Contacts of the helix formed by residues 106 - 121 (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 ASN 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ALA* 3.2 28.8 + - + +
104A PRO 3.4 0.6 - - - -
105A ASN* 1.3 73.6 - - - +
107A VAL* 1.3 60.5 + - - +
108A ASP* 3.1 27.3 + - - +
109A CSX 3.1 22.4 + - - +
110A LEU* 3.0 28.6 + - - +
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Residues in contact with VAL 107 (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 3.3 3.8 + - - +
106A ASN* 1.3 73.4 + - - +
108A ASP* 1.3 73.5 + - - +
110A LEU* 3.4 7.3 + - - -
111A GLU* 2.9 31.0 + - - +
133A ILE* 3.6 24.4 - - + +
136A LEU* 4.1 27.1 - - + -
137A GLU* 3.8 27.6 - - + +
140A ASN* 4.0 12.9 - - - +
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Residues in contact with ASP 108 (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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106A ASN* 3.1 11.9 + - - +
107A VAL* 1.3 88.4 - - - +
109A CSX 1.3 65.9 + - - +
111A GLU* 3.6 17.6 - - - +
112A ALA* 3.3 22.0 + - - +
140A ASN* 5.2 1.9 + - - -
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Residues in contact with CSX 109 (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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96A TYR* 4.8 3.1 - - - +
99A LEU* 4.0 29.3 + - + +
100A LEU* 3.6 25.6 - - + +
103A ALA* 4.3 6.1 - - - +
106A ASN* 3.1 33.3 + - + +
108A ASP* 1.3 74.8 + - - +
110A LEU* 1.3 65.8 + - - +
112A ALA* 3.5 6.7 + - - +
113A CYS* 3.4 25.1 + - - -
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Residues in contact with LEU 110 (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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100A LEU* 3.5 18.4 - - + -
104A PRO 3.7 14.8 - - - +
106A ASN 3.0 15.8 + - - +
107A VAL* 3.4 4.2 + - - +
109A CSX 1.3 76.6 + - - +
111A GLU* 1.3 62.0 + - - +
113A CYS* 3.2 5.0 + - - +
114A ALA* 3.0 23.4 + - - +
129A MSE 3.4 30.4 - - + +
132A LYS* 4.2 29.2 - - + +
133A ILE* 3.7 26.2 - - + +
136A LEU* 3.6 31.4 - - + -
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Residues in contact with GLU 111 (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 2.9 18.1 + - - +
108A ASP* 3.6 21.5 - - - +
110A LEU* 1.3 75.0 - - - +
112A ALA* 1.3 62.2 + - - +
114A ALA* 3.4 5.1 + - - +
115A GLU* 3.2 28.4 + - + +
130A TYR* 4.4 5.1 + - + -
133A ILE* 3.4 15.4 - - + +
140A ASN* 4.8 4.3 + - - +
142A ALA* 3.2 33.1 - - + +
250A ZN 2.3 34.9 - - - -
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Residues in contact with ALA 112 (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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96A TYR* 3.3 43.2 - - + -
108A ASP 3.3 13.6 + - - +
109A CSX 3.8 6.1 - - - +
110A LEU 3.3 0.2 - - - -
111A GLU* 1.3 81.8 - - - +
113A CYS* 1.3 61.7 + - - +
115A GLU* 3.7 10.2 + - - +
116A MSE 3.6 23.9 + - - +
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Residues in contact with CYS 113 (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* 4.0 13.4 - - + -
96A TYR* 3.4 40.8 - - - -
97A LYS* 3.7 6.7 - - - -
100A LEU* 3.7 19.5 - - - -
109A CSX 3.4 12.7 + - - -
110A LEU 3.2 2.1 + - - +
112A ALA* 1.3 75.2 - - - +
114A ALA* 1.3 64.5 + - - +
116A MSE 3.2 7.2 + - - +
117A GLN* 3.1 24.1 + - - +
129A MSE 3.5 24.9 - - + -
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Residues in contact with ALA 114 (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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110A LEU 3.0 16.2 + - - +
111A GLU* 3.4 6.7 + - - +
113A CYS* 1.3 76.1 - - - +
115A GLU* 1.3 61.9 + - - +
117A GLN* 3.3 4.8 + - - +
118A VAL* 3.2 26.3 + - - +
126A ALA* 3.6 6.7 - - - +
129A MSE 3.9 23.7 - - + -
130A TYR* 3.6 34.5 - - + +
133A ILE* 5.3 0.2 - - + -
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Residues in contact with GLU 115 (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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84A LYS* 5.0 8.3 - - - +
111A GLU* 3.2 16.8 + - + +
112A ALA* 3.9 7.3 - - - +
113A CYS 3.3 0.2 - - - -
114A ALA* 1.3 76.2 - - - +
116A MSE 1.3 76.3 + - + +
118A VAL* 3.4 7.7 + - - +
119A CYS* 3.2 26.6 + - - -
130A TYR* 3.2 20.0 + - - +
142A ALA* 5.7 0.3 - - - +
250A ZN 2.0 37.8 - - - -
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Residues in contact with MSE 116 (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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84A LYS* 3.7 36.8 - - + -
89A TYR* 3.9 17.3 - - + +
92A ALA* 3.5 26.9 - - + -
93A TYR* 4.1 21.5 - - + +
96A TYR* 3.9 16.2 - - + -
112A ALA 3.6 13.7 + - - +
113A CYS* 3.2 8.9 + - - +
115A GLU* 1.3 92.1 - - + +
117A GLN* 1.3 59.7 + - - +
119A CYS* 3.3 18.2 + - - +
120A ARG* 3.0 35.4 + - - +
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Residues in contact with GLN 117 (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* 3.2 35.1 + - + -
113A CYS 3.1 19.6 + - - +
114A ALA 3.3 2.2 + - - +
116A MSE 1.3 75.6 - - - +
118A VAL* 1.3 60.0 + - - +
120A ARG* 3.1 29.8 + - - +
121A GLY 3.2 3.3 + - - -
122A GLN* 2.8 49.2 + - - +
125A ASP* 2.7 29.9 + - - +
126A ALA* 3.6 24.0 - - + +
129A MSE 4.6 7.1 - - - -
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Residues in contact with VAL 118 (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 3.2 16.7 + - - +
115A GLU* 3.6 8.5 - - - +
116A MSE 3.3 0.4 - - - -
117A GLN* 1.3 74.5 - - - +
119A CYS* 1.3 65.8 + - - +
121A GLY* 3.4 11.3 + - - -
122A GLN 4.6 2.5 - - - -
123A GLU* 5.4 3.8 - - - +
126A ALA* 3.4 17.7 - - + -
130A TYR* 4.1 5.2 - - + +
146A PHE* 3.7 37.9 - - + -
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Residues in contact with CYS 119 (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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89A TYR* 3.4 55.4 - - + -
115A GLU* 3.2 15.8 + - - +
116A MSE 3.3 13.2 + - - +
118A VAL* 1.3 82.7 - - - +
120A ARG* 1.3 60.4 + - - +
121A GLY* 3.4 0.9 + - - -
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Residues in contact with ARG 120 (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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89A TYR* 3.5 37.2 - - + +
90A ASP* 3.1 28.8 + - - +
93A TYR* 3.4 29.0 - - - -
116A MSE 3.0 19.2 + - - +
117A GLN* 3.1 31.6 + - - +
118A VAL 3.4 0.2 - - - -
119A CYS* 1.3 76.2 - - - +
121A GLY* 1.3 56.3 + - - +
122A GLN* 3.6 23.6 + - + +
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Residues in contact with GLY 121 (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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117A GLN 3.2 3.2 + - - -
118A VAL 3.4 8.4 + - - -
119A CYS 3.3 4.0 - - - -
120A ARG* 1.3 78.1 - - - +
122A GLN* 1.3 62.1 + - - +
123A GLU* 2.8 15.5 + - - +
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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