Contacts of the helix formed by residues 226 - 230 (chain B) in PDB entry 1UZL
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 SER 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PHE* 6.4 3.1 - - - -
40B HIS* 5.3 3.4 - - - -
132B PHE* 6.1 1.2 - - - -
134B ARG* 4.8 7.6 + - - -
222B SER 3.2 9.6 + - - -
223B PHE* 2.7 25.8 + - - -
224B LEU 4.1 1.2 - - - +
225B ALA* 1.3 82.1 - - - +
227B GLU* 1.3 65.1 + - - +
228B ASP* 3.2 22.8 + - - +
229B ALA* 3.3 14.6 + - - +
230B SER 4.6 0.2 + - - -
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLU* 5.9 0.2 - - - +
11B PRO* 3.6 34.8 - - + +
12B PRO* 3.4 21.4 - - - +
13B PHE* 4.9 2.5 - - + -
14B VAL* 3.7 27.1 - - + +
16B ARG* 3.0 25.9 + - - -
132B PHE* 4.2 7.8 - - - -
134B ARG* 5.6 1.7 + - - +
226B SER* 1.3 76.5 - - - +
228B ASP* 1.3 60.8 + - - +
229B ALA 3.3 0.9 + - - -
230B SER* 3.5 19.4 + - - -
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 2.7 45.7 + - - -
215A ALA 5.0 1.9 - - - +
216A GLU* 4.2 18.9 - - - +
219A GLY* 3.8 13.5 - - - +
220A VAL* 4.6 3.5 - - - +
10B LYS* 4.3 6.6 - - - -
11B PRO* 3.1 20.1 - - - +
223B PHE* 4.0 22.5 - - + -
226B SER* 3.1 13.4 + - - +
227B GLU* 1.3 78.1 - - - +
229B ALA* 1.3 58.2 + - - +
230B SER* 3.4 2.8 + - - -
231B TYR 5.1 0.7 + - - -
232B ILE* 5.2 0.3 - - - +
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ARG* 5.1 4.7 + - - +
177B THR* 5.3 0.9 + - - +
179B ASN* 5.1 1.9 + - - +
223B PHE* 3.4 28.9 - - + +
224B LEU* 3.6 34.1 - - + +
226B SER* 3.3 5.3 + - - +
227B GLU 3.3 1.8 - - - -
228B ASP* 1.3 77.7 - - - +
230B SER* 1.3 63.5 + - - +
231B TYR 3.3 2.5 - - - -
232B ILE* 3.0 30.6 + - + +
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ARG* 4.0 13.2 + - - -
216A GLU* 2.9 30.2 + - - +
134B ARG* 3.7 27.6 + - - +
175B ASN* 4.9 3.3 - - - +
177B THR* 3.9 17.7 - - - +
226B SER 4.6 0.6 + - - -
227B GLU* 3.5 15.8 + - - -
228B ASP 3.4 2.3 + - - -
229B ALA* 1.3 76.5 - - - +
231B TYR* 1.3 56.0 + - - +
232B ILE 3.3 2.7 + - - -
233B SER* 5.5 0.2 - - - -
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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