Contacts of the strand formed by residues 148 - 155 (chain D) in PDB entry 5OA3
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 LYS 148 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13342 G 5.3 0.6 + - - -
138D VAL 3.7 1.4 - - - +
139D SER* 3.3 2.6 - - - -
140D GLY 2.9 32.9 + - - +
142D LEU* 3.8 39.9 - - + +
143D ARG* 3.1 40.0 - - - +
146D ARG* 4.0 6.4 + - + -
147D ALA* 1.3 77.2 - - - +
149D SER* 1.3 61.5 + - - +
150D MET* 4.2 4.0 - - + -
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Residues in contact with SER 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D VAL* 3.7 23.0 - - - +
138D VAL 3.3 4.0 - - - -
139D SER* 3.7 14.3 - - - -
147D ALA 4.2 0.6 + - - -
148D LYS* 1.3 75.5 - - - +
150D MET* 1.3 62.6 + - - +
151D LYS* 4.0 3.3 + - - +
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Residues in contact with MET 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D VAL* 4.1 16.6 - - - -
116D ARG* 3.3 43.1 - - + +
136D VAL 3.7 1.2 - - - +
137D VAL* 3.3 4.7 - - - +
138D VAL* 2.9 38.6 + - + +
142D LEU* 3.5 29.4 - - + -
148D LYS* 5.4 3.6 - - + -
149D SER* 1.3 76.5 - - - +
151D LYS* 1.3 58.7 + - - +
152D PHE* 3.5 35.0 - - + -
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Residues in contact with LYS 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14852 U 2.7 42.6 + - - -
14862 A 3.6 28.6 + - - +
135D GLU* 3.5 24.2 - - + +
136D VAL 3.4 2.9 - - - -
137D VAL* 3.8 23.6 - - + -
149D SER* 4.0 4.4 + - - +
150D MET* 1.3 74.8 - - - +
152D PHE* 1.3 70.2 + - - +
153D VAL* 3.6 20.2 + - + +
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Residues in contact with PHE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C GLU* 5.4 6.5 - - - +
115D VAL* 5.0 0.4 - - + -
116D ARG* 4.9 6.1 - - + -
119D CYS* 3.9 33.7 - - + -
120D TYR* 4.0 35.2 - + + -
123D LEU* 3.4 26.5 - - + +
135D GLU* 3.3 3.6 - - - -
136D VAL* 2.9 53.1 + - + -
138D VAL* 4.5 5.2 - - + -
150D MET* 3.5 56.3 - - + -
151D LYS* 1.3 77.4 - - - +
153D VAL* 1.3 62.6 + - - +
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Residues in contact with VAL 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14852 U 5.9 3.4 - - - +
14862 A 5.3 2.2 - - - +
146C GLU* 4.7 11.0 + - - +
123D LEU* 4.8 1.2 - - - +
134D CYS 3.9 6.5 - - - +
135D GLU* 3.7 14.1 - - + +
151D LYS* 3.6 37.2 + - + +
152D PHE* 1.3 75.9 - - - +
154D ASP* 1.3 69.9 + - - +
155D GLY 4.7 7.9 - - - +
157D MET* 5.7 7.9 - - + -
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Residues in contact with ASP 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D LEU* 3.5 32.0 - - + +
124D ARG* 5.7 0.9 - - - -
127D MET* 3.2 32.5 - - + +
134D CYS 2.9 39.7 + - - +
152D PHE 4.2 0.2 + - - -
153D VAL* 1.3 77.9 - - - +
155D GLY* 1.3 74.1 + - - +
156D LEU 4.2 0.2 - - - +
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Residues in contact with GLY 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D MET* 4.6 4.7 - - - -
132D LYS 3.9 7.9 - - - -
133D GLY* 4.2 0.4 - - - -
153D VAL* 4.7 9.6 - - - +
154D ASP* 1.3 80.1 + - - +
156D LEU* 1.3 68.5 - - - +
157D MET* 3.9 1.4 + - - +
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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