Contacts of the strand formed by residues 154 - 158 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H TRP* 3.4 6.9 - - - -
151H HIS 3.1 29.4 + - - +
153H GLU* 1.3 89.5 + - - +
155H CYS* 1.3 66.4 + - - +
156H TYR* 3.5 25.3 + - + +
187H ASP* 5.5 2.2 + - - -
265H GLN* 3.2 25.7 + - - +
266H LYS 2.9 19.4 - - - +
267H LYS* 3.5 17.3 + - - +
268H ALA* 3.9 0.4 - - - +
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Residues in contact with CYS 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H PRO 3.3 14.8 - - - -
144H CYS* 2.0 53.6 - - + -
145H PRO* 4.3 3.8 - - + -
148H TRP* 3.4 18.1 - - + -
149H ILE 3.6 0.9 - - - -
154H ASN* 1.3 73.9 - - - +
156H TYR* 1.3 64.1 + - - +
265H GLN* 3.1 6.1 - - - -
266H LYS* 2.7 39.3 + - + +
267H LYS 4.0 4.0 - - - -
268H ALA* 3.8 11.9 - - - -
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Residues in contact with TYR 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H TRP* 3.2 8.3 - - - -
149H ILE* 2.7 57.1 + - + +
151H HIS* 3.6 28.1 + + + -
154H ASN* 3.5 32.1 + - + +
155H CYS* 1.3 73.6 - - - +
157H LEU* 1.3 61.7 + - - +
158H PHE* 5.0 7.2 - - + -
180H LEU* 4.3 13.7 - - + -
187H ASP* 4.2 15.8 + - + +
190H PHE* 3.5 39.4 - + + -
191H ILE* 4.5 9.2 - - + -
263H ILE* 4.7 7.4 - - + -
264H CYS 3.2 4.9 - - - +
265H GLN* 3.7 35.5 + - + -
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Residues in contact with LEU 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ASP* 3.5 28.9 - - + +
148H TRP* 3.4 50.7 - - + +
156H TYR* 1.3 75.9 - - - +
158H PHE* 1.3 77.7 + - - +
159H SER* 3.7 3.0 + - - +
175H LEU* 3.5 23.8 - - + -
263H ILE* 3.4 6.5 - - - +
264H CYS* 2.8 41.3 + - + +
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Residues in contact with PHE 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193G GLN* 4.9 8.3 + - - -
197G TYR* 3.5 42.1 - + + +
149H ILE* 3.9 27.6 - - + -
156H TYR* 5.0 6.5 - - + -
157H LEU* 1.3 90.0 - - - +
159H SER* 1.3 66.5 + - - +
160H SER* 3.8 0.5 + - - -
190H PHE* 5.8 0.9 - + - -
191H ILE* 5.2 3.8 - - + -
194H ALA* 3.6 26.9 - - + -
195H ILE* 3.1 36.1 - - + -
202H PHE* 3.5 24.2 - + + -
262H SER 4.0 3.1 - - - -
263H ILE* 4.1 19.1 - - + -
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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