Contacts of the strand formed by residues 147 - 153 (chain A) in PDB entry 5J3S
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 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A PHE* 3.6 29.6 - - + -
115A SER 3.4 7.7 + - - +
116A LEU* 3.1 11.8 - - + -
117A ILE 3.1 20.3 + - - -
145A PRO* 3.9 2.6 - - - +
146A ASP* 1.3 83.8 - - + +
148A ILE* 1.3 69.9 + - - +
149A PHE* 3.5 33.7 - - + -
182A ILE* 4.2 1.8 - - + -
183A MET 3.4 10.1 - - - +
184A LEU* 4.0 8.1 - - + -
189A VAL* 4.4 6.7 - - + -
222A LEU* 3.6 24.5 - - + -
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Residues in contact with ILE 148 (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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117A ILE* 3.5 11.9 - - + +
140A LEU* 3.6 39.9 - - + -
145A PRO* 3.6 20.6 - - + -
147A VAL* 1.3 81.5 - - - +
149A PHE* 1.3 64.9 + - - +
150A LEU* 3.7 30.3 - - + -
168A TYR* 3.9 24.7 - - + -
181A ALA 3.8 0.3 - - - +
182A ILE* 3.3 10.0 - - - +
183A MET* 2.9 50.3 + - + -
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Residues in contact with PHE 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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116A LEU* 3.7 31.0 - - + -
117A ILE 2.8 12.2 + - - +
118A THR* 3.4 12.0 - - - +
119A TRP 3.0 26.0 + - - -
147A VAL* 3.5 27.1 - - + -
148A ILE* 1.3 72.3 - - - +
150A LEU* 1.3 61.6 + - - +
151A GLN* 3.2 8.2 + - - +
181A ALA 3.6 3.1 - - - -
182A ILE* 3.7 17.9 - - + -
222A LEU* 3.6 32.1 - - + -
223A MET 3.4 16.6 - - - -
224A THR* 3.5 30.1 - - - +
258A ILE 4.3 2.9 - - - -
260A ALA* 3.8 18.8 - - + +
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Residues in contact with LEU 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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117A ILE* 6.1 0.2 - - + -
119A TRP* 3.4 20.4 - - + +
121A ILE* 3.8 22.7 - - + -
136A VAL* 5.2 6.1 - - + -
140A LEU* 5.3 4.3 - - + -
148A ILE* 3.7 20.0 - - + -
149A PHE* 1.3 75.4 - - - +
151A GLN* 1.3 64.4 + - - +
153A VAL* 4.0 15.5 - - + -
161A LEU* 3.5 33.2 - - + -
180A THR* 3.3 5.7 - - - -
181A ALA* 2.8 43.5 + - + +
183A MET* 3.7 24.5 - - + -
224A THR* 4.5 0.5 + - - -
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Residues in contact with GLN 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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118A THR* 3.9 2.0 - - - +
119A TRP 3.3 5.8 + - - -
120A ASN* 3.2 35.1 + - + +
121A ILE* 3.3 14.6 + - - +
149A PHE* 3.2 25.0 + - - +
150A LEU* 1.3 75.4 - - - +
152A GLU* 1.3 74.0 + - - +
153A VAL* 3.6 1.8 - - - -
180A THR* 3.7 13.5 - - + +
224A THR* 3.0 22.4 + - - -
225A SER 3.4 20.4 - - - +
226A HIS* 3.5 17.5 - - - +
261A GLY* 3.4 10.5 - - - -
262A ASP* 3.6 18.9 + - + +
316A ASP* 3.7 5.2 - - - +
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Residues in contact with GLU 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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120A ASN* 3.1 26.8 + - - +
121A ILE* 3.4 4.9 - - - +
122A ASP* 2.8 33.1 - - - +
123A GLY* 2.9 25.7 + - - +
124A LEU* 3.9 23.8 + - + +
151A GLN* 1.3 73.7 - - - +
153A VAL* 1.3 58.6 + - - +
178A TYR* 4.0 31.5 - - + -
179A PHE 3.4 8.3 + - - -
180A THR* 5.0 0.6 - - - +
206A ARG* 5.2 1.2 + - - -
226A HIS* 3.3 30.0 + - + -
229A SER* 5.3 0.5 + - - -
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Residues in contact with VAL 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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121A ILE* 3.7 19.3 - - + -
150A LEU* 4.0 19.1 - - + -
151A GLN 3.9 7.9 - - - +
152A GLU* 1.3 76.1 - - - +
154A ILE* 1.3 74.0 + - - +
157A TYR* 3.7 16.4 - - + -
158A TYR* 3.7 18.6 - - + +
161A LEU* 5.0 4.9 - - + -
178A TYR* 3.3 4.5 - - - -
179A PHE* 2.9 53.4 + - + +
181A ALA* 4.3 12.1 - - + -
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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