Contacts of the strand formed by residues 224 - 229 (chain A) in PDB entry 1L8A
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 VAL 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A LEU* 3.4 15.3 - - + +
138A TYR* 3.7 20.0 - - + -
201A ALA* 3.6 28.7 - - + +
204A GLN* 4.1 7.2 - - + -
205A ALA* 3.7 21.3 - - + +
208A LEU* 3.7 29.8 - - + -
223A THR* 1.3 76.0 - - - +
225A TYR* 1.3 61.1 + - - +
252A ASN 2.7 14.3 + - - +
253A LEU* 3.5 7.8 - - + +
254A VAL 2.8 27.2 + - - +
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Residues in contact with TYR 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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124A PHE* 3.9 22.3 + - + +
125A PHE* 3.6 27.1 - + - -
135A ASP* 3.8 20.2 + - + -
136A LEU 2.8 9.8 + - - +
137A VAL* 4.2 12.7 - - + +
138A TYR* 2.6 37.3 + - - +
223A THR* 3.7 27.6 + - + +
224A VAL* 1.3 71.5 - - - +
226A ALA* 1.3 58.8 + - - +
227A PHE* 3.7 19.2 + + + -
254A VAL* 3.5 31.5 - - + +
256A VAL* 4.3 3.8 - - + -
373A PHE* 3.8 34.6 + + - -
376A ALA* 6.1 0.2 - - + -
377A GLN* 5.3 6.8 + - - +
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Residues in contact with ALA 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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138A TYR* 3.9 7.9 - - + -
197A GLY 4.6 0.2 - - - +
198A PRO* 4.5 1.8 - - + -
201A ALA* 3.8 22.4 - - + -
224A VAL 4.1 0.8 + - - -
225A TYR* 1.3 72.3 - - - +
227A PHE* 1.3 64.6 + - - +
228A LEU* 3.5 16.9 + - + +
253A LEU* 5.0 0.6 - - + +
254A VAL 3.0 7.5 + - - -
255A PHE* 3.6 28.6 - - + -
256A VAL* 2.8 28.7 + - - -
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Residues in contact with PHE 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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113A SER* 6.1 0.9 - - - -
116A ILE* 3.7 27.4 - - + -
117A TYR* 3.1 44.6 - + - +
120A CYS* 4.0 13.7 - - - -
125A PHE* 3.5 35.0 - + - -
137A VAL* 3.8 16.8 - - + -
138A TYR 3.0 17.5 + - - +
140A GLN* 3.5 23.2 - - + +
191A THR* 5.9 0.9 - - - -
225A TYR* 3.7 21.3 - + + -
226A ALA* 1.3 70.9 - - - +
228A LEU* 1.3 64.3 + - - +
232A GLU* 4.6 1.0 - - - +
256A VAL* 3.5 25.6 - - + -
373A PHE* 4.4 0.7 - + - -
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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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138A TYR* 6.2 0.7 - - + -
140A GLN* 4.1 7.2 + - - +
197A GLY* 4.6 2.2 - - - -
198A PRO* 3.6 35.9 - - + -
226A ALA* 3.7 17.3 - - + +
227A PHE* 1.3 80.9 - - - +
229A GLY* 1.3 55.5 + - - +
232A GLU* 3.6 12.8 - - - +
233A MET* 3.4 33.7 - - + -
255A PHE* 3.6 36.3 - - + -
256A VAL 2.8 8.2 + - - +
257A ILE* 4.1 8.5 - - + -
258A ASN* 2.8 35.4 + - - +
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Residues in contact with GLY 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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140A GLN* 3.7 12.7 + - - -
228A LEU* 1.3 75.6 - - - +
230A ASP* 1.3 64.6 + - - -
231A GLY 3.3 2.2 - - - -
232A GLU* 3.3 16.8 + - - +
233A MET* 3.3 17.7 + - - +
257A ILE* 3.9 3.1 - - - -
258A ASN* 4.0 4.9 - - - -
887B TPP 3.6 21.5 - - - -
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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