Contacts of the strand formed by residues 226 - 230 (chain A) in PDB entry 1T32
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 GLU 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU* 3.6 8.2 - - - +
168A CYS* 3.9 1.2 - - - -
172A PHE* 4.3 3.8 - - - -
181A ILE 3.6 1.7 - - - +
182A CYS* 3.7 3.3 - - - -
183A VAL* 2.8 43.0 + - - +
189A ALA* 3.6 11.5 - - - +
190A ALA* 2.6 54.5 + - - +
213A VAL* 5.9 0.2 - - - -
215A TYR 3.7 10.3 - - - +
216A GLY* 4.1 8.3 - - - -
217A LYS 5.5 0.2 - - - +
220A GLY 5.2 1.2 - - - +
221A VAL 5.7 0.2 - - - +
224A PRO* 4.8 4.9 - - + -
225A PRO* 1.3 74.6 - - - +
227A VAL* 1.3 63.1 + - - +
228A PHE* 3.4 22.9 + - + -
901A OHH 3.1 12.3 - - + -
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A CYS* 4.2 2.5 - - - -
172A PHE* 3.5 35.2 - - + -
175A TYR* 4.1 15.5 - - + -
180A GLN* 3.6 34.5 - - + +
181A ILE 3.5 3.8 - - - +
213A VAL* 4.7 0.9 - - - +
214A SER* 3.2 8.0 + - - -
215A TYR* 2.8 57.4 + - + +
226A GLU* 1.3 75.4 - - - +
228A PHE* 1.3 77.2 + - - +
901A OHH 5.4 0.3 - - - -
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Residues in contact with PHE 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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138A VAL* 3.8 8.3 - - + -
160A LEU* 4.4 2.0 - - + -
180A GLN* 3.2 8.0 - - - +
181A ILE* 2.8 45.4 + - + -
183A VAL* 3.5 34.8 - - + -
190A ALA* 4.1 5.6 - - + -
199A LEU* 3.7 38.6 - - + -
212A ILE 3.2 21.3 - - - +
213A VAL* 3.3 33.7 - - + -
214A SER* 4.2 1.1 - - - +
226A GLU* 3.4 31.4 - - + -
227A VAL* 1.3 83.0 - - - +
229A THR* 1.3 61.9 + - - +
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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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101A ASN* 5.4 0.2 - - - -
102A ASP* 2.7 45.0 + - - +
103A ILE* 4.1 9.0 - - + -
179A ARG 3.8 5.8 - - - +
180A GLN* 4.4 4.5 - - + +
181A ILE* 4.5 0.4 - - - -
211A GLY* 3.1 9.0 - - - -
212A ILE* 2.8 43.3 + - + +
214A SER* 3.9 7.0 + - - -
228A PHE* 1.3 71.6 - - - +
230A ARG* 1.3 63.6 + - - +
231A VAL 3.3 2.4 + - - -
234A PHE* 3.5 31.6 - - + -
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Residues in contact with ARG 230 (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 GLN 6.1 0.2 - - - -
128A GLU 4.2 4.0 + - - +
129A GLY* 3.9 7.3 - - - -
130A LEU* 3.7 38.4 + - - +
165A ASP* 4.2 11.9 + - - -
177A PRO 3.0 28.6 + - - -
178A ARG* 3.1 14.5 + - - +
179A ARG 2.8 24.7 + - - +
180A GLN 3.0 13.5 + - - -
181A ILE* 3.8 33.0 - - + +
210A HIS* 3.7 7.9 + - - +
228A PHE 3.7 1.2 + - - -
229A THR* 1.3 69.2 - - - +
231A VAL* 1.3 66.6 + - - +
232A SER* 3.5 23.8 - - - +
233A SER* 3.2 11.7 + - - -
234A PHE* 3.3 15.3 - - - -
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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