Contacts of the helix formed by residues 126 - 135 (chain A) in PDB entry 2D68
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 PRO 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A GLU* 3.6 11.9 - - - +
81A PHE* 4.0 22.9 - - + -
84A PHE* 3.8 27.5 - - + -
85A PHE* 3.9 8.5 - - + -
107A ARG* 3.7 3.6 - - - +
122A THR 5.1 0.7 - - - +
125A GLY* 1.3 87.8 - - - +
127A LEU* 1.3 66.3 + - - +
128A LEU 4.3 3.4 - - - +
129A LEU* 2.9 24.3 + - + +
130A GLU* 3.8 2.3 + - - +
65B PHE* 3.8 37.0 - - + -
74B VAL* 4.7 0.7 - - + -
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Residues in contact with LEU 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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77A LEU* 3.8 12.8 - - + -
80A GLU* 2.8 17.9 + - - +
107A ARG* 3.7 46.6 - - + +
110A LEU* 3.8 22.0 - - + -
111A ALA* 3.7 41.7 - - + +
114A LEU* 4.7 2.0 - - + -
116A ILE* 4.1 22.9 - - + +
118A GLU* 4.4 3.8 - - - +
122A THR* 5.6 1.6 - - - -
126A PRO* 1.3 71.5 - - - +
128A LEU* 1.3 63.9 + - - +
130A GLU* 2.9 19.8 + - + +
131A VAL* 3.4 11.6 + - - +
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Residues in contact with LEU 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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77A LEU* 3.9 48.4 - - + +
80A GLU* 4.5 0.8 + - - -
81A PHE* 5.0 2.2 - - + -
126A PRO* 3.2 6.1 - - + +
127A LEU* 1.3 77.4 - - - +
129A LEU* 1.3 61.7 + - - +
131A VAL* 3.4 15.6 + - + +
132A ILE* 3.0 27.6 + - + +
74B VAL* 3.8 25.6 - - + +
78B VAL* 3.7 29.4 - - + -
128B LEU* 3.8 35.9 - - + -
132B ILE* 4.9 2.9 - - + -
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Residues in contact with LEU 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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124A GLY 5.7 0.2 - - - -
125A GLY* 4.2 16.4 - - - -
126A PRO* 2.9 24.3 + - + +
128A LEU* 1.3 80.3 - - - +
130A GLU* 1.3 57.6 + - - +
132A ILE 3.4 0.2 + - - -
133A ARG* 2.8 71.0 + - - +
65B PHE* 3.9 27.8 - - + -
68B THR* 5.5 0.9 - - - +
70B ASP* 3.7 33.9 - - + -
71B GLY 4.4 0.7 - - - +
74B VAL* 3.9 8.4 - - + +
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Residues in contact with GLU 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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116A ILE* 3.9 32.7 - - + +
117A ILE 5.5 0.3 - - - +
121A GLY 4.7 0.7 - - - +
122A THR* 3.6 31.2 - - + +
126A PRO 3.8 1.3 + - - +
127A LEU* 2.9 15.1 + - + +
129A LEU* 1.3 79.0 - - - +
131A VAL* 1.3 64.2 + - - +
133A ARG* 3.6 20.8 + - - +
134A ARG* 3.1 60.9 + - - +
135B TRP* 4.6 1.1 - - + -
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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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77A LEU* 5.2 0.4 - - + -
114A LEU* 4.8 6.7 - - + -
116A ILE* 4.2 9.6 - - + -
127A LEU 3.4 11.2 + - - +
128A LEU* 3.4 16.8 + - + +
129A LEU 3.3 0.4 - - - -
130A GLU* 1.3 77.2 - - - +
132A ILE* 1.3 60.6 + - + +
134A ARG 3.3 2.8 + - - -
135A TRP* 3.0 28.1 + - + +
131B VAL* 3.7 29.6 - - + -
132B ILE* 4.4 13.7 - - + -
135B TRP* 3.7 49.4 - - + +
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Residues in contact with ILE 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 LEU* 3.0 22.1 + - + +
129A LEU 4.0 1.1 - - - +
131A VAL* 1.3 74.9 - - + +
133A ARG* 1.3 67.7 + - - +
134A ARG 3.2 0.5 + - - -
135A TRP* 3.3 18.8 + - + +
70B ASP* 4.0 31.3 - - + +
73B LEU* 3.8 22.0 - - + -
74B VAL* 3.7 16.4 - - + -
77B LEU* 3.7 28.5 - - + -
114B LEU* 4.0 20.0 - - + -
128B LEU* 5.7 0.9 - - + -
131B VAL* 4.3 17.9 - - + -
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Residues in contact with ARG 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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121A GLY 3.2 26.3 + - - -
122A THR* 5.1 1.6 - - - +
125A GLY 5.8 1.6 - - - +
129A LEU* 2.8 56.4 + - - +
130A GLU* 3.6 18.1 + - - +
132A ILE* 1.3 74.9 - - - +
134A ARG* 1.3 64.2 + - + +
135A TRP* 3.8 2.1 + - - +
70B ASP* 3.6 24.3 + - - +
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Residues in contact with ARG 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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115A GLY 4.6 12.1 + - - -
116A ILE* 4.9 4.4 - - - +
117A ILE 5.7 0.8 - - - +
130A GLU* 3.1 48.2 + - - +
131A VAL 3.7 1.6 - - - -
132A ILE 3.1 0.4 - - - -
133A ARG* 1.3 81.4 - - + +
135A TRP* 1.3 66.6 + - - +
135B TRP* 3.7 38.6 - - + -
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Residues in contact with TRP 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 VAL* 3.0 15.7 + - + +
132A ILE* 3.3 22.3 + - + +
133A ARG 4.8 1.6 - - - +
134A ARG* 1.3 82.9 - - - +
113B ASP 5.6 0.7 - - - -
114B LEU* 2.8 53.2 + - + +
116B ILE* 4.1 13.5 - - + -
131B VAL* 3.6 46.4 - - + -
134B ARG* 3.7 60.6 - - + -
135B TRP* 5.1 6.7 - + - -
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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