Contacts of the strand formed by residues 132 - 139 (chain A) in PDB entry 4ED5
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 ILE 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLU* 3.6 56.1 - - + +
126A PHE* 4.1 9.2 - - + -
127A SER* 3.8 18.2 - - - +
130A GLY 3.4 9.3 + - - +
131A ARG* 1.3 81.8 + - - +
133A ILE* 1.3 64.1 + - - +
134A ASN* 3.8 20.6 - - - +
135A SER* 4.5 3.8 - - - -
152A ILE* 4.3 9.2 - - + -
153A ARG 3.5 9.0 - - - +
154A PHE* 4.0 12.8 - - + -
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Residues in contact with ILE 133 (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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92A LYS* 3.6 14.2 + - - +
97A ARG* 3.5 46.7 - - - +
131A ARG* 3.8 23.8 - - - +
132A ILE* 1.3 74.3 - - - +
134A ASN* 1.3 67.7 + - - +
153A ARG* 2.7 17.4 + - + +
154A PHE 3.8 16.8 - - - +
155A ASP* 3.8 11.0 - - + +
8D U 3.3 38.1 - - + +
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Residues in contact with ASN 134 (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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26A TYR* 4.8 2.9 - - - +
92A LYS* 4.3 4.9 - - + +
107A ASN* 5.1 1.9 - - - +
123A GLU* 5.3 1.1 - - - -
132A ILE* 3.6 6.1 - - - +
133A ILE* 1.3 79.1 - - - +
135A SER* 1.3 62.4 + - - +
152A ILE* 3.7 0.3 - - - -
153A ARG* 2.9 62.8 + - - +
8D U 3.5 33.5 - - - +
102D GOL 2.8 38.3 + - - -
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Residues in contact with SER 135 (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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119A GLN* 2.7 32.4 + - - +
122A VAL* 5.9 1.8 - - - -
123A GLU* 2.3 42.7 + - - +
132A ILE* 4.5 2.0 - - - -
134A ASN* 1.3 77.8 + - - +
136A ARG* 1.3 64.0 + - - +
151A PHE 3.1 15.5 - - - -
152A ILE* 4.2 9.9 - - - -
102D GOL 3.8 8.6 - - - -
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Residues in contact with ARG 136 (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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119A GLN* 4.2 6.4 - - - +
135A SER* 1.3 78.8 + - - +
137A VAL* 1.3 78.8 + - - +
138A LEU* 3.7 25.1 + - + -
150A ALA* 3.0 6.6 - - - +
151A PHE* 2.7 37.5 + - + -
202A GOL 5.0 5.6 + - - -
4D U 3.6 12.6 - - - +
5D U 3.2 62.1 + - - -
102D GOL 3.5 23.7 + - - +
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Residues in contact with VAL 137 (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 LEU* 5.9 1.6 - - + -
117A MET 4.4 4.5 - - - +
118A THR 4.3 0.2 - - - -
119A GLN* 3.8 31.2 - - + +
122A VAL* 3.9 23.8 - - + -
136A ARG* 1.3 85.8 + - - +
138A LEU* 1.3 63.6 + - - +
139A VAL* 3.7 1.6 + - - +
146A SER* 3.3 29.8 - - - +
148A GLY* 5.4 0.9 - - - -
149A VAL 3.6 9.9 - - - +
150A ALA* 3.9 6.5 - - + -
202A GOL 2.8 48.4 + - - +
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Residues in contact with LEU 138 (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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136A ARG* 3.7 22.7 - - + -
137A VAL* 1.3 72.4 - - - +
139A VAL* 1.3 55.1 + - - +
146A SER* 3.6 5.2 + - - -
147A ARG* 2.8 41.5 + - - +
149A VAL* 2.9 36.7 + - + +
150A ALA* 5.2 0.2 - - - -
151A PHE* 4.2 8.7 - - + -
3D U 3.8 31.2 - - - -
4D U 3.5 31.4 - - - +
5D U 4.2 5.8 - - - +
101D GOL 3.9 20.2 - - - +
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Residues in contact with VAL 139 (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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137A VAL 3.7 1.1 + - - +
138A LEU* 1.3 74.1 - - - +
140A ASP* 1.3 69.8 + - - +
141A GLN* 3.4 13.9 + - + +
144A GLY* 3.4 35.4 - - - +
145A LEU 3.5 4.3 - - - +
146A SER* 4.5 3.6 - - - -
147A ARG* 3.9 4.0 - - - -
202A GOL 3.1 40.4 - - - +
5D U 5.5 1.6 + - - -
101D GOL 3.0 18.5 + - - -
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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