Contacts of the helix formed by residues 125 - 133 (chain B) in PDB entry 4XQ2
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 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B THR* 1.3 85.3 - - - +
126B GLU* 1.3 73.7 + - + +
128B ILE* 3.1 25.4 + - + +
129B ALA* 3.7 5.4 + - - +
157B GLU* 5.7 7.2 - - + +
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B THR* 3.2 9.8 - - - +
125B PRO* 1.3 90.1 - - + +
127B GLY* 1.3 60.3 + - - +
128B ILE 3.0 3.3 + - - -
129B ALA* 3.5 13.0 + - - +
130B ALA* 4.3 4.3 + - - +
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA* 4.1 4.8 - - - +
121B ASP* 2.8 28.8 - - - +
122B LEU* 4.2 0.2 - - - +
124B THR* 3.2 8.1 + - - -
126B GLU* 1.3 76.0 - - - +
128B ILE* 1.3 60.0 + - - +
129B ALA 3.6 0.2 - - - -
130B ALA* 4.5 9.1 - - - +
131B ALA* 3.7 18.4 + - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ASP 4.1 0.4 - - - -
122B LEU* 4.0 27.3 - - + +
124B THR 3.1 25.8 - - - +
125B PRO* 3.1 14.0 + - + +
126B GLU 3.0 1.8 + - - -
127B GLY* 1.3 77.5 - - - +
129B ALA* 1.3 68.6 + - + +
130B ALA 3.3 0.2 - - - -
131B ALA* 3.5 2.9 + - - +
132B LEU* 3.1 44.2 + - + +
154B ASP* 6.0 2.5 - - + -
157B GLU* 4.6 15.7 - - + +
158B VAL* 3.5 29.8 - - + -
161B ARG* 4.2 16.8 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PRO 3.7 4.2 + - - +
126B GLU 3.5 9.0 + - - +
128B ILE* 1.3 84.9 - - + +
130B ALA* 1.3 56.7 + - - +
132B LEU* 3.4 6.1 + - - +
133B ALA* 3.0 28.1 + - - +
161B ARG* 5.4 8.1 - - + -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ARG* 4.8 14.4 + - - +
120B ALA* 6.3 0.7 - - + -
126B GLU 4.3 7.8 + - - +
127B GLY* 5.0 6.5 - - - +
128B ILE 3.3 0.6 - - - -
129B ALA* 1.3 74.2 - - - +
131B ALA* 1.3 67.8 + - - +
132B LEU 3.0 0.9 - - - -
133B ALA* 3.0 16.5 + - - +
134B GLU* 3.4 10.7 + - - +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 3.0 42.7 - - + +
118B ARG* 4.4 13.2 - - + +
120B ALA* 3.4 30.2 - - + +
122B LEU* 4.6 4.7 - - + -
127B GLY 3.7 12.3 + - - +
128B ILE 3.5 4.0 + - - +
130B ALA* 1.3 79.8 - - - +
132B LEU* 1.3 60.9 + - + +
134B GLU* 3.4 11.0 - - - +
137B LEU* 4.5 0.3 - - - +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 5.3 2.9 - - + -
122B LEU* 6.1 2.2 - - + -
128B ILE* 3.1 30.1 + - + +
129B ALA* 3.7 6.5 - - - +
130B ALA 3.0 1.2 - - - -
131B ALA* 1.3 78.3 - - + +
133B ALA* 1.3 50.7 + - - +
134B GLU 3.1 4.7 + - - -
137B LEU* 3.3 24.9 - - + +
140B VAL* 3.7 24.5 - - + -
158B VAL* 4.3 9.0 - - + +
161B ARG* 3.5 39.5 - - + +
162B ALA* 3.7 15.0 - - + +
165B ARG* 2.2 47.5 + - + -
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ALA 3.0 16.2 + - - +
130B ALA* 3.0 9.1 + - - +
132B LEU* 1.3 74.0 - - - +
134B GLU* 1.3 66.4 + - - +
135B PRO* 3.3 7.8 - - - +
165B ARG* 3.9 12.7 + - - +
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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