Contacts of the helix formed by residues 123 - 132 (chain A) in PDB entry 3WBR
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 THR 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A GLN* 5.2 3.6 + - - -
121A ILE* 3.6 7.2 - - - +
122A ASN* 1.3 85.7 - - + +
124A ARG* 1.3 59.7 + - - +
125A GLU* 3.5 18.2 + - - +
126A GLU* 3.0 25.2 + - - +
127A GLN* 3.0 23.4 + - - +
165B VAL* 3.8 9.2 - - - -
167B PHE* 4.5 1.6 - - - -
91D GLN* 5.6 4.3 + - - +
122D ASN* 5.0 8.7 - - + +
123D THR* 3.6 30.2 - - + +
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Residues in contact with ARG 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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123A THR* 1.3 73.3 - - - +
125A GLU* 1.3 70.4 + - - +
127A GLN* 3.2 5.9 + - - +
128A ASP* 2.8 66.2 + - - +
131A ILE* 5.5 2.0 - - - +
165B VAL* 4.0 7.1 - - + +
167B PHE* 3.5 36.8 - - + -
92D SER* 5.0 6.1 - - - +
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Residues in contact with GLU 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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90A PHE* 3.9 14.6 - - + -
91A GLN* 5.2 0.2 - - - +
123A THR* 3.6 19.0 - - - +
124A ARG* 1.3 82.2 + - + +
126A GLU* 1.3 57.3 + - - +
128A ASP* 3.4 8.7 + - - +
129A PHE* 2.9 27.5 + - - +
91D GLN* 3.4 50.7 - - + +
92D SER* 2.5 30.3 + - - -
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Residues in contact with GLU 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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90A PHE* 4.0 13.2 - - + -
91A GLN* 5.4 2.5 - - - +
95A TYR* 2.5 31.2 + - + +
119A VAL* 4.4 0.3 - - - +
120A VAL 3.3 8.9 - - - +
121A ILE* 4.0 4.3 - - + -
122A ASN* 2.8 38.7 + - - +
123A THR* 3.0 21.4 + - - +
125A GLU* 1.3 74.7 - - - +
127A GLN* 1.3 65.9 + - - +
129A PHE* 3.2 2.9 + - - +
130A ILE* 3.0 40.8 + - + +
207A LYS* 2.6 25.0 + - - +
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Residues in contact with GLN 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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121A ILE* 3.6 19.3 - - + +
123A THR 3.0 7.9 + - - +
124A ARG* 3.2 10.5 + - - +
126A GLU* 1.3 76.0 - - - +
128A ASP* 1.3 70.6 + - - +
130A ILE* 3.3 5.4 + - - +
131A ILE* 3.1 36.2 + - + +
183A ILE* 3.6 23.4 - - - +
191A TRP* 4.6 9.1 + - - +
192A GLY* 4.7 3.4 - - - -
193A TRP* 3.1 20.2 + - - +
167B PHE* 3.7 53.3 - - + +
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Residues in contact with ASP 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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124A ARG* 2.8 63.4 + - - +
125A GLU* 3.6 8.6 - - - +
127A GLN* 1.3 75.6 - - - +
129A PHE* 1.3 65.6 - - - +
131A ILE* 3.4 29.6 - - - +
132A GLN* 3.5 18.9 + - - +
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Residues in contact with PHE 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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88A THR* 3.5 26.2 - - + -
89A SER 3.5 16.4 - - - -
90A PHE* 3.5 49.4 - + + -
95A TYR* 3.8 26.0 - + + -
125A GLU 2.9 15.0 + - - +
126A GLU 3.7 6.1 - - - +
128A ASP* 1.3 77.2 - - - +
130A ILE* 1.3 68.4 + - + +
132A GLN* 3.4 15.2 + - - +
133A ASN* 2.7 51.9 + - + -
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Residues in contact with ILE 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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95A TYR* 4.0 20.0 - - + -
97A ILE* 5.8 0.9 - - + -
119A VAL* 3.6 27.8 - - + -
121A ILE* 3.7 19.3 - - + -
126A GLU* 3.0 35.3 + - + +
127A GLN* 3.6 4.3 - - - +
129A PHE* 1.3 83.2 - - + +
131A ILE* 1.3 58.6 + - - +
133A ASN* 2.8 23.4 + - - +
134A LEU* 3.2 23.9 + - + +
183A ILE* 4.8 8.7 - - + -
205A ILE* 3.9 30.5 - - + -
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Residues in contact with ILE 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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124A ARG* 5.5 1.6 - - - +
127A GLN* 3.1 20.3 + - + +
128A ASP* 3.4 32.8 - - - +
130A ILE* 1.3 76.5 - - + +
132A GLN* 1.3 61.5 + - + +
133A ASN 3.1 0.2 - - - -
134A LEU* 3.3 25.2 + - - +
183A ILE* 3.6 29.8 - - + -
191A TRP* 3.7 52.2 + - + -
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Residues in contact with GLN 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 ASP* 3.5 15.0 + - - +
129A PHE* 3.4 19.5 + - - +
131A ILE* 1.3 81.2 - - + +
133A ASN* 1.3 65.8 + - - +
134A LEU 3.4 2.9 - - - +
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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