Contacts of the helix formed by residues 122 - 137 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B GLN* 2.8 41.2 + - - +
120B ARG* 3.9 33.7 + - + +
121B GLY* 1.3 77.9 + - - +
123B GLU* 1.3 57.8 + - - +
124B LYS 3.4 2.7 - - - +
125B ASP* 3.5 8.9 + - + +
126B ALA* 2.9 28.9 + - - +
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Residues in contact with GLU 123 (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 GLN 4.2 0.2 + - - -
118B VAL* 5.4 4.7 - - - +
121B GLY* 3.3 9.2 + - - +
122B GLN* 1.3 72.5 - - - +
124B LYS* 1.3 64.7 + - - +
126B ALA* 3.7 6.6 - - - +
127B LEU* 3.0 27.9 + - - +
150B TYR* 5.5 13.9 - - + +
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Residues in contact with LYS 124 (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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122B GLN* 3.4 1.0 - - - -
123B GLU* 1.3 80.1 - - - +
125B ASP* 1.3 63.4 + - - +
127B LEU* 3.3 9.0 + - + +
128B ARG* 3.2 19.3 + - - +
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Residues in contact with ASP 125 (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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93B TYR* 4.3 4.7 + - - -
117B GLN* 2.6 36.0 + - - +
122B GLN* 3.5 11.8 + - + +
124B LYS* 1.3 79.4 - - - +
126B ALA* 1.3 62.4 + - - +
128B ARG* 2.9 43.7 + - - +
129B MSE 3.2 25.6 + - - +
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Residues in contact with ALA 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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114B ALA* 3.5 15.8 - - - +
117B GLN* 3.6 11.1 - - + +
118B VAL* 3.5 32.1 - - + +
122B GLN 2.9 19.1 + - - +
123B GLU* 3.7 6.5 - - - +
125B ASP* 1.3 74.9 - - - +
127B LEU* 1.3 63.6 + - - +
129B MSE 3.3 4.6 + - - +
130B TYR* 3.1 29.4 + - + -
146B PHE* 5.5 1.3 - - + -
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Residues in contact with LEU 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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123B GLU 3.0 17.4 + - - +
124B LYS* 3.6 8.7 - - + +
125B ASP 3.3 0.2 - - - -
126B ALA* 1.3 74.0 - - - +
128B ARG* 1.3 63.8 + - - +
130B TYR* 3.4 5.0 + - - +
131B GLU* 3.0 47.1 + - - +
146B PHE* 4.2 9.1 - - + -
147B LEU* 3.6 26.7 - - + -
150B TYR* 3.7 46.7 - - + +
151B TYR* 4.9 5.6 - - + +
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Residues in contact with ARG 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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93B TYR* 5.9 0.2 + - - -
124B LYS 3.2 12.7 + - - +
125B ASP* 2.9 39.3 + - - +
126B ALA 3.3 0.2 - - - -
127B LEU* 1.3 75.9 - - - +
129B MSE 1.3 87.9 + - - +
131B GLU* 3.4 9.0 + - - +
132B LYS* 2.9 44.9 + - + +
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Residues in contact with MSE 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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93B TYR* 5.0 4.7 - - + -
100B LEU* 3.8 12.1 - - + -
110B LEU* 3.7 33.0 - - + +
113B CYS* 3.5 34.5 - - + -
114B ALA* 3.7 21.3 - - + -
117B GLN* 4.4 6.7 - - - -
125B ASP* 3.2 24.3 + - - +
126B ALA 3.3 6.9 + - - +
128B ARG* 1.3 103.5 - - - +
130B TYR* 1.3 55.4 + - - +
132B LYS* 3.2 9.3 + - - +
133B ILE* 3.0 32.2 + - - +
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Residues in contact with TYR 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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111B GLU* 4.9 9.0 - - + -
114B ALA* 3.7 21.3 - - + -
115B GLU* 3.3 29.6 + - - +
118B VAL* 4.2 8.8 - - + +
126B ALA 3.1 24.1 + - - -
127B LEU* 3.4 5.6 + - - +
129B MSE 1.3 76.0 - - - +
131B GLU* 1.3 61.7 + - - +
133B ILE* 3.4 16.5 + - + +
134B LEU* 3.2 24.9 + - - +
142B ALA 4.3 8.7 - - - -
143B ALA* 3.8 21.0 - - + +
146B PHE* 3.3 59.7 - + + +
147B LEU* 4.2 19.1 - - + -
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Residues in contact with GLU 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 LEU* 3.0 36.3 + - - +
128B ARG* 3.8 7.2 - - - +
130B TYR* 1.3 73.4 - - - +
132B LYS* 1.3 64.2 + - - +
134B LEU* 3.3 10.3 + - + +
135B GLN* 3.2 20.1 + - - +
147B LEU* 4.3 16.4 - - + +
151B TYR* 3.4 22.9 + - - -
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Residues in contact with LYS 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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104B PRO* 3.6 27.8 + - - +
105B ASN* 4.5 14.1 + - - -
110B LEU* 4.1 23.7 - - + +
128B ARG* 2.9 28.7 + - + +
129B MSE 3.2 11.2 + - - +
131B GLU* 1.3 72.6 - - - +
133B ILE* 1.3 66.5 + - - +
135B GLN* 3.1 18.7 + - - +
136B LEU* 3.1 29.0 + - + +
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Residues in contact with ILE 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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107B VAL* 3.7 14.1 - - + +
110B LEU* 3.6 24.9 - - + -
111B GLU* 3.5 38.6 - - + +
114B ALA* 5.3 0.2 - - + -
129B MSE 3.0 19.1 + - - +
130B TYR* 3.4 23.8 - - + +
132B LYS* 1.3 75.0 - - - +
134B LEU* 1.4 56.8 + - - +
136B LEU* 3.2 5.1 + - - +
137B GLU* 2.9 26.7 + - - +
140B ASN* 3.3 38.6 - - + +
143B ALA* 3.7 8.5 - - + +
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Residues in contact with LEU 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 TYR 3.2 10.8 + - - +
131B GLU* 3.7 10.3 - - + +
132B LYS 3.2 0.2 - - - -
133B ILE* 1.4 73.8 - - - +
135B GLN* 1.3 65.8 + - - +
137B GLU 3.5 6.5 - - - +
138B ALA* 3.2 36.3 + - - +
140B ASN* 4.4 1.3 - - + +
143B ALA* 3.5 22.2 - - + +
144B ASN* 3.7 33.4 - - - +
147B LEU* 3.3 28.9 - - + -
198B SER* 5.0 2.5 - - - +
201B LYS* 6.1 1.6 - - - +
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Residues in contact with GLN 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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131B GLU 3.2 11.2 + - - +
132B LYS* 3.1 23.8 + - + +
134B LEU* 1.3 78.1 - - - +
136B LEU* 1.3 64.0 + - + +
138B ALA 5.1 0.5 + - - -
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Residues in contact with LEU 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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105B ASN* 3.4 49.8 - - + +
107B VAL* 4.1 11.4 - - + -
110B LEU* 3.6 27.4 - - + -
132B LYS* 3.1 23.9 + - + +
133B ILE 3.6 5.6 - - - +
135B GLN* 1.3 80.9 - - + +
137B GLU* 1.3 58.6 + - - +
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Residues in contact with GLU 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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107B VAL* 3.6 19.9 - - + +
133B ILE 2.9 16.2 + - - +
134B LEU* 3.3 6.8 - - - +
136B LEU* 1.3 77.6 - - - +
138B ALA* 1.3 62.6 + - - +
139B ASP* 3.1 15.2 - - - +
140B ASN* 3.0 43.3 + - + +
260B ZN 2.1 31.2 - - - -
301B EDO 3.4 11.7 + - - +
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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