Contacts of the helix formed by residues 133 - 146 (chain D) in PDB entry 2ZNZ
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 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D SER* 4.4 3.4 - - - +
87D MET* 4.2 9.6 - - - -
131D THR* 2.8 21.0 + - - -
132D LYS* 1.3 89.3 - - - +
134D SER* 1.3 62.8 + - - +
135D GLU* 3.1 13.8 + - - +
136D GLU* 2.7 36.8 + - - +
137D LEU* 3.2 8.3 + - - +
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Residues in contact with SER 134 (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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87D MET* 3.8 24.0 - - - +
133D ASN* 1.3 75.0 - - - +
135D GLU* 1.3 60.1 + - - +
137D LEU* 3.3 7.4 + - - +
138D ASN* 3.0 26.2 + - - +
157D ILE* 5.0 6.8 - - - +
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Residues in contact with GLU 135 (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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133D ASN* 3.1 12.6 + - - +
134D SER* 1.3 76.9 - - - +
136D GLU* 1.3 63.7 + - - +
138D ASN* 3.4 9.2 + - + +
139D ASN* 3.0 39.6 + - - +
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Residues in contact with GLU 136 (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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85D TYR* 4.3 6.8 - - - -
112D GLU* 4.4 6.1 - - - +
131D THR* 3.5 14.0 - - - +
132D LYS* 3.3 40.8 + - - +
133D ASN* 2.7 26.2 + - - +
135D GLU* 1.3 72.0 - - - +
137D LEU* 1.3 62.3 + - - +
139D ASN* 3.4 13.6 + - + +
140D PHE* 3.1 51.2 + - + -
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Residues in contact with LEU 137 (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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87D MET* 3.8 27.8 - - + -
89D ALA* 4.3 5.8 - - + -
91D ILE* 4.6 5.4 - - + -
129D ILE* 3.9 30.7 - - + -
131D THR* 3.7 22.8 + - + +
133D ASN 3.2 8.6 + - - +
134D SER* 3.4 11.2 - - - +
136D GLU* 1.3 73.8 - - - +
138D ASN* 1.3 60.3 + - - +
140D PHE* 3.1 3.7 + - - -
141D LEU* 2.9 48.2 + - + +
155D THR* 4.2 9.9 - - + -
157D ILE* 4.0 22.2 - - + -
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Residues in contact with ASN 138 (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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134D SER 3.0 13.7 + - - +
135D GLU* 3.6 11.2 - - + +
137D LEU* 1.3 74.3 - - - +
139D ASN* 1.3 59.7 + - - +
141D LEU* 3.2 8.5 + - - +
142D ASP* 2.9 36.3 + - - -
172D LYS* 2.8 38.8 + - - +
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Residues in contact with ASN 139 (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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135D GLU* 3.0 32.4 + - - +
136D GLU* 3.4 17.5 - - + +
137D LEU 3.3 0.2 - - - -
138D ASN* 1.3 77.6 + - - +
140D PHE* 1.3 59.1 + - + +
142D ASP* 3.4 14.4 - - - +
143D LEU* 3.2 32.7 + - + +
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Residues in contact with PHE 140 (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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91D ILE* 5.9 0.2 - - + -
110D TYR* 4.1 26.2 - + + -
112D GLU* 3.3 46.7 - - + -
113D ILE* 5.8 1.6 - - + -
129D ILE* 3.8 24.5 - - + -
131D THR* 3.7 12.8 - - + -
136D GLU* 3.1 47.6 + - + -
137D LEU* 3.7 5.8 - - + +
139D ASN* 1.3 76.1 - - + +
141D LEU* 1.3 60.5 + - - +
143D LEU* 3.2 20.7 + - + +
144D ILE* 2.8 38.4 + - + +
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Residues in contact with LEU 141 (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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91D ILE* 3.8 28.3 - - + -
137D LEU* 2.9 32.0 + - + +
138D ASN* 3.2 13.0 + - - +
140D PHE* 1.3 72.3 - - - +
142D ASP* 1.3 62.3 + - - +
144D ILE* 3.5 4.7 + - + +
145D GLY* 3.0 25.6 + - - -
153D THR* 3.9 13.7 + - + +
155D THR* 3.2 31.6 - - + +
172D LYS* 3.6 43.5 - - + +
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Residues in contact with ASP 142 (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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138D ASN* 2.9 23.2 + - - +
139D ASN* 3.4 18.1 - - - +
141D LEU* 1.3 76.3 - - - +
143D LEU* 1.3 63.0 + - + +
145D GLY* 3.4 3.0 + - - -
146D SER* 3.3 26.3 + - - -
172D LYS* 2.8 23.5 + - - -
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Residues in contact with LEU 143 (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 TYR* 4.4 28.7 + - + +
139D ASN* 3.2 18.6 + - + +
140D PHE* 3.2 32.5 + - + +
142D ASP* 1.3 79.6 - - + +
144D ILE* 1.3 60.9 + - + +
146D SER* 3.4 14.6 + - - -
147D ILE* 3.5 16.0 + - - +
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Residues in contact with ILE 144 (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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91D ILE* 3.6 31.9 - - + -
93D VAL* 4.7 7.6 - - + -
107D LEU* 3.8 26.7 - - + -
110D TYR* 5.6 3.6 - - + -
113D ILE* 4.2 19.7 - - + -
127D VAL* 5.1 1.6 - - + -
129D ILE* 4.7 3.8 - - + -
140D PHE* 2.8 29.5 + - + +
141D LEU* 3.9 7.0 - - + +
143D LEU* 1.3 71.6 - - + +
145D GLY* 1.3 64.9 + - - +
147D ILE* 3.2 18.9 + - + +
150D VAL* 3.4 23.3 - - + +
153D THR* 3.7 24.2 - - + -
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Residues in contact with GLY 145 (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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141D LEU 3.0 16.9 + - - -
142D ASP* 3.8 2.9 - - - -
143D LEU 3.3 0.2 - - - -
144D ILE* 1.3 79.2 - - - +
146D SER* 1.3 58.9 + - - +
147D ILE 3.5 6.8 + - - +
150D VAL* 3.9 22.2 - - - +
152D GLY* 6.4 0.2 - - - -
153D THR* 5.1 2.4 - - - +
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Residues in contact with SER 146 (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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142D ASP 3.3 15.4 + - - -
143D LEU* 3.4 9.2 + - - -
144D ILE 3.2 0.8 - - - -
145D GLY* 1.3 73.7 - - - +
147D ILE* 1.3 64.8 + - - +
148D PRO* 3.4 8.3 - - - +
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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