Contacts of the helix formed by residues 123 - 132 (chain A) in PDB entry 1C3Q
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 ASN 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ARG* 4.1 2.8 - - - +
122A GLY* 1.3 77.3 - - - -
124A ALA* 1.3 65.8 + - - +
125A ALA* 3.1 10.3 + - - +
126A GLU* 2.8 53.4 + - - +
127A ILE* 3.1 18.7 + - - +
167A ILE* 3.7 2.0 - - - -
168A THR 3.9 15.9 - - - +
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Residues in contact with ALA 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 ASN* 1.3 74.6 - - - +
125A ALA* 1.3 62.7 + - - +
127A ILE* 3.3 0.6 + - - -
128A ALA* 2.9 25.3 + - - +
150A ILE* 3.5 32.8 - - + -
153A LEU* 3.7 11.5 - - + +
167A ILE* 3.3 17.7 - - + +
168A THR 4.7 1.4 + - - -
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Residues in contact with ALA 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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98A ALA 4.7 0.7 - - - +
123A ASN* 3.1 10.5 + - - +
124A ALA* 1.3 78.4 - - - +
126A GLU* 1.3 58.1 + - + +
128A ALA* 3.3 5.6 + - - +
129A HIS* 2.9 47.6 + - + +
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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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94A ASP* 4.6 2.4 - - - +
95A PRO* 3.6 29.5 - - + +
96A VAL* 3.5 8.2 - - - +
97A GLY* 2.8 24.4 + - - +
98A ALA* 3.7 19.7 - - + +
121A ARG* 5.3 1.0 + - - -
122A GLY* 3.5 8.7 - - - -
123A ASN* 2.8 54.2 + - - +
125A ALA* 1.3 73.8 - - + +
127A ILE* 1.3 59.9 + - - +
130A THR* 2.7 35.1 + - - -
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Residues in contact with ILE 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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95A PRO* 4.5 7.0 - - + -
120A ILE* 3.9 30.5 - - + +
122A GLY* 4.3 15.3 - - - +
123A ASN 3.1 14.9 + - - +
124A ALA 3.8 6.1 - - - +
126A GLU* 1.3 76.0 - - - +
128A ALA* 1.3 59.6 + - - +
130A THR* 3.6 5.0 - - + +
131A VAL* 3.0 33.2 + - + +
153A LEU* 4.4 6.5 - - + -
157A ALA* 4.0 26.7 - - + -
165A ILE* 4.2 18.2 - - + -
167A ILE* 3.8 27.1 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.8 + - - +
125A ALA* 3.3 7.8 + - - +
127A ILE* 1.3 78.4 - - - +
129A HIS* 1.3 59.0 + - + +
131A VAL* 4.8 0.8 - - - +
132A GLY* 2.9 28.6 + - - +
138A ILE* 5.4 3.8 - - + +
153A LEU* 4.2 21.1 - - + +
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Residues in contact with HIS 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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98A ALA 3.9 5.2 - - - +
99A GLY* 3.6 41.4 + - - +
105A THR* 3.8 7.7 + - + +
109A ARG* 2.8 32.1 + - - -
125A ALA* 2.9 37.7 + - + +
126A GLU 4.1 0.9 - - - +
128A ALA* 1.3 80.6 - - + +
130A THR* 1.3 54.8 + - - +
132A GLY* 3.8 3.0 + - - +
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Residues in contact with THR 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 PRO* 4.0 10.6 - - + +
98A ALA* 3.4 18.1 - - - +
105A THR* 4.8 3.6 - - - -
108A ALA* 4.2 12.9 - - + +
109A ARG* 2.9 33.8 + - + +
112A ILE* 3.5 31.9 - - + -
120A ILE* 5.8 3.4 - - + -
126A GLU 2.7 23.1 + - - -
127A ILE* 3.6 7.9 - - + -
129A HIS* 1.3 77.2 - - - +
131A VAL* 1.3 66.4 + - + +
133A VAL* 4.9 1.6 - - - +
161A LEU* 5.2 1.3 - - + -
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Residues in contact with VAL 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 ILE* 3.0 20.2 + - + +
128A ALA* 4.8 0.4 - - - +
130A THR* 1.3 77.7 - - + +
132A GLY* 1.3 59.6 + - - +
133A VAL* 2.8 21.4 + - - +
137A LEU* 4.4 8.9 - - + +
138A ILE* 4.0 26.7 - - + -
153A LEU* 6.1 0.4 - - + -
157A ALA* 3.9 17.7 - - + -
160A LYS* 4.3 28.7 + - + -
161A LEU* 3.6 32.5 - - + -
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Residues in contact with GLY 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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109A ARG* 3.5 12.6 + - - -
128A ALA 2.9 20.6 + - - -
129A HIS* 3.8 2.5 + - - +
130A THR 3.4 1.8 - - - -
131A VAL* 1.3 73.3 - - - +
133A VAL* 1.3 60.5 + - - -
134A THR 3.0 21.0 + - - +
137A LEU* 5.0 1.3 - - - -
138A ILE* 4.9 10.5 - - - +
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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