Contacts of the strand formed by residues 142 - 147 (chain A) in PDB entry 5I2Y
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 ALA 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A GLN 3.4 12.1 - - - +
124A ALA* 4.0 16.1 - - + +
141A GLY* 1.3 75.1 - - - -
143A THR* 1.3 57.1 + - - +
144A LEU* 4.3 3.6 - - + -
156A LEU* 3.4 5.2 - - - +
157A VAL* 2.7 38.5 + - + -
162A LEU* 3.9 5.5 - - + +
174A PHE* 3.5 38.6 - - + -
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Residues in contact with THR 143 (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 LEU* 2.9 37.8 + - + +
122A GLN* 2.7 31.5 + - - +
141A GLY 4.3 2.3 + - - -
142A ALA* 1.3 75.4 + - - +
144A LEU* 1.3 66.1 + - - +
154A ARG* 3.9 33.4 - - + +
155A CYS 3.3 6.5 - - - +
156A LEU* 3.9 14.5 - - + +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.6 28.0 - - + -
119A GLU 3.5 3.1 - - - -
120A VAL* 3.9 17.7 - - + -
121A LEU* 4.2 5.6 - - - +
142A ALA* 4.3 2.9 - - + -
143A THR* 1.3 82.0 - - - +
145A LEU* 1.3 60.2 + - - +
146A VAL* 4.2 8.7 - - + -
153A VAL 3.6 0.2 - - - +
154A ARG* 3.3 6.8 - - - +
155A CYS* 2.8 34.7 + - + +
157A VAL* 3.7 28.3 - - + -
174A PHE* 3.9 35.9 - - + -
182A LEU* 3.9 22.4 - - + -
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Residues in contact with LEU 145 (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 LEU* 3.8 1.9 - - - +
118A LEU* 2.8 47.3 + - + +
119A GLU* 2.8 39.1 + - + +
121A LEU* 4.3 14.5 - - + +
144A LEU* 1.3 72.5 - - - +
146A VAL* 1.3 59.6 + - - +
152A SER* 3.7 28.7 - - - +
153A VAL* 3.5 15.0 - - - +
154A ARG* 4.3 4.9 - - + +
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TRP* 4.9 5.4 - - + -
99A ILE* 4.0 1.1 - - + +
115A GLY* 4.2 14.4 - - - -
116A GLN 3.3 11.7 - - - +
117A LEU* 4.7 2.7 - - + -
118A LEU* 4.7 0.2 - - - -
144A LEU* 4.2 12.1 - - + -
145A LEU* 1.3 77.3 - - - +
147A SER* 1.3 70.0 + - - +
151A HIS 3.9 0.2 - - - +
152A SER* 3.0 4.3 - - - -
153A VAL* 2.8 43.4 + - + +
155A CYS* 3.6 30.7 - - + -
182A LEU* 4.1 25.8 - - + -
184A LEU* 4.8 11.2 - - + -
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Residues in contact with SER 147 (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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99A ILE* 4.4 0.7 - - - -
115A GLY* 3.3 6.4 - - - -
116A GLN* 2.7 45.3 + - - -
118A LEU* 3.6 34.8 - - - +
146A VAL* 1.3 77.0 - - - +
148A ASP* 1.3 62.2 + - - +
149A GLY* 3.0 16.7 + - - -
151A HIS 3.3 10.5 + - - -
152A SER* 4.1 1.8 - - - +
219A LEU 5.2 0.3 + - - -
221A VAL* 4.0 12.9 - - - +
93B LEU* 3.8 1.5 - - - +
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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