Contacts of the strand formed by residues 146 - 154 (chain B) 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 SER 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B PRO 4.6 0.9 + - - -
115B ARG* 3.0 56.3 + - - +
117B MET 4.6 4.5 + - - -
137B VAL* 3.6 19.8 - - - +
138B LEU 3.9 6.7 - - - -
139B VAL* 4.2 6.6 - - - +
144B GLY 4.0 1.4 + - - -
145B LEU* 1.3 77.2 - - - +
147B ARG* 1.3 61.2 + - - +
148B GLY* 3.3 11.1 + - - -
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 5.0 0.6 + - - -
112B GLY 5.5 1.2 + - - -
115B ARG* 2.8 31.8 + - - +
138B LEU* 3.1 37.8 + - - +
139B VAL 4.4 8.5 + - - -
140B ASP* 3.7 31.9 - - + +
145B LEU 4.0 0.9 - - - +
146B SER* 1.3 73.6 + - - +
148B GLY* 1.3 58.4 + - - +
149B VAL* 3.1 30.6 + - + +
2C U 3.5 9.9 - - - -
3C U 3.3 24.5 + - - -
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B SER* 3.4 3.1 - - - -
112B GLY* 3.3 10.5 + - - -
113B LEU* 3.0 57.8 + - - +
114B PRO 4.6 1.8 - - - -
115B ARG* 4.1 3.4 - - - +
137B VAL* 5.3 2.0 - - - -
146B SER* 3.3 12.8 + - - -
147B ARG* 1.3 78.6 - - - +
149B VAL* 1.3 58.2 + - - +
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 3.4 44.0 - - + +
110B ILE 3.1 4.5 - - - +
111B SER* 4.0 16.8 - - - -
112B GLY 5.2 0.2 - - - +
137B VAL* 3.5 6.2 - - - +
138B LEU* 2.9 43.3 + - + -
147B ARG* 3.1 35.0 - - + +
148B GLY* 1.3 80.8 - - - +
150B ALA* 1.3 66.6 + - - +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU 3.8 0.2 - - - +
109B TYR* 3.6 5.7 - - - -
110B ILE* 2.7 43.4 + - + +
113B LEU* 3.9 20.6 - - + +
122B VAL* 4.3 15.7 - - + -
136B ARG 3.0 17.0 - - - +
137B VAL* 4.2 4.7 - - + -
138B LEU* 4.6 1.1 - - - +
148B GLY 4.3 0.2 - - - -
149B VAL* 1.3 78.3 - - - +
151B PHE* 1.3 67.9 + - - +
152B ILE* 4.2 0.9 - - + -
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Residues in contact with PHE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASN* 4.0 10.1 - - - +
108B LEU 3.2 15.0 - - - -
109B TYR* 3.9 13.5 - + - -
134B ASN* 6.4 2.0 - - - -
135B SER* 3.2 5.3 - - - -
136B ARG* 2.9 33.3 + - + +
138B LEU* 3.9 17.5 - - + -
150B ALA* 1.3 74.5 - - - +
152B ILE* 1.3 64.2 + - - +
153B ARG 4.2 0.2 - - - -
184B ALA* 3.9 20.0 - - + -
3C U 3.3 39.7 - - - -
4C U 3.3 77.8 - + - +
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ASN* 3.6 2.6 - - - -
108B LEU* 2.7 41.8 + - + +
110B ILE* 3.5 26.4 - - + +
122B VAL* 3.9 32.1 - - + +
123B GLU* 4.6 2.0 - - - -
126B PHE* 4.4 9.2 - - + -
132B ILE* 4.0 26.2 - - + -
134B ASN 3.6 1.8 - - - -
135B SER* 3.5 26.0 - - - -
136B ARG 5.3 0.2 - - - +
150B ALA* 4.2 0.9 - - + -
151B PHE* 1.3 74.1 - - - +
153B ARG* 1.3 60.8 + - - +
154B PHE* 3.9 28.6 + - + -
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ARG* 4.7 2.4 - - - +
103B ILE 3.2 14.5 + - - -
104B LYS 3.2 25.9 + - - -
106B ALA* 3.7 9.8 - - - +
107B ASN* 3.6 35.1 + - - +
132B ILE* 3.6 4.2 - - - +
133B ILE* 2.8 46.8 + - + -
134B ASN* 2.9 32.7 + - - +
151B PHE 4.2 0.2 - - - -
152B ILE* 1.3 73.3 - - - +
154B PHE* 1.3 71.7 + - - +
8C U 3.1 63.8 + - - +
9C U 3.4 3.8 + - - -
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Residues in contact with PHE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ARG* 4.4 0.9 + - - -
106B ALA* 2.9 22.0 + - - +
108B LEU* 3.6 26.5 - - + -
126B PHE* 3.2 39.7 - + + -
129B PHE* 3.7 20.2 - + + -
130B GLY 3.8 13.9 - - - -
131B ARG 3.3 16.4 - - - -
132B ILE* 3.8 8.7 - - + -
133B ILE* 3.8 3.6 - - - +
152B ILE* 3.9 10.8 - - + -
153B ARG* 1.3 87.3 + - - +
155B ASP* 1.3 66.6 + - - +
156B LYS 3.7 12.8 - - - +
159B GLU* 3.5 18.8 - - + +
160B ALA* 3.6 18.6 - - + +
163B ALA* 3.9 10.1 - - + -
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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