Contacts of the helix formed by residues 122 - 137 (chain A) in PDB entry 3URZ
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 GLN 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLN* 2.8 41.2 + - - +
120A ARG* 4.4 26.8 + - + +
121A GLY* 1.3 73.5 - - - +
123A GLU* 1.3 58.1 + - - +
124A LYS 3.5 2.2 - - - -
125A ASP* 4.2 13.4 + - + +
126A ALA* 3.1 28.8 + - - +
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A VAL* 5.5 4.5 - - - +
121A GLY 2.8 14.1 + - - +
122A GLN* 1.3 69.8 - - - +
124A LYS* 1.3 61.0 + - - +
126A ALA* 3.5 5.3 + - - +
127A LEU* 3.0 28.6 + - - +
146A PHE* 6.5 0.4 - - + -
150A TYR* 3.1 40.3 + - + +
154A THR* 5.1 3.8 - - - +
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Residues in contact with LYS 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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122A GLN 3.5 0.2 - - - -
123A GLU* 1.3 77.3 - - - +
125A ASP* 1.3 64.1 + - - +
127A LEU* 3.3 13.5 + - + +
128A ARG* 3.2 20.6 + - - +
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Residues in contact with ASP 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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93A TYR* 4.2 4.2 + - - -
117A GLN* 2.7 31.3 + - - +
122A GLN* 3.8 18.1 + - + +
123A GLU 3.5 0.4 - - - -
124A LYS* 1.3 75.2 - - - +
126A ALA* 1.3 64.4 + - - +
128A ARG* 2.8 40.0 + - - +
129A MSE 3.3 23.1 + - - +
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Residues in contact with ALA 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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114A ALA* 3.6 7.7 - - - +
117A GLN* 3.6 17.8 - - + +
118A VAL* 3.4 33.2 - - + -
122A GLN 3.1 21.3 + - - +
123A GLU* 3.7 4.3 - - - +
125A ASP* 1.3 73.6 - - - +
127A LEU* 1.3 65.6 + - - +
129A MSE 3.4 3.2 + - - +
130A TYR* 3.2 29.9 + - - -
146A PHE* 5.5 1.1 - - + -
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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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123A GLU 3.0 17.4 + - - +
124A LYS* 3.3 12.8 + - + +
126A ALA* 1.3 77.1 - - - +
128A ARG* 1.3 60.5 + - - +
130A TYR* 3.6 5.4 + - - +
131A GLU* 3.1 29.6 + - + +
146A PHE* 4.7 5.8 - - + -
147A LEU* 3.6 29.7 - - + +
150A TYR* 3.6 42.6 - - + +
151A TYR* 4.5 11.9 - - + +
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Residues in contact with ARG 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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93A TYR* 5.6 2.0 + - - -
124A LYS 3.2 12.1 + - - +
125A ASP* 2.8 35.1 + - - +
126A ALA 3.2 0.2 - - - -
127A LEU* 1.3 76.1 - - - +
129A MSE 1.3 82.7 + - - +
131A GLU* 3.2 10.4 + - - +
132A LYS* 2.9 48.9 + - + +
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Residues in contact with MSE 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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93A TYR* 4.8 7.4 - - - -
100A LEU* 3.4 33.0 - - + -
110A LEU* 3.4 28.8 - - + +
113A CYS* 3.5 27.8 - - + -
114A ALA* 3.9 21.3 - - + -
117A GLN* 4.6 11.7 - - - -
125A ASP* 3.3 14.8 + - - +
126A ALA 3.4 2.6 + - - +
128A ARG* 1.3 100.7 - - - +
130A TYR* 1.3 57.0 + - - +
132A LYS* 3.3 10.0 + - - +
133A ILE* 3.1 32.4 + - - +
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Residues in contact with TYR 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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111A GLU* 4.8 9.9 - - + -
114A ALA* 3.6 23.6 - - + -
115A GLU* 3.2 31.2 + - - +
118A VAL* 4.1 10.0 - - + +
126A ALA 3.2 24.5 + - - +
127A LEU 4.0 3.8 - - - +
128A ARG 3.3 0.2 - - - -
129A MSE 1.3 73.4 - - - +
131A GLU* 1.3 64.1 + - - +
133A ILE* 3.3 15.5 + - + +
134A LEU* 3.3 24.3 + - - +
142A ALA* 4.5 5.2 - - + -
143A ALA* 3.7 27.3 - - + +
146A PHE* 3.4 55.2 - + + +
147A LEU* 4.1 19.3 - - + -
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Residues in contact with GLU 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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127A LEU* 3.1 23.4 + - + +
128A ARG* 3.6 8.2 - - - +
130A TYR* 1.3 75.2 - - - +
132A LYS* 1.3 62.9 + - - +
134A LEU* 3.3 14.7 + - + +
135A GLN* 3.2 19.8 + - - +
147A LEU* 4.5 8.2 - - + +
151A TYR* 5.5 5.9 + - - -
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Residues in contact with LYS 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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104A PRO* 4.2 19.1 + - - +
105A ASN* 4.7 10.5 + - - -
110A LEU* 4.2 28.5 - - + +
128A ARG* 2.9 32.2 + - + +
129A MSE 3.5 11.7 - - + +
130A TYR 3.3 0.2 - - - -
131A GLU* 1.3 75.1 - - - +
133A ILE* 1.3 63.7 + - - +
135A GLN* 3.3 18.2 + - - +
136A LEU* 3.2 27.5 + - + +
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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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107A VAL* 3.6 18.6 - - + +
110A LEU* 3.7 22.4 - - + -
111A GLU* 3.4 38.4 - - + +
114A ALA* 5.3 0.4 - - + -
129A MSE 3.1 18.6 + - - +
130A TYR* 3.5 25.1 - - + +
131A GLU 3.3 0.2 - - - -
132A LYS* 1.3 75.5 - - - +
134A LEU* 1.3 51.3 + - - +
136A LEU* 3.2 4.8 + - - +
137A GLU* 2.8 32.7 + - - +
140A ASN* 3.2 37.2 - - + +
143A ALA* 3.7 7.2 - - + +
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Residues in contact with LEU 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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130A TYR 3.3 10.0 + - - +
131A GLU* 3.3 14.8 + - + +
133A ILE* 1.3 78.6 - - - +
135A GLN* 1.3 59.1 + - - +
137A GLU 3.2 21.0 - - - +
138A ALA* 3.3 24.6 + - - +
140A ASN* 4.6 1.1 - - + +
143A ALA* 3.7 20.0 - - + -
144A ASN* 3.2 30.3 - - - +
147A LEU* 3.3 27.6 - - + -
198A SER* 5.1 3.6 - - - +
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Residues in contact with GLN 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 GLU 3.2 10.6 + - - +
132A LYS* 3.5 21.6 - - - +
134A LEU* 1.3 76.6 - - - +
136A LEU* 1.3 64.7 + - + +
137A GLU 5.1 0.2 - - - -
138A ALA 5.2 0.3 + - - -
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Residues in contact with LEU 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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105A ASN* 3.2 51.8 - - + +
107A VAL* 4.1 11.7 - - + -
110A LEU* 3.6 28.0 - - + -
132A LYS* 3.2 16.3 + - + +
133A ILE 3.2 7.0 + - - +
135A GLN* 1.3 80.4 - - + +
137A GLU* 1.3 59.6 + - - +
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Residues in contact with GLU 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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107A VAL* 3.8 19.9 - - + +
133A ILE 2.8 18.6 + - - +
134A LEU* 3.2 12.1 - - - +
135A GLN 3.4 0.4 - - - -
136A LEU* 1.3 75.3 - - - +
138A ALA* 1.3 64.0 + - - +
139A ASP* 3.7 5.4 - - - +
140A ASN* 3.1 40.2 + - + +
260A ZN 2.1 39.8 - - - -
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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