Contacts of the strand formed by residues 148 - 154 (chain A) in PDB entry 4R54
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 ARG 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A LEU* 4.9 1.2 - - - +
147A ASP* 1.3 85.7 + - + +
149A ILE* 1.3 70.1 + - - +
150A ILE* 3.6 20.8 - - - +
237A ILE* 4.6 1.1 - - - -
238A ALA* 3.1 24.3 - - + +
257A TYR* 4.9 6.7 - - + -
258A ILE* 3.3 5.2 - - - +
259A GLU* 3.1 63.1 + - + +
148B ARG* 5.1 3.6 - - - +
257B TYR* 2.9 24.2 + - - -
259B GLU* 2.9 24.2 + - - -
310B ASP* 3.3 26.3 + - - -
312B ASP* 5.8 0.8 - - - +
313B ALA* 3.8 10.3 - - - +
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Residues in contact with ILE 149 (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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133A MET* 3.9 30.1 - - + -
134A MET* 4.7 1.1 - - + -
137A LEU* 3.5 20.9 - - + -
146A LEU* 4.4 10.1 - - + -
148A ARG* 1.3 80.9 + - - +
150A ILE* 1.3 77.2 + - - +
151A VAL* 4.4 4.3 - - + -
228A THR* 4.0 26.9 - - + -
237A ILE* 4.3 11.2 - - + -
238A ALA 2.7 11.0 + - - +
239A VAL* 3.4 11.6 - - + -
240A SER* 3.2 23.0 + - - +
256A VAL* 4.3 8.1 - - + -
257A TYR 3.3 9.9 - - - +
258A ILE* 4.0 9.4 - - + -
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Residues in contact with ILE 150 (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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148A ARG* 3.6 26.0 - - - +
149A ILE* 1.3 77.5 - - - +
151A VAL* 1.3 67.6 + - - +
152A SER* 5.4 3.6 - - - +
240A SER* 3.4 4.9 - - - +
241A ALA* 5.9 0.2 - - - -
255A SER 4.0 1.2 - - - +
256A VAL* 3.9 0.2 - - - -
257A TYR* 2.8 51.4 + - + +
150B ILE* 4.0 20.6 - - + -
257B TYR* 3.6 44.6 - - + -
310B ASP* 4.8 1.8 - - - +
318B HIS* 3.9 26.0 - - + +
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Residues in contact with VAL 151 (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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133A MET* 4.0 16.6 - - + -
149A ILE* 4.4 6.5 - - + -
150A ILE* 1.3 79.5 - - - +
152A SER* 1.3 73.9 + - - +
153A THR* 4.2 2.2 - - + -
224A MET* 3.7 27.1 - - + -
239A VAL* 5.0 3.1 - - + -
240A SER 3.2 6.7 + - - +
241A ALA* 3.2 28.1 - - + +
242A THR* 2.9 25.2 + - - +
254A GLU* 4.1 8.3 - - + -
255A SER 3.4 11.7 - - - +
256A VAL* 4.0 17.0 - - + -
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Residues in contact with SER 152 (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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150A ILE* 5.4 4.2 - - - +
151A VAL* 1.3 75.9 + - - +
153A THR* 1.3 62.8 + - - +
154A TYR* 3.7 3.1 - - - -
242A THR* 3.2 7.1 - - - -
254A GLU* 3.7 0.9 - - - -
255A SER 2.9 31.5 + - - -
152B SER* 4.0 21.9 + - - -
154B TYR* 3.5 15.3 - - - -
255B SER* 2.7 32.0 + - - -
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Residues in contact with THR 153 (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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129A SER* 4.5 0.9 - - - +
151A VAL* 4.2 3.8 - - + -
152A SER* 1.3 73.7 - - - +
154A TYR* 1.3 65.0 + - - +
155A GLN* 2.7 34.2 + - - +
224A MET* 3.8 29.2 - - + -
242A THR 2.8 9.4 + - - +
243A CYS* 3.1 20.5 - - - -
244A VAL* 3.1 16.1 + - - +
253A SER 3.7 6.5 - - - -
254A GLU* 4.1 17.9 - - + +
154B TYR* 2.8 17.7 + - - -
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Residues in contact with TYR 154 (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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152A SER* 3.7 14.6 - - - -
153A THR* 1.3 78.8 - - - +
155A GLN* 1.3 60.0 + - - +
156A ALA 3.9 0.3 + - - -
244A VAL 3.6 2.9 - - - -
246A ILE* 3.8 21.6 - - + +
248A VAL* 5.8 0.3 - - - +
251A ALA 4.3 1.7 - - - +
252A HIS* 3.6 1.9 - - - -
253A SER* 2.8 44.7 + - - +
255A SER* 4.0 6.0 - - - -
320A TRP* 3.7 21.5 - + - -
152B SER* 3.5 18.4 - - - -
153B THR 2.8 24.4 + - - -
154B TYR* 3.3 44.1 - + - -
205B ALA* 4.8 0.7 - - + -
244B VAL* 3.4 28.9 - - + +
246B ILE* 4.0 16.4 - - + -
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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