Contacts of the strand formed by residues 223 - 228 (chain A) in PDB entry 3Q29
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 THR 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ASN* 4.4 2.4 + - - +
122A LEU* 4.1 9.6 - - - +
146A SER* 2.8 27.5 + - - -
147A ALA 3.4 0.5 + - - -
148A LEU 3.3 15.6 + - - -
149A MET* 3.5 21.2 + - + +
214A ALA 4.8 0.2 - - - +
217A ALA* 3.9 8.1 - - + -
218A PHE* 3.6 42.0 - - + +
221A GLY 4.6 0.7 - - - -
222A GLU* 1.3 81.0 + - - +
224A ALA* 1.3 62.5 + - - +
225A MET 3.6 15.3 - - - +
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Residues in contact with ALA 224 (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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118A TYR* 3.3 1.2 - - - +
119A ASN* 2.9 29.0 + - - -
122A LEU* 4.1 18.5 - - + +
123A LEU* 4.1 24.7 - - + +
140A LEU* 3.8 19.1 - - + -
146A SER 2.8 15.0 + - - +
147A ALA 3.6 7.9 - - - +
218A PHE* 3.4 2.4 - - - -
223A THR* 1.3 73.8 + - - +
225A MET* 1.3 64.1 + - - +
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Residues in contact with MET 225 (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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116A LEU* 3.9 22.4 - - + -
117A ILE 3.2 7.4 - - - +
118A TYR* 4.0 9.9 - - + -
123A LEU* 3.7 10.1 - - + -
127A PRO* 3.5 40.6 - - + -
133A ILE* 4.1 18.8 - - + -
136A LEU* 3.8 19.1 - - + -
147A ALA* 2.8 29.9 + - + +
148A LEU* 3.5 11.6 - - + -
149A MET 3.0 24.3 + - - +
218A PHE* 3.8 5.4 - - - -
223A THR* 3.4 6.9 - - - +
224A ALA* 1.3 85.7 - - - +
226A THR* 1.3 62.6 + - - +
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Residues in contact with THR 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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116A LEU* 3.8 2.9 - - - +
117A ILE* 2.9 59.2 + - + +
148A LEU* 4.0 2.9 - - - -
149A MET 2.9 21.3 + - - -
150A PHE* 4.2 2.9 - - - +
214A ALA* 4.3 8.7 + - - +
215A GLU* 5.6 1.5 - - - -
218A PHE* 3.8 31.0 - - + -
219A ASN* 5.9 0.2 - - - +
225A MET* 1.3 73.2 - - - +
227A ILE* 1.3 77.5 + - - +
228A ASN* 4.8 8.5 + - + +
236A ILE* 5.2 2.2 - - + -
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Residues in contact with ILE 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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114A LEU* 3.9 30.3 - - + -
115A SER 3.6 10.1 - - - +
116A LEU* 4.4 7.0 - - + -
130A TRP* 3.8 35.0 - - + -
148A LEU* 4.2 11.4 - - + -
150A PHE* 3.7 33.1 - - + +
151A ASN 5.1 0.5 + - - -
157A PHE* 3.6 23.7 - - + +
160A PRO* 5.4 2.9 - - + -
226A THR* 1.3 82.9 + - - +
228A ASN* 1.3 71.2 + - - +
248A LEU* 4.2 20.2 - - + -
249A PRO* 5.7 0.4 - - + -
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Residues in contact with ASN 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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114A LEU* 3.3 12.6 - - - -
115A SER* 3.1 28.1 + - - +
117A ILE* 3.9 24.2 - - + +
157A PHE* 3.8 3.9 - - - -
211A TYR* 3.3 33.4 + - - -
215A GLU* 5.4 8.1 - - - +
226A THR* 4.2 9.7 + - + +
227A ILE* 1.3 80.2 + - - +
229A GLY* 1.3 68.4 + - - +
231A TRP* 3.1 23.0 + - - -
232A ALA* 3.6 16.3 - - + +
233A TRP* 5.2 0.5 + - - -
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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