Contacts of the helix formed by residues 106 - 120 (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 ASN 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B ALA* 3.2 32.2 + - + +
104B PRO 3.4 0.4 - - - -
105B ASN* 1.3 74.5 - - - +
107B VAL* 1.3 60.0 + - - +
108B ASP* 3.0 26.9 + - - +
109B CSX 3.2 23.5 + - - +
110B LEU* 3.0 28.6 + - - +
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Residues in contact with VAL 107 (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 3.3 5.1 + - - +
106B ASN* 1.3 72.7 + - - +
108B ASP* 1.3 70.5 + - - +
110B LEU* 3.7 9.0 - - - +
111B GLU* 3.0 29.7 + - - +
133B ILE* 3.7 20.4 - - + +
136B LEU* 4.1 29.2 - - + -
137B GLU* 3.6 19.5 - - + +
140B ASN* 3.5 23.9 + - - +
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Residues in contact with ASP 108 (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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106B ASN* 3.0 13.5 + - - +
107B VAL* 1.3 85.8 - - - +
109B CSX 1.3 66.4 + - - +
111B GLU* 3.5 18.8 + - - +
112B ALA* 3.2 22.9 + - - +
140B ASN* 5.3 1.4 + - - -
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Residues in contact with CSX 109 (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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96B TYR* 4.8 3.4 - - - +
99B LEU* 3.9 30.1 - - + +
100B LEU* 3.8 25.1 - - + +
103B ALA* 4.6 5.4 - - - -
106B ASN* 3.2 34.2 + - + +
108B ASP* 1.3 74.6 + - - +
110B LEU* 1.3 64.7 + - - +
112B ALA* 3.6 6.2 + - - +
113B CYS* 3.2 27.9 + - - -
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Residues in contact with LEU 110 (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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100B LEU* 3.7 22.9 - - + -
104B PRO 3.9 12.6 - - - +
106B ASN 3.0 18.3 + - - +
107B VAL* 3.7 4.7 - - - +
109B CSX 1.3 77.0 + - - +
111B GLU* 1.3 55.3 + - - +
113B CYS* 3.2 4.0 + - - +
114B ALA* 2.9 30.5 + - - +
128B ARG* 6.2 0.4 - - - +
129B MSE 3.7 28.6 - - + +
132B LYS* 4.1 26.2 - - + +
133B ILE* 3.6 26.7 - - + -
136B LEU* 3.6 31.9 - - + -
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Residues in contact with GLU 111 (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 3.0 15.6 + - - +
108B ASP* 3.6 20.9 - - - +
109B CSX 3.4 0.2 - - - -
110B LEU* 1.3 76.1 - - - +
112B ALA* 1.3 61.0 + - - +
114B ALA* 3.4 4.8 + - - +
115B GLU* 3.1 33.3 + - + +
130B TYR* 4.4 5.8 + - + -
133B ILE* 3.5 14.9 - - + +
140B ASN* 5.0 4.3 + - - +
142B ALA* 3.3 31.7 - - + +
250B ZN 2.0 37.3 - - - -
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Residues in contact with ALA 112 (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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84B LYS* 6.2 0.7 - - - +
96B TYR* 3.4 41.2 - - + -
108B ASP 3.2 13.9 + - - +
109B CSX 3.9 5.4 - - - +
110B LEU 3.4 0.2 - - - -
111B GLU* 1.3 80.7 - - - +
113B CYS* 1.3 61.0 + - - +
115B GLU* 3.6 12.0 + - - +
116B MSE 3.4 26.3 + - - +
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Residues in contact with CYS 113 (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* 4.2 10.9 - - + -
96B TYR* 3.3 42.2 - - - -
97B LYS* 3.7 7.2 - - - -
100B LEU* 3.9 17.7 - - - -
109B CSX 3.2 13.8 + - - -
110B LEU 3.2 4.5 + - - +
112B ALA* 1.3 75.9 - - - +
114B ALA* 1.3 65.4 + - - +
116B MSE 3.2 8.3 + - - +
117B GLN* 3.1 23.4 + - - +
129B MSE 3.5 25.1 - - + -
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Residues in contact with ALA 114 (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 LEU 2.9 16.3 + - - +
111B GLU* 3.4 5.4 + - - +
113B CYS* 1.3 75.3 - - - +
115B GLU* 1.3 61.8 + - - +
117B GLN* 3.1 15.7 + - - +
118B VAL* 3.1 12.3 + - - +
126B ALA* 3.5 11.3 - - - +
129B MSE 3.7 28.4 - - + -
130B TYR* 3.7 31.9 - - + +
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Residues in contact with GLU 115 (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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84B LYS* 4.8 12.1 + - - +
111B GLU* 3.1 21.3 + - - +
112B ALA* 3.8 9.3 - - - +
114B ALA* 1.3 77.0 - - - +
116B MSE 1.3 73.3 + - + +
118B VAL* 3.3 8.2 + - - +
119B CYS* 3.2 26.7 + - - -
130B TYR* 3.3 20.2 + - - +
142B ALA* 5.3 1.0 - - - +
250B ZN 2.1 37.5 - - - -
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Residues in contact with MSE 116 (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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84B LYS* 3.7 33.2 - - + -
89B TYR* 3.9 18.5 - - + +
92B ALA* 3.4 27.6 - - + -
93B TYR* 4.0 22.0 - - + +
96B TYR* 3.7 18.6 - - + -
112B ALA 3.4 13.4 + - - +
113B CYS* 3.2 8.8 + - - +
115B GLU* 1.3 95.7 - - + +
117B GLN* 1.3 56.3 + - - +
119B CYS* 3.3 19.1 + - - +
120B ARG* 3.0 34.8 + - - +
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Residues in contact with GLN 117 (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* 3.5 28.8 + - + -
113B CYS 3.1 12.8 + - - +
114B ALA 3.1 9.7 + - - +
116B MSE 1.3 73.1 - - - +
118B VAL* 1.3 59.2 + - - +
120B ARG* 2.7 35.1 + - - +
121B GLY 3.3 2.4 + - - -
122B GLN* 2.8 56.2 + - - +
125B ASP* 2.6 38.5 + - - +
126B ALA* 3.6 7.9 - - + +
129B MSE 4.4 6.5 - - - -
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Residues in contact with VAL 118 (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 3.1 8.5 + - - +
115B GLU* 3.3 10.7 + - - +
117B GLN* 1.3 74.8 - - - +
119B CYS* 1.3 66.6 + - - +
121B GLY* 3.1 14.9 + - - -
122B GLN 4.9 2.2 - - - +
123B GLU* 5.3 4.3 - - - +
126B ALA* 3.5 22.9 - - + -
130B TYR* 4.2 4.9 - - + +
146B PHE* 3.8 34.8 - - + -
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Residues in contact with CYS 119 (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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89B TYR* 3.4 52.8 - - + -
115B GLU* 3.2 15.6 + - - +
116B MSE 3.3 21.1 + - - +
118B VAL* 1.3 80.2 - - - +
120B ARG* 1.3 56.7 + - - +
121B GLY 3.3 1.4 + - - -
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Residues in contact with ARG 120 (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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89B TYR* 3.5 33.4 - - + -
90B ASP* 2.7 35.2 + - - +
93B TYR* 3.7 27.6 - - - -
116B MSE 3.0 16.2 + - - +
117B GLN* 2.7 43.8 + - - +
118B VAL 3.2 0.4 - - - -
119B CYS* 1.3 75.5 - - - +
121B GLY* 1.3 61.9 + - - +
122B GLN* 3.5 28.8 + - + +
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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