Contacts of the helix formed by residues 119 - 129 (chain A) in PDB entry 1A6Y
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 GLU 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A SER* 2.9 34.2 + - - +
112A HIS* 4.7 0.5 + - - -
118A CYS* 1.3 73.3 - - - +
120A GLY* 1.3 57.5 + - - +
122A LYS* 3.0 28.7 + - - +
123A GLY* 3.0 28.6 + - - -
605C A 5.7 0.3 + - - -
631D G 3.8 4.7 - - + +
632D A 3.6 45.8 + - + +
633D C 2.6 35.5 + - + -
634D C 5.0 2.0 + - - -
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Residues in contact with GLY 120 (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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118A CYS* 2.9 7.2 + - - +
119A GLU* 1.3 81.4 - - - +
121A CYS* 1.3 57.5 + - - +
124A PHE* 2.8 31.0 + - - +
150A ARG* 5.0 2.4 - - - +
157A ARG* 3.1 11.0 + - - -
631D G 3.4 39.3 + - - +
632D A 4.6 0.6 + - - -
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Residues in contact with CYS 121 (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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101A CYS* 3.7 11.9 - - - -
103A VAL* 3.8 23.8 - - + -
104A CYS* 3.9 6.5 - - - -
117A ALA* 4.7 4.3 - - + -
118A CYS* 3.0 5.3 + - - +
120A GLY* 1.3 76.2 - - - +
122A LYS* 1.3 61.9 + - - +
124A PHE* 3.7 3.7 - - - +
125A PHE* 2.8 29.8 + - - +
157A ARG* 3.0 30.8 - - - +
161A CYS* 4.4 8.0 - - - -
166A MET* 3.9 4.1 - - + +
550A ZN 2.2 35.0 - - - -
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Residues in contact with LYS 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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112A HIS* 2.8 45.3 + - + +
113A TYR* 3.8 17.6 - - + +
117A ALA* 4.7 0.8 - - + +
118A CYS 3.0 11.8 + - - +
119A GLU* 3.0 34.1 + - - +
121A CYS* 1.3 75.8 - - - +
123A GLY* 1.3 59.2 + - - +
125A PHE* 2.6 24.4 + - - +
126A ARG* 2.9 17.4 + - - +
166A MET* 4.2 11.5 - - - +
605C A 3.3 27.1 + - + +
606C G 2.8 35.3 + - - +
607C G 5.1 0.4 - - - -
633D C 4.6 1.1 - - - +
634D C 4.6 0.4 - - - +
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Residues in contact with GLY 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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119A GLU 3.0 11.4 + - - -
122A LYS* 1.3 80.9 - - - +
124A PHE* 1.3 63.9 + - - +
126A ARG* 3.2 29.5 - - - +
127A ARG* 3.0 41.0 + - - +
631D G 5.0 2.2 - - - -
632D A 5.8 0.9 - - - -
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Residues in contact with PHE 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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120A GLY 2.8 24.1 + - - +
121A CYS 3.9 1.8 - - - +
122A LYS 3.2 0.2 - - - -
123A GLY* 1.3 74.8 - - - +
125A PHE* 1.3 55.6 + - - +
127A ARG* 3.7 13.9 - - - +
128A SER* 2.5 40.6 + - - -
134A TYR* 3.0 43.7 - + - -
154A GLN* 3.6 18.4 - - + -
157A ARG* 3.2 52.9 - - + +
158A PHE* 3.6 18.6 - + - -
161A CYS* 4.3 8.7 - - - -
630D T 3.6 27.1 - - - -
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Residues in contact with PHE 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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113A TYR* 3.4 42.8 - + + -
121A CYS 2.8 17.9 + - - +
122A LYS 2.6 12.9 + - - +
124A PHE* 1.3 71.4 - - - +
126A ARG* 1.3 57.0 + - - +
127A ARG 3.0 1.1 - - - -
128A SER* 2.7 24.8 + - - -
129A ILE* 3.1 35.9 + - + +
158A PHE* 3.3 32.3 - + - -
161A CYS* 3.9 17.0 - - + -
162A LEU* 3.6 15.0 - - + -
166A MET* 4.0 29.6 - - + -
167A SER* 3.9 16.4 - - - -
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Residues in contact with ARG 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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113A TYR* 3.0 27.2 + - - +
122A LYS* 2.9 10.6 + - - +
123A GLY* 3.2 31.3 + - - +
125A PHE* 1.3 75.7 - - - +
127A ARG* 1.3 70.1 + - - +
129A ILE* 3.9 9.6 - - + -
130A GLN* 2.7 49.6 + - + +
168A ARG* 6.0 0.2 - - - +
606C G 3.3 46.2 + - + +
607C G 2.9 41.8 + - - -
608C T 3.0 23.2 + - - +
631D G 5.0 0.2 + - - -
632D A 4.2 3.4 - - - +
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Residues in contact with ARG 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 GLY* 3.0 33.2 + - - +
124A PHE* 3.7 17.7 - - - +
126A ARG* 1.3 92.9 - - + +
128A SER* 1.3 56.7 + - - +
130A GLN* 4.7 2.7 - - - +
131A GLN* 2.5 53.5 + - - +
133A ILE* 3.3 2.2 - - + +
134A TYR* 5.0 5.6 - - - +
629D G 4.6 6.3 - - - -
630D T 2.7 72.6 + - - +
631D G 2.4 40.3 + - - -
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Residues in contact with SER 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 PHE* 2.5 29.5 + - - -
125A PHE 2.7 12.6 + - - -
127A ARG* 1.3 74.3 - - - +
129A ILE* 1.3 55.8 + - - -
131A GLN 3.5 12.6 - - - +
133A ILE* 3.9 16.1 - - - +
134A TYR* 3.0 24.8 + - - -
158A PHE* 3.3 36.0 - - - -
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Residues in contact with ILE 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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113A TYR* 4.3 9.9 - - + -
125A PHE* 3.1 53.8 + - + +
126A ARG* 3.5 12.1 - - - +
128A SER* 1.3 75.7 - - - +
130A GLN* 1.3 63.1 + - - +
131A GLN 2.9 17.3 + - - +
158A PHE* 4.1 9.0 - - + -
162A LEU* 5.5 0.9 - - + -
168A ARG* 3.7 36.6 - - + +
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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