Contacts of the helix formed by residues 109 - 123 (chain D) in PDB entry 2ZU6
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 THR 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107D ALA* 3.2 2.7 - - - +
108D PRO* 1.3 90.9 - - + +
110D ARG* 1.3 54.4 + - - +
111D GLU* 3.5 7.1 + - - +
112D LEU* 3.0 22.3 + - - +
113D ALA* 2.7 34.0 + - - +
158D THR* 3.7 10.3 - - - -
190D ARG* 3.4 17.5 - - - +
210E GLU* 3.5 30.7 - - - +
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Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D THR* 1.3 67.9 - - - +
111D GLU* 1.3 68.5 + - - +
113D ALA* 3.1 9.3 + - - +
114D GLN* 2.8 23.7 + - - +
134D CYS 4.4 3.6 - - - +
135D ILE* 3.1 54.3 + - + +
136D GLY 5.6 0.8 - - - -
137D GLY* 5.6 2.8 - - - +
158D THR* 3.8 4.5 - - + +
161D ARG* 5.2 1.3 - - - +
206E SER* 5.6 6.3 + - - -
210E GLU* 2.9 33.5 + - - +
250E LEU* 4.6 19.4 - - - +
253E ASP* 2.5 38.1 + - - +
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D THR* 3.2 8.3 + - - +
110D ARG* 1.3 78.8 - - - +
112D LEU* 1.3 64.1 + - - +
114D GLN* 2.8 19.9 + - + +
115D GLN* 2.9 34.7 + - + +
173E GLN* 3.9 19.5 - - - +
210E GLU* 4.2 1.6 + - - -
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D GLY* 5.6 0.4 - - - -
81D GLY* 5.3 0.9 - - - -
82D LYS* 4.0 18.8 - - + +
107D ALA* 4.0 10.8 - - + -
108D PRO* 3.4 27.6 - - + -
109D THR* 3.0 21.6 + - - +
111D GLU* 1.3 74.6 - - - +
113D ALA* 1.3 67.6 + - - +
114D GLN 2.9 0.9 + - - -
115D GLN* 3.1 24.7 + - + +
116D ILE* 3.0 30.7 + - + +
182D ASP* 4.1 13.2 - - - +
183D GLU* 3.4 26.0 - - + +
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Residues in contact with ALA 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ALA* 4.0 6.8 - - + +
109D THR 2.7 19.1 + - - +
110D ARG* 3.3 14.6 - - - +
112D LEU* 1.3 73.0 - - - +
114D GLN* 1.3 56.3 + - - +
116D ILE 3.4 0.3 + - - -
117D GLN* 3.0 24.4 + - - +
133D ALA* 4.2 2.7 - - + -
135D ILE* 4.6 7.4 - - + -
156D VAL* 3.3 35.3 - - + +
157D GLY* 4.0 17.9 - - - -
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Residues in contact with GLN 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ARG 2.8 12.6 + - - +
111D GLU* 2.8 18.3 + - + +
113D ALA* 1.3 68.8 - - - +
115D GLN* 1.3 65.3 + - - +
117D GLN* 3.1 25.2 + - - +
118D LYS* 2.8 49.6 + - + +
133D ALA* 4.2 9.2 - - + +
135D ILE* 4.1 23.5 - - + +
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Residues in contact with GLN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D LYS* 2.9 56.5 + - + +
111D GLU* 2.9 39.9 + - + +
112D LEU* 3.5 20.2 - - - +
114D GLN* 1.3 78.4 - - - +
116D ILE* 1.3 66.6 + - - +
118D LYS* 3.1 14.6 + - - +
119D VAL* 3.1 15.0 + - - +
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Residues in contact with ILE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D GLY* 3.8 30.1 - - - +
86D PHE* 4.3 16.6 - - + -
105D VAL* 4.1 21.8 - - + -
107D ALA* 4.3 14.8 - - + -
112D LEU* 3.0 25.7 + - + +
113D ALA 3.7 5.8 - - - +
115D GLN* 1.3 74.9 - - - +
117D GLN* 1.3 66.2 + - - +
119D VAL* 3.3 4.2 + - - +
120D VAL* 2.9 34.7 + - + +
156D VAL* 4.3 14.8 - - + -
182D ASP* 3.3 25.8 - - - +
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Residues in contact with GLN 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ALA 3.0 7.2 + - - +
114D GLN* 3.1 20.0 + - - +
116D ILE* 1.3 76.0 - - - +
118D LYS* 1.3 79.3 + - - +
120D VAL* 2.9 12.0 + - - +
121D MET* 2.9 32.4 + - - +
131D CYS* 2.8 47.9 + - - +
132D HIS* 4.7 1.0 - - - +
133D ALA* 3.7 32.5 - - + +
156D VAL* 4.2 2.9 - - + +
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Residues in contact with LYS 118 (chain D).
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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114D GLN* 2.8 45.6 + - + +
115D GLN* 3.3 12.1 - - - +
117D GLN* 1.3 79.3 + - - +
119D VAL* 1.3 55.7 + - + +
121D MET* 3.2 3.1 + - - +
122D ALA* 2.7 36.2 + - - +
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Residues in contact with VAL 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D GLY 4.3 4.0 - - - +
82D LYS* 3.0 38.1 - - + +
83D THR 4.1 9.2 - - - +
84D ALA* 4.2 9.6 - - + +
87D ALA* 4.0 16.6 - - + -
115D GLN 3.1 9.0 + - - +
116D ILE 3.6 7.9 - - - +
118D LYS* 1.3 82.4 - - + +
120D VAL* 1.3 64.6 + - + +
122D ALA* 3.4 14.4 - - + +
123D LEU* 3.3 18.8 - - + +
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Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D PHE* 5.4 2.0 - - + -
87D ALA* 3.9 22.4 - - + -
90D ILE* 5.6 3.8 - - + -
91D LEU* 3.5 12.8 - - + +
116D ILE* 2.9 33.4 + - + +
117D GLN 2.9 8.0 + - - +
119D VAL* 1.3 76.1 - - + +
121D MET* 1.3 63.2 + - + +
123D LEU 3.2 5.5 + - - -
124D GLY* 2.8 23.0 + - - -
131D CYS* 3.5 35.4 - - + -
154D ILE* 3.7 24.0 - - + -
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Residues in contact with MET 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D GLN* 2.9 38.5 + - - +
118D LYS* 3.9 2.9 - - - +
120D VAL* 1.3 77.1 - - + +
122D ALA* 1.3 59.7 + - - +
124D GLY* 2.4 28.7 + - - -
125D ASP* 2.4 36.9 + - - +
129D ALA* 2.8 35.4 - - + +
130D SER* 3.7 2.7 - - - -
131D CYS* 3.4 35.4 - - + +
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Residues in contact with ALA 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LYS 2.7 22.4 + - - +
119D VAL* 3.4 14.1 - - + +
121D MET* 1.3 72.7 - - - +
123D LEU* 1.3 66.6 + - + +
124D GLY 3.5 0.7 + - - -
125D ASP* 4.8 5.5 + - - +
126D TYR* 5.7 1.2 + - - +
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Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ALA* 4.0 30.1 - - + +
87D ALA* 3.9 19.1 - - + -
88D ILE* 4.8 15.3 - - + -
91D LEU* 3.7 19.1 - - + +
119D VAL* 3.3 18.6 + - + +
120D VAL 3.2 3.8 + - - -
121D MET 3.1 0.4 - - - -
122D ALA* 1.3 80.7 - - + +
124D GLY* 1.3 59.1 + - - +
125D ASP 3.9 0.4 - - - -
126D TYR* 4.9 5.7 - - - +
127D MET* 3.7 16.5 + - - +
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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