Contacts of the helix formed by residues 129 - 140 (chain A) in PDB entry 2L9N
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ALA* 4.5 0.2 - - - -
127A PRO 4.8 1.6 + - - -
128A TYR* 1.3 76.1 - - - +
130A VAL* 1.3 68.1 + - + +
131A ILE* 3.8 23.5 - - + +
132A LEU* 2.8 35.2 + - - +
133A ILE* 3.1 16.8 + - - +
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Residues in contact with VAL 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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109A ARG* 5.2 4.3 - - + +
112A ALA* 3.4 39.7 - - + +
113A THR* 4.0 11.4 - - + +
116A ALA* 3.8 9.4 - - + +
129A THR* 1.3 79.0 - - + +
131A ILE* 1.3 62.9 + - + +
133A ILE* 3.4 3.5 + - - -
134A GLU* 3.0 36.5 + - + +
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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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129A THR* 3.8 22.0 - - + +
130A VAL* 1.3 83.7 - - + +
132A LEU* 1.3 66.6 + - + +
134A GLU* 4.4 13.0 - - + +
135A ARG* 3.0 47.8 + - - +
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Residues in contact with LEU 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 TYR* 3.9 34.1 - - + -
129A THR* 2.8 32.0 + - - +
131A ILE* 1.3 84.0 - - + +
133A ILE* 1.3 63.7 + - - +
135A ARG* 3.4 7.7 + - + +
136A ALA* 3.1 25.3 + - - +
165A MET* 4.4 16.4 - - + +
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Residues in contact with ILE 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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111A ILE* 4.9 0.9 - - + +
112A ALA* 3.2 35.4 - - - +
115A VAL* 3.7 34.5 - - + +
116A ALA* 3.4 28.5 - - + +
128A TYR* 4.4 16.8 - - + -
129A THR 3.1 12.9 + - - +
130A VAL* 3.9 2.9 - - - +
132A LEU* 1.3 75.9 - - - +
134A GLU* 1.3 58.2 + - - +
136A ALA* 3.6 4.9 + - - +
137A MET* 3.0 36.0 + - - +
161A LEU* 4.0 18.2 - - + +
165A MET* 6.0 0.2 - - - -
167A ILE* 5.4 0.7 - - + -
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Residues in contact with GLU 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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108A PHE* 3.2 45.7 - - + +
109A ARG* 5.0 2.5 - - - -
112A ALA* 3.9 16.2 - - + -
130A VAL* 3.0 22.1 + - + +
131A ILE* 3.9 14.6 - - + +
133A ILE* 1.3 74.9 - - - +
135A ARG* 1.3 64.8 + - - +
137A MET* 3.3 6.9 + - - +
138A LYS* 3.0 24.8 + - - +
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Residues in contact with ARG 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 ILE* 3.0 39.8 + - - +
132A LEU* 3.7 9.0 - - + +
134A GLU* 1.3 76.3 - - - +
136A ALA* 1.3 50.6 + - - +
138A LYS* 3.2 5.5 + - - +
139A ASP* 2.7 47.8 + - - +
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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 LEU 3.1 14.4 + - - +
133A ILE* 3.9 2.7 - - - +
135A ARG* 1.3 79.6 - - - +
137A MET* 1.3 57.3 + - - +
139A ASP* 3.7 7.4 - - - +
140A ILE* 2.9 35.0 + - - +
161A LEU* 3.9 20.4 - - + -
164A LYS* 4.5 14.3 + - + +
165A MET* 3.8 23.8 - - + -
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Residues in contact with MET 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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108A PHE* 3.6 18.8 - - + -
111A ILE* 3.8 26.7 - - + -
133A ILE* 3.0 23.1 + - - +
134A GLU* 3.5 7.0 - - - +
136A ALA* 1.3 76.4 - - - +
138A LYS* 1.3 59.1 + - - +
140A ILE* 3.1 9.9 - - - +
142A TYR* 2.7 73.2 + - + +
144A VAL* 3.6 28.0 - - + -
153A GLN* 6.5 0.9 - - + -
157A VAL* 3.5 25.4 - - + -
161A LEU* 4.4 4.6 - - + +
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Residues in contact with LYS 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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108A PHE* 5.1 8.3 - - + -
134A GLU 3.0 15.5 + - - +
135A ARG* 3.7 5.4 - - - +
137A MET* 1.3 73.2 - - - +
139A ASP* 1.3 63.8 + - - +
140A ILE 3.1 1.8 - - - -
141A HIS* 3.0 22.4 + - - +
142A TYR 4.6 5.4 - - - +
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Residues in contact with ASP 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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135A ARG* 2.7 31.5 + - - +
136A ALA* 3.7 5.8 - - - +
138A LYS* 1.3 74.2 - - - +
140A ILE* 1.3 56.8 + - - +
141A HIS* 3.2 10.4 + - - -
164A LYS* 3.4 24.9 + - - +
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Residues in contact with ILE 140 (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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136A ALA 2.9 25.6 + - - +
137A MET* 3.1 17.9 - - - +
139A ASP* 1.3 75.8 - - - +
141A HIS* 1.3 68.2 - - - +
142A TYR* 3.7 17.1 - - + -
160A GLN* 4.1 31.7 + - + +
161A LEU* 5.2 7.0 - - + -
163A GLU* 3.8 37.0 - - + +
164A LYS* 4.5 19.5 - - + +
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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