Contacts of the helix formed by residues 128 - 139 (chain A) in PDB entry 1CXQ
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 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A SER* 2.7 29.2 + - - -
124A SER 3.2 11.2 + - - -
126A PHE 3.5 0.4 - - - -
127A THR* 1.3 79.7 + - - +
129A LYS* 1.3 65.0 + - - +
130A SER* 3.6 4.8 + - - -
131A THR* 3.0 21.1 + - - -
132A ARG* 2.9 26.4 + - - +
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Residues in contact with LYS 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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127A THR 3.7 0.8 + - - -
128A SER* 1.3 73.2 - - - +
130A SER* 1.3 62.7 + - - +
132A ARG* 3.4 6.4 + - - +
133A GLU* 2.9 27.4 + - + +
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Residues in contact with SER 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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98A SER* 4.2 8.3 - - - -
99A VAL* 4.9 5.9 - - - +
102A GLN* 2.9 20.8 + - - -
128A SER* 3.2 8.4 - - - -
129A LYS* 1.3 80.4 - - - +
131A THR* 1.3 56.8 + - - +
133A GLU* 3.3 5.5 + - - +
134A TRP* 3.0 28.4 + - - +
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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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98A SER* 3.4 6.2 + - - -
101A ALA* 4.9 0.2 - - - +
102A GLN* 3.1 20.9 + - + +
105A TRP* 3.6 30.5 - - + -
125A CYS 2.8 23.2 + - - +
126A PHE* 3.5 22.9 - - - +
128A SER* 3.0 15.9 + - - -
130A SER* 1.3 73.9 - - - +
132A ARG* 1.3 66.3 + - - +
134A TRP* 3.2 2.5 + - - +
135A LEU* 3.0 29.1 + - + +
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Residues in contact with ARG 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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126A PHE 4.2 10.3 - - - +
127A THR* 3.6 25.3 + - - +
128A SER 2.9 14.3 + - - +
129A LYS* 3.8 6.5 - - - +
131A THR* 1.3 75.5 - - - +
133A GLU* 1.3 58.7 + - - +
135A LEU* 3.5 6.5 + - - +
136A ALA* 3.0 29.4 + - - +
142A HIS* 4.6 12.3 + - - +
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Residues in contact with GLU 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 LYS* 2.9 21.7 + - + +
130A SER* 3.7 5.8 - - - +
132A ARG* 1.3 77.7 - - - +
134A TRP* 1.3 58.8 + - - +
136A ALA* 3.3 10.9 + - - +
137A ARG* 2.9 42.9 + - - +
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Residues in contact with TRP 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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102A GLN* 3.4 52.7 + - + +
105A TRP* 3.5 42.4 - + + -
106A ALA* 3.8 16.4 - - + -
109A ILE* 3.9 10.3 - - + -
130A SER 3.0 17.5 + - - +
131A THR 3.6 4.0 - - - +
133A GLU* 1.3 75.3 - - - +
135A LEU* 1.3 81.6 + - + +
137A ARG* 3.3 45.5 + - - +
138A TRP* 3.2 50.5 + + - +
140A ILE* 4.8 1.8 - - + -
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Residues in contact with LEU 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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105A TRP* 3.9 30.1 - - + -
118A ILE* 3.9 23.1 - - + -
131A THR* 3.0 24.8 + - + +
132A ARG* 3.9 4.7 - - - +
134A TRP* 1.3 93.7 - - + +
136A ALA* 1.3 61.9 + - - +
138A TRP* 3.2 4.5 + - - +
139A GLY 3.0 16.6 + - - -
140A ILE* 3.1 35.9 + - + +
142A HIS* 3.6 39.5 - - + +
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Residues in contact with ALA 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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132A ARG 3.0 18.3 + - - +
133A GLU* 3.3 15.7 + - - +
135A LEU* 1.3 75.6 - - - +
137A ARG* 1.3 62.9 + - - +
139A GLY* 3.0 14.7 + - - +
140A ILE 4.7 1.8 + - - +
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Residues in contact with ARG 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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102A GLN* 5.6 0.2 + - - -
133A GLU* 2.9 27.8 + - - +
134A TRP* 3.3 49.6 - - - +
136A ALA* 1.3 77.3 - - - +
138A TRP* 1.3 70.2 + - - +
139A GLY 3.6 0.2 + - - -
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Residues in contact with TRP 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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106A ALA* 5.5 5.8 - - + -
109A ILE* 3.8 40.2 - - + -
114A ARG* 3.1 59.7 + - + +
134A TRP* 3.2 52.6 + + - +
135A LEU* 3.2 6.8 + - - +
136A ALA 3.2 0.6 - - - -
137A ARG* 1.3 90.6 - - + +
139A GLY* 1.3 60.0 + - - +
140A ILE* 3.6 20.1 + - + -
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Residues in contact with GLY 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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114A ARG* 5.2 2.6 - - - -
115A PRO 4.9 2.3 - - - +
116A LYS* 4.6 3.5 - - - +
135A LEU 3.0 1.0 + - - -
136A ALA* 3.0 17.9 + - - -
137A ARG 3.3 0.8 + - - -
138A TRP* 1.3 77.8 - - - +
140A ILE* 1.3 61.0 + - - +
141A ALA 4.0 1.2 + - - -
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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