Contacts of the helix formed by residues 121 - 135 (chain A) in PDB entry 3BFR
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ILE* 3.8 11.8 + - - +
116A ASP* 3.6 10.0 + - - -
119A PHE* 3.2 5.4 + - - +
120A GLY* 1.3 80.1 - - - +
122A LEU* 1.3 64.1 + - - +
123A ASP* 3.5 10.5 + - - +
124A GLU* 3.3 31.5 + - - +
125A LEU 3.4 8.8 + - - -
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Residues in contact with LEU 122 (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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104A GLY 5.9 1.3 - - - +
106A PRO* 3.9 18.6 - - + -
107A PRO* 3.7 33.9 - - + -
115A ILE* 3.9 18.8 - - + +
116A ASP* 4.1 3.4 + - - +
121A SER* 1.3 72.9 - - - +
123A ASP* 1.3 62.1 + - - +
125A LEU* 3.1 6.6 + - + +
126A ILE* 2.9 44.7 + - + +
203A TRP* 3.6 40.2 - - + +
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Residues in contact with ASP 123 (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 SER* 3.3 9.2 + - - +
122A LEU* 1.3 82.3 - - - +
124A GLU* 1.3 58.4 + - + +
126A ILE* 3.7 15.6 - - - +
127A LYS* 2.9 45.6 + - - +
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Residues in contact with GLU 124 (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 PHE* 3.3 30.5 - - + +
120A GLY* 5.4 0.7 - - - -
121A SER* 3.3 15.3 + - - +
122A LEU 3.2 0.8 - - - -
123A ASP* 1.3 76.5 - - + +
125A LEU* 1.3 59.0 + - - +
127A LYS* 3.4 35.0 + - - +
128A LEU* 3.0 27.5 + - - +
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Residues in contact with LEU 125 (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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115A ILE* 3.6 37.9 - - + -
119A PHE* 3.7 41.3 - - + +
121A SER 3.4 6.2 + - - +
122A LEU* 3.1 9.7 + - + +
124A GLU* 1.3 73.6 - - - +
126A ILE* 1.3 56.9 + - - +
128A LEU* 3.4 2.9 + - + +
129A THR* 2.8 38.0 + - - +
144A ILE* 4.1 24.5 - - + -
154A LEU* 4.9 0.4 - - + -
156A VAL* 3.6 26.9 - - + -
203A TRP* 4.2 17.0 - - + -
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Residues in contact with ILE 126 (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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122A LEU* 2.9 41.4 + - + +
123A ASP* 3.7 15.5 - - - +
125A LEU* 1.3 76.2 - - - +
127A LYS* 1.3 58.3 + - + +
129A THR* 3.2 7.5 + - - -
130A ASN* 2.9 37.2 + - - +
198A TRP* 3.5 61.2 - - + +
203A TRP* 4.4 10.5 - - + +
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Residues in contact with LYS 127 (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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123A ASP* 2.9 29.5 + - - +
124A GLU* 3.5 32.5 + - - +
125A LEU 3.3 0.2 - - - -
126A ILE* 1.3 78.1 - - + +
128A LEU* 1.3 62.0 + - - +
130A ASN* 3.4 9.2 + - - +
131A THR* 3.0 26.3 + - - -
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Residues in contact with LEU 128 (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 PHE* 3.7 31.4 - - + -
124A GLU 3.0 13.6 + - - +
125A LEU* 3.6 8.1 - - + +
127A LYS* 1.3 74.9 - - - +
129A THR* 1.3 63.1 + - - +
131A THR* 3.1 13.4 + - + -
132A LYS* 3.0 44.9 + - + +
155A ASP* 5.3 3.1 - - - +
156A VAL* 3.9 25.1 - - + +
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Residues in contact with THR 129 (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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125A LEU 2.8 21.8 + - - -
126A ILE 3.2 4.2 + - - -
128A LEU* 1.3 77.2 - - - +
130A ASN* 1.3 57.6 + - - +
132A LYS* 3.1 3.3 + - - +
133A LEU* 2.8 37.0 + - + +
142A ALA* 4.2 9.9 - - + -
144A ILE* 3.6 17.8 - - + +
156A VAL* 3.6 33.8 - - + +
175A ILE* 4.7 4.7 - - + -
198A TRP* 3.6 28.9 - - + -
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Residues in contact with ASN 130 (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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126A ILE* 2.9 35.4 + - - +
127A LYS* 3.7 7.8 - - - +
129A THR* 1.3 75.0 - - - +
131A THR* 1.3 58.3 + - - +
133A LEU* 3.7 9.7 - - - +
134A ALA* 3.0 29.1 + - - +
194A PHE* 3.2 28.6 + - + +
195A LYS* 4.2 10.9 - - - +
198A TRP* 2.8 25.5 + - - +
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Residues in contact with THR 131 (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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127A LYS 3.0 14.8 + - - -
128A LEU* 3.1 17.0 + - + -
130A ASN* 1.3 77.0 - - - +
132A LYS* 1.3 58.3 + - + +
134A ALA* 3.5 5.6 + - - +
135A GLY* 3.0 25.1 + - - -
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Residues in contact with LYS 132 (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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128A LEU* 3.0 38.0 + - + +
129A THR 3.4 7.0 - - - +
131A THR* 1.3 75.4 - - + +
133A LEU* 1.3 62.3 + - - +
135A GLY 3.3 2.6 + - - -
136A VAL* 3.3 7.8 + - - +
142A ALA* 4.4 5.4 - - + -
155A ASP* 5.0 3.2 + - - -
156A VAL* 3.2 45.9 + - + +
157A VAL* 5.0 1.2 - - - +
158A GLN* 2.6 49.9 + - + +
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Residues in contact with LEU 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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129A THR* 2.8 30.0 + - + +
130A ASN* 3.7 21.8 - - - +
131A THR 3.3 0.2 - - - -
132A LYS* 1.3 74.7 - - - +
134A ALA* 1.3 64.6 + - - +
136A VAL* 3.2 23.0 + - - +
142A ALA* 3.6 24.2 - - + +
175A ILE* 3.6 44.6 - - + +
177A ALA* 4.0 17.2 - - + +
190A LYS* 5.2 1.2 + - - +
194A PHE* 3.6 34.8 - - + -
198A TRP* 4.6 2.5 - - + +
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Residues in contact with ALA 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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130A ASN 3.0 17.9 + - - +
131A THR* 3.9 4.9 - - - +
133A LEU* 1.3 76.5 - - - +
135A GLY* 1.3 59.4 + - - +
136A VAL 3.3 2.2 + - - +
137A GLN* 5.4 1.6 - - - +
190A LYS* 3.4 29.2 + - + +
191A ALA* 5.8 6.1 - - + -
194A PHE* 3.6 16.3 - - + -
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Residues in contact with GLY 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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131A THR 3.0 13.4 + - - -
132A LYS 3.3 4.0 + - - -
133A LEU 3.1 0.6 - - - -
134A ALA* 1.3 76.0 - - - +
136A VAL* 1.3 61.4 + - - +
137A GLN* 3.2 18.6 + - - +
158A GLN* 3.3 18.5 + - - +
160A TYR* 3.7 5.4 + - - -
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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