Contacts of the helix formed by residues 123 - 133 (chain D) in PDB entry 1NTZ
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 GLY 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D VAL* 3.6 25.5 - - - +
120D ARG* 5.1 1.0 - - - +
122D GLY* 1.3 77.4 - - - +
124D GLU* 1.3 73.0 + - - +
125D ASP* 3.1 8.3 + - - +
126D TYR* 3.4 7.8 + - - +
127D VAL* 3.7 13.5 + - - +
191D ARG* 5.1 1.8 - - - -
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Residues in contact with GLU 124 (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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12D TRP* 3.5 33.1 + - + -
14D HIS* 2.5 34.1 + - - +
117D VAL* 3.8 19.5 - - + -
123D GLY* 1.3 77.9 - - - -
125D ASP* 1.3 54.3 + - - +
127D VAL* 3.3 2.8 + - - +
128D PHE* 2.6 37.9 + - - +
187D CYS* 3.7 28.4 - - + +
191D ARG* 2.9 26.1 + - + -
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Residues in contact with ASP 125 (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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7D PRO* 4.0 8.5 - - + -
8D PRO 3.2 25.7 - - - +
9D SER* 3.9 5.7 + - - -
10D TYR* 3.5 22.3 + - + +
12D TRP* 2.3 40.4 + - - -
122D GLY* 5.0 3.6 - - - -
123D GLY 4.5 7.7 + - - +
124D GLU* 1.3 76.5 - - - +
126D TYR* 1.3 59.9 + - - +
128D PHE* 4.4 1.6 - - - -
129D SER* 2.8 35.5 + - - -
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Residues in contact with TYR 126 (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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4D GLU* 5.4 3.4 - - - -
7D PRO* 3.8 22.5 - - + +
120D ARG* 4.0 24.0 - - + -
121D HIS 3.8 24.5 - - - +
122D GLY 4.0 4.5 - - - +
123D GLY 3.4 10.5 + - - +
124D GLU 3.4 0.6 - - - -
125D ASP* 1.3 76.8 - - - +
127D VAL* 1.3 67.2 + - + +
129D SER* 3.8 1.4 - - - -
130D LEU* 2.9 37.2 + - + +
152D TYR* 3.2 31.9 + + + +
153D PHE* 3.6 5.4 - - - -
154D PRO* 3.4 21.2 - - + +
242D HEM 2.8 39.3 + - + -
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Residues in contact with VAL 127 (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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116D ILE* 3.7 26.9 - - + -
117D VAL* 5.3 4.0 - - + -
120D ARG* 5.3 2.7 - - + -
123D GLY 3.7 10.5 + - - +
124D GLU* 3.3 7.7 + - - +
126D TYR* 1.3 85.7 - - + +
128D PHE* 1.3 60.2 + - - +
130D LEU* 3.1 5.0 + - + +
131D LEU* 2.9 50.2 + - + +
187D CYS* 3.9 10.5 - - - -
190D LEU* 4.6 10.3 - - + -
242D HEM 3.7 28.5 - - + -
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Residues in contact with PHE 128 (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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10D TYR* 3.6 43.5 - + - -
12D TRP* 3.6 28.3 - + + -
124D GLU 2.6 22.7 + - - +
125D ASP* 3.9 2.5 - - - +
127D VAL* 1.3 71.8 - - - +
129D SER* 1.3 59.8 + - - +
131D LEU* 4.0 3.0 - - - +
132D THR* 2.9 57.5 + - + -
180D SER* 3.9 9.2 - - - -
183D ALA* 3.6 32.1 - - + -
184D LYS 3.8 5.4 - - - -
187D CYS* 3.5 7.3 - - - -
69H VAL* 6.2 0.2 - - + -
73H LEU* 4.1 13.5 - - + -
74H PHE* 3.6 25.6 - + - -
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Residues in contact with SER 129 (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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7D PRO* 4.2 1.8 - - - -
8D PRO* 3.3 12.3 - - - +
10D TYR* 3.1 26.2 + - - -
125D ASP 2.8 24.3 + - - -
126D TYR 4.0 1.3 - - - -
128D PHE* 1.3 76.3 - - - +
130D LEU* 1.3 57.6 + - - +
132D THR* 5.1 1.6 - - - -
133D GLY* 2.9 26.7 + - - +
152D TYR* 3.3 40.7 - - - -
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Residues in contact with LEU 130 (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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126D TYR* 2.9 25.8 + - + +
127D VAL* 3.3 5.8 - - - +
128D PHE 3.1 0.2 - - - -
129D SER* 1.3 80.9 - - - +
131D LEU* 1.3 71.2 + - + +
133D GLY 3.2 7.4 + - - -
134D TYR* 3.6 5.4 - - - +
150D ASN* 3.2 43.6 + - + +
152D TYR* 3.4 28.4 - - - +
153D PHE* 4.2 16.6 - - + -
158D ILE* 5.1 3.1 - - + -
160D MET* 4.9 9.9 - - + -
242D HEM 4.2 43.1 - - + -
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Residues in contact with LEU 131 (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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127D VAL* 2.9 35.9 + - + +
128D PHE 4.1 2.0 - - - +
130D LEU* 1.3 75.5 - - + +
132D THR* 1.3 61.2 + - - +
134D TYR* 3.3 21.4 - - + -
160D MET* 3.7 29.4 - - + -
163D PRO* 4.5 2.0 - - + -
164D ILE* 3.6 39.9 - - + +
179D MET* 3.9 14.4 - - - +
183D ALA* 4.7 4.5 - - + -
186D VAL* 3.9 13.2 - - + -
187D CYS* 4.5 3.4 - - - -
242D HEM 3.6 34.3 - - + -
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Residues in contact with THR 132 (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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10D TYR* 5.0 5.8 - - - +
128D PHE* 2.9 42.9 + - + +
129D SER* 4.9 1.1 - - - +
131D LEU* 1.3 77.2 - - - +
133D GLY* 1.3 61.7 - - - +
134D TYR* 3.1 8.4 + - - +
179D MET* 4.0 21.4 + - - +
180D SER* 4.1 6.6 - - - -
183D ALA* 3.9 17.4 - - - +
17H LEU* 3.8 37.1 - - + +
21H ARG* 3.7 10.0 + - - +
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Residues in contact with GLY 133 (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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129D SER 2.9 19.4 + - - +
130D LEU 3.2 6.5 + - - -
132D THR* 1.3 77.8 - - - +
134D TYR* 1.3 64.3 + - - +
135D CYS* 3.6 1.4 + - - +
150D ASN* 3.8 1.9 - - - +
151D PRO* 3.5 23.4 - - - +
152D TYR* 4.4 8.6 - - - -
21H ARG* 3.6 15.9 - - - -
62H LEU* 6.1 0.7 - - - +
66H ASP* 5.9 0.7 - - - -
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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