Contacts of the strand formed by residues 225 - 229 (chain D) in PDB entry 1ZBU
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D TYR* 3.7 9.9 - - - -
129D TYR* 3.2 25.8 - - + +
131D CYS* 4.3 4.7 - - + +
214D MSE 3.5 27.9 - - + +
219D LEU* 3.6 22.2 - - + -
220D GLY* 3.3 29.4 - - - -
223D TYR 4.3 2.0 - - - +
224D LYS* 1.3 77.2 - - - +
226D SER* 1.3 76.4 + - - +
227D LEU* 3.9 15.0 - - + -
253D PHE* 3.8 10.6 - - - +
338D GLY* 4.7 0.2 - - - -
339D THR* 2.7 63.3 + - - +
340D PRO 2.9 20.3 + - - -
342D PRO* 3.3 12.8 - - + +
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Residues in contact with SER 226 (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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127D TYR* 3.7 31.4 - - - -
129D TYR 3.2 5.6 + - - -
130D ILE* 3.6 3.8 - - - -
131D CYS* 2.7 33.4 + - - +
225D TYR* 1.3 84.3 - - - +
227D LEU* 1.3 72.8 + - - +
258D ILE* 3.6 9.5 - - - +
318D ILE* 3.3 20.7 - - - +
339D THR* 3.2 9.0 - - - -
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Residues in contact with LEU 227 (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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131D CYS* 3.4 16.2 - - + +
133D ILE* 4.4 19.5 - - + -
214D MSE 4.6 2.0 - - + -
225D TYR* 3.9 24.0 - - + -
226D SER* 1.3 82.6 + - - +
228D LEU* 1.3 55.4 + - - +
229D THR* 5.3 1.8 - - + -
235D MSE 3.7 35.7 - - + -
253D PHE* 4.0 22.9 - - + +
254D ALA* 4.2 11.7 - - + -
256D LYS 3.9 10.5 + - - +
257D TRP* 3.5 14.7 - - + -
258D ILE* 2.7 32.1 + - - +
339D THR* 4.1 3.5 + - + -
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Residues in contact with LEU 228 (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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130D ILE* 3.6 23.3 - - + -
131D CYS 3.1 7.0 + - - +
132D ILE* 3.4 20.2 - - + +
133D ILE 3.3 23.0 + - - -
227D LEU* 1.3 77.7 - - - +
229D THR* 1.3 66.3 + - - +
258D ILE* 3.2 28.5 - - + +
260D ILE* 3.8 26.9 - - + -
302D ILE* 3.4 33.2 - - + +
306D ALA* 4.4 4.0 - - + -
316D LEU* 3.9 20.0 - - + -
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Residues in contact with THR 229 (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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132D ILE* 5.5 0.9 - - - -
133D ILE* 3.1 27.6 - - + +
227D LEU* 5.3 2.2 - - + -
228D LEU* 1.3 82.4 - - - +
230D ASP* 1.3 59.5 + - - +
231D GLY 2.7 31.1 + - - -
234D ASP* 3.9 21.9 - - + +
235D MSE 4.2 20.6 - - + +
257D TRP* 3.5 17.7 - - + -
258D ILE 2.9 6.9 + - - +
259D ASN* 3.7 0.2 - - - -
260D ILE* 3.1 26.5 + - - +
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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