 1YPO
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 ASN 154 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149F ILE 3.7 0.2 - - - +
150F TRP* 3.6 6.1 - - - -
151F HIS 2.9 30.5 + - - +
152F GLY 3.2 1.0 + - - -
153F GLU* 1.3 94.4 - - - +
155F CYS* 1.3 67.3 + - - +
156F TYR* 3.4 32.7 + - + +
187F ASP* 5.4 4.2 + - - -
265F GLN* 4.0 21.4 + - + +
266F LYS 3.5 8.0 - - - +
267F LYS* 3.7 18.5 + - - +
268F ALA* 4.0 1.8 - - - +
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Residues in contact with CYS 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F PRO 3.4 11.4 - - - -
144F CYS* 2.0 50.7 - - + -
145F PRO* 4.2 4.5 - - + -
148F TRP* 3.6 19.6 - - + -
149F ILE 3.3 5.2 - - - +
154F ASN* 1.3 74.4 - - - +
156F TYR* 1.3 62.2 + - - +
265F GLN* 3.2 25.3 - - - +
266F LYS* 2.8 18.3 + - + +
267F LYS 3.8 6.3 - - - -
268F ALA* 3.7 13.7 - - - -
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Residues in contact with TYR 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F TRP* 3.3 7.0 - - - -
149F ILE* 2.7 53.0 + - + +
151F HIS* 3.9 19.7 + + + -
154F ASN* 3.4 38.2 + - + -
155F CYS* 1.3 74.4 - - - +
157F LEU* 1.3 60.7 + - - +
158F PHE* 4.0 20.9 + - + -
180F LEU* 4.1 11.9 - - + +
181F LYS 5.6 0.5 + - - -
187F ASP* 4.7 13.2 + - - +
190F PHE* 3.4 29.7 - + + -
191F ILE* 4.0 15.5 - - + -
263F ILE* 4.3 10.5 - - + -
264F CYS 3.4 1.1 - - - -
265F GLN* 3.8 33.0 + - + -
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Residues in contact with LEU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F ASP* 3.1 30.1 - - + +
148F TRP* 3.7 36.6 - - + +
156F TYR* 1.3 75.6 - - - +
158F PHE* 1.3 65.3 + - - +
159F SER* 3.4 14.7 + - - +
175F LEU* 3.4 33.2 - - + -
263F ILE* 3.3 7.3 - - - -
264F CYS* 2.8 43.8 + - + +
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Residues in contact with PHE 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E ILE* 6.2 1.1 - - + -
194E ALA* 5.8 2.1 - - - -
197E TYR* 3.3 34.3 + + + +
149F ILE* 3.4 32.1 - - + -
156F TYR* 4.0 24.0 - - + -
157F LEU* 1.3 80.7 - - - +
159F SER* 1.3 70.6 + - - +
160F SER* 3.5 1.4 + - - -
190F PHE* 4.7 2.2 - + - -
191F ILE* 4.5 9.2 - - + -
194F ALA* 3.9 22.7 - - + -
195F ILE* 3.3 34.8 - - + -
197F TYR* 5.6 3.4 - - - -
202F PHE* 4.3 6.3 - + + -
262F SER 3.9 5.2 - - - -
263F ILE* 3.8 23.3 - - + -
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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