Contacts of the strand formed by residues 153 - 156 (chain D) in PDB entry 1YCH
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 MET 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D VAL* 3.7 6.7 - - + -
79D VAL 3.9 11.0 - - - +
80D ASN* 3.1 45.4 + - - +
103D LEU 3.6 24.0 - - - +
104D CYS* 4.0 4.9 - - - -
105D THR* 3.7 31.0 - - + -
126D VAL* 4.6 4.7 - - + -
141D PHE* 3.5 33.2 - - + -
142D ILE 3.4 13.0 - - - +
143D GLU* 4.1 3.8 - - - -
144D ALA* 3.8 4.9 - - - +
151D ASP 5.5 0.2 - - - +
152D SER* 1.3 79.5 - - - +
154D PHE* 1.3 74.5 + - - +
165D PRO 4.4 4.0 - - - +
166D ASN* 4.5 1.4 - - - +
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Residues in contact with PHE 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASN* 3.9 0.4 - - - -
141D PHE* 3.6 3.5 - - - -
142D ILE* 2.8 45.4 + - + +
144D ALA* 3.6 22.2 - - + -
147D LEU* 4.2 18.2 - - + -
152D SER* 5.9 0.9 - - - -
153D MET* 1.3 88.9 - - - +
155D THR* 1.3 61.8 + - - +
163D LEU* 4.1 21.1 - - + -
164D LEU 3.7 4.5 - - - -
165D PRO* 3.6 34.1 - - + -
168D ALA* 4.0 20.4 - - + -
169D PHE* 4.8 8.5 - + - -
210D LYS* 4.1 20.0 - - + -
214D ILE* 4.2 18.8 - - + -
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Residues in contact with THR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D VAL* 4.6 3.8 - - + -
78D VAL* 3.5 15.7 - - + +
80D ASN* 2.8 27.6 + - - -
139D LEU* 4.2 24.0 - - + -
140D THR 3.6 8.5 - - - +
141D PHE* 3.7 15.4 - - + -
154D PHE* 1.3 72.7 + - - +
156D TYR* 1.3 64.9 + - - +
157D VAL* 5.2 0.7 - - + -
162D LEU 4.0 0.3 - - - +
163D LEU* 3.8 3.7 - - - +
164D LEU* 2.8 55.5 + - + +
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Residues in contact with TYR 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LEU* 3.5 3.6 - - - -
140D THR* 2.8 55.5 + - + +
142D ILE* 4.9 10.8 - - + -
154D PHE 4.3 0.2 - - - -
155D THR* 1.3 76.3 - - - +
157D VAL* 1.3 60.4 + - - +
158D PRO* 3.7 26.7 + - + +
161D ALA* 3.6 22.8 - - - -
162D LEU 3.4 14.1 - - - -
163D LEU* 4.0 18.2 - - + -
219D LEU* 3.5 35.2 - - + +
220D ALA* 2.4 46.2 + - - +
221D ILE* 4.7 5.6 - - + -
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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