Contacts of the strand formed by residues 154 - 158 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E TRP* 3.8 5.5 - - - -
151E HIS 3.1 29.9 + - - +
152E GLY 3.3 0.6 - - - -
153E GLU* 1.3 101.5 + - - +
155E CYS* 1.3 66.2 - - - +
156E TYR* 3.3 34.8 + - + +
183E ASN* 5.5 5.3 + - - +
187E ASP* 5.0 4.0 + - - -
265E GLN* 3.9 18.3 + - - +
266E LYS 3.3 14.1 - - - +
267E LYS* 3.8 7.8 + - - +
268E ALA* 4.1 0.2 - - - -
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Residues in contact with CYS 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E PRO 3.4 12.1 - - - -
144E CYS* 2.0 49.8 - - + -
145E PRO* 4.3 4.3 - - + -
148E TRP* 3.6 18.7 - - + -
149E ILE 3.3 4.9 - - - +
154E ASN* 1.3 71.2 - - - +
156E TYR* 1.3 62.8 + - - +
265E GLN* 2.9 26.7 - - - +
266E LYS* 2.7 17.6 + - + +
267E LYS 4.1 2.7 - - - -
268E ALA* 3.4 16.2 - - - -
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Residues in contact with TYR 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E TRP* 3.3 5.4 - - - -
149E ILE* 2.8 52.4 + - + +
151E HIS* 3.8 18.8 + + + -
154E ASN* 3.3 42.4 + - + -
155E CYS* 1.3 76.7 - - - +
157E LEU* 1.3 60.8 + - - +
158E PHE* 3.9 18.8 - - + -
180E LEU* 3.7 15.4 - - + +
187E ASP* 3.9 18.3 + - + -
190E PHE* 3.8 25.4 - + + -
191E ILE* 3.8 15.7 - - + -
263E ILE* 4.2 3.8 - - + -
264E CYS 3.2 4.9 - - - +
265E GLN* 3.5 33.6 + - + -
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Residues in contact with LEU 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E ASP* 4.1 17.9 - - + +
148E TRP* 3.5 50.0 - - + +
156E TYR* 1.3 73.6 - - - +
158E PHE* 1.3 69.4 + - - +
159E SER* 3.6 14.3 + - - +
175E LEU* 3.6 33.7 - - + -
263E ILE* 3.3 6.9 - - - +
264E CYS* 2.8 42.0 + - + +
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Residues in contact with PHE 158 (chain E).
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* 3.7 26.2 - - + -
156E TYR* 3.9 20.9 - - + -
157E LEU* 1.3 86.2 - - - +
159E SER* 1.3 65.9 + - - +
160E SER* 3.6 1.7 + - - -
190E PHE* 5.4 0.9 - + - -
191E ILE* 4.3 16.6 - - + -
194E ALA* 3.9 25.4 - - + -
195E ILE* 3.1 36.3 - - + -
202E PHE* 4.1 11.9 - + + -
262E SER 3.9 5.4 - - - -
263E ILE* 4.0 14.8 - - + +
193F GLN 5.5 1.7 - - - +
197F TYR* 3.6 34.7 - - + +
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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