Contacts of the helix formed by residues 125 - 138 (chain B) in PDB entry 5XVO
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 TYR 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B LEU* 3.1 24.6 + - + +
121B ALA* 4.1 0.6 + - - -
123B ARG* 3.4 37.2 - - + -
124B ASP* 1.3 80.5 - - - +
126B GLY* 1.3 65.0 + - - +
127B GLN* 2.8 6.3 + - - -
128B LYS* 3.3 8.8 + - + -
129B ALA* 3.1 19.9 + - - +
158B THR* 3.5 49.2 + - + -
159B LEU* 4.5 7.9 + - + -
230B TYR* 4.3 14.0 + - - -
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Residues in contact with GLY 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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121B ALA* 4.8 6.7 - - - +
124B ASP* 3.3 6.5 + - - +
125B TYR* 1.3 75.3 - - - +
127B GLN* 1.3 62.4 + - - +
129B ALA* 3.5 7.2 - - - +
130B ALA* 3.3 20.8 + - - +
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Residues in contact with GLN 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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125B TYR* 2.8 6.8 + - - -
126B GLY* 1.3 72.6 - - - +
128B LYS* 1.3 66.4 + - + +
129B ALA 3.2 0.9 - - - -
130B ALA* 3.3 8.6 + - - +
131B ALA* 3.2 18.4 + - - +
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Residues in contact with LYS 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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120B LEU* 4.2 11.7 - - + -
125B TYR* 3.3 11.2 + - + +
127B GLN* 1.3 77.5 - - + +
129B ALA* 1.3 63.8 + - - +
131B ALA* 3.2 12.5 - - + +
132B LEU* 3.1 25.8 + - - +
154B SER* 4.3 15.6 + - - +
158B THR* 3.7 37.4 + - + +
46Q G 5.8 1.4 + - - -
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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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117B SER* 3.1 50.0 + - - +
120B LEU* 4.1 7.2 - - + +
121B ALA* 3.9 16.4 - - + +
125B TYR 3.1 17.2 + - - +
126B GLY 3.5 7.4 - - - +
128B LYS* 1.3 77.7 - - - +
130B ALA* 1.3 61.2 + - - +
132B LEU 3.3 0.7 + - - -
133B LEU* 3.3 12.5 + - + +
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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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126B GLY 3.3 9.6 + - - +
127B GLN* 3.3 10.9 + - - +
129B ALA* 1.3 78.6 - - - +
131B ALA* 1.3 63.1 + - - +
133B LEU* 3.2 15.3 + - + +
134B ALA* 3.1 21.7 + - - +
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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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127B GLN 3.2 7.5 + - - +
128B LYS* 3.2 22.6 + - + +
129B ALA 3.2 0.2 - - - -
130B ALA* 1.3 79.2 - - - +
132B LEU* 1.3 63.2 + - + +
134B ALA* 3.2 10.7 + - - +
135B MET* 3.0 29.3 + - + +
154B SER* 5.6 2.5 - - - +
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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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113B ILE* 3.6 11.7 - - + +
116B GLN* 3.7 31.0 - - + +
117B SER* 2.7 25.6 - - - +
120B LEU* 3.7 22.4 - - + -
128B LYS 3.1 15.8 + - - +
129B ALA 3.7 2.0 - - - +
130B ALA 3.3 0.4 - - - -
131B ALA* 1.3 79.5 - - + +
133B LEU* 1.3 64.0 + - - +
134B ALA 3.0 1.8 - - - -
135B MET* 3.0 12.2 + - - +
136B ARG 2.9 19.6 + - - -
151B ALA* 4.1 31.4 - - + +
154B SER* 4.0 22.2 - - - +
155B TYR* 4.2 2.9 - - + +
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Residues in contact with LEU 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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114B THR* 4.3 13.9 - - + +
117B SER* 3.9 18.4 - - - +
129B ALA* 3.3 14.5 + - + +
130B ALA* 3.2 15.2 + - - +
132B LEU* 1.3 76.6 - - - +
134B ALA* 1.3 56.0 + - - +
136B ARG* 3.4 34.3 + - + +
137B ALA* 3.1 27.2 + - - +
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Residues in contact with ALA 134 (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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130B ALA 3.1 12.1 + - - +
131B ALA* 3.3 13.9 - - - +
132B LEU 3.0 0.4 - - - -
133B LEU* 1.3 74.5 - - - +
135B MET* 1.3 66.7 + - + +
137B ALA* 3.2 15.5 + - - +
138B GLU* 3.3 23.0 + - - +
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Residues in contact with MET 135 (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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113B ILE* 5.2 1.6 - - + -
131B ALA* 3.0 19.3 - - - +
132B LEU* 3.0 16.4 + - - +
134B ALA* 1.3 77.4 - - + +
136B ARG* 1.3 63.4 + - - +
138B GLU* 3.2 14.9 + - - +
139B LEU* 3.6 3.5 + - - +
147B ARG* 3.5 50.8 - - + +
150B HIS* 3.5 29.8 - - + +
151B ALA* 3.6 29.6 - - + +
154B SER* 5.3 3.6 - - - -
45Q G 4.6 17.3 - - - +
46Q G 6.2 0.2 - - - +
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Residues in contact with ARG 136 (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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110B ALA* 3.7 23.5 - - + +
113B ILE* 4.0 12.7 - - + +
114B THR* 3.1 38.3 - - - +
132B LEU 2.9 12.3 + - - +
133B LEU* 3.4 26.5 + - - +
134B ALA 3.2 0.2 - - - -
135B MET* 1.3 77.4 - - - +
137B ALA* 1.3 64.8 + - - +
139B LEU* 3.1 37.2 + - + +
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Residues in contact with ALA 137 (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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133B LEU 3.1 14.2 + - - +
134B ALA* 3.2 11.6 + - - +
136B ARG* 1.3 78.7 - - - +
138B GLU* 1.3 60.0 + - + +
139B LEU 3.3 3.7 + - - +
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Residues in contact with GLU 138 (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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134B ALA* 3.5 17.8 - - - +
135B MET* 3.2 11.8 + - - +
136B ARG 3.1 0.8 - - - -
137B ALA* 1.3 80.2 - - + +
139B LEU* 1.3 63.2 + - - +
140B ARG* 3.5 10.2 + - - +
145B ALA* 5.7 2.3 - - - +
147B ARG* 3.3 40.2 + - - +
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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