Contacts of the strand formed by residues 225 - 229 (chain A) in PDB entry 1W0H
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 TYR 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A TYR* 3.7 12.6 - - - -
129A TYR 3.1 18.2 - - - +
130A ILE* 5.3 0.2 - - - -
131A CYS* 4.4 9.9 - - - -
214A MSE 3.5 28.4 - - + +
219A LEU* 3.6 27.3 + - + -
220A GLY* 3.6 34.8 - - - -
224A LYS* 1.3 79.3 + - - +
226A SER* 1.3 74.3 + - - +
227A LEU* 4.2 13.7 - - + -
253A PHE* 3.2 30.8 - + + +
256A LYS* 5.9 0.7 + - - -
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TYR* 3.7 26.5 - - - -
129A TYR 3.3 5.6 + - - -
130A ILE* 3.4 5.2 - - - +
131A CYS 2.9 24.1 + - - -
225A TYR* 1.3 85.7 - - - +
227A LEU* 1.3 65.4 + - - +
258A ILE* 3.6 14.1 - - - +
318A ILE* 2.8 33.6 - - - +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A CYS* 3.3 26.7 - - + +
133A ILE* 4.0 22.0 - - + -
214A MSE 4.5 2.7 - - + -
225A TYR* 4.2 11.1 - - + -
226A SER* 1.3 81.4 + - - +
228A LEU* 1.3 60.7 + - - +
229A THR* 4.9 3.4 - - + -
235A MSE 4.0 14.8 - - + -
253A PHE* 3.8 28.3 - - + +
254A ALA* 3.7 37.7 - - + -
256A LYS 4.4 3.3 + - - +
257A TRP* 3.5 12.6 - - + -
258A ILE* 2.8 24.0 + - - +
318A ILE* 4.9 1.6 - - - +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ILE* 3.4 23.3 - - + -
131A CYS 2.9 7.6 + - - +
132A ILE* 3.4 29.9 - - + +
133A ILE 3.4 7.1 + - - -
227A LEU* 1.3 75.7 - - - +
229A THR* 1.3 67.6 + - - +
258A ILE* 3.2 33.2 - - + +
260A ILE* 3.9 20.2 - - + -
302A ILE* 3.4 31.6 - - + -
306A ALA* 3.9 23.1 - - + -
316A LEU* 4.1 13.2 - - + -
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Residues in contact with THR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 5.4 0.7 - - - -
133A ILE* 4.3 6.5 - - + +
227A LEU* 4.9 1.8 - - + -
228A LEU* 1.3 87.5 - - - +
230A ASP* 1.3 58.9 + - - +
231A GLY 3.0 24.0 + - - +
234A ASP* 5.4 0.2 - - - -
235A MSE 3.5 37.5 - - + -
257A TRP* 3.3 37.3 - - + -
258A ILE 2.9 5.7 + - - -
259A ASN* 4.0 0.9 - - - -
260A ILE* 2.9 30.6 + - - +
302A ILE* 4.7 2.7 - - - -
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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