Contacts of the helix formed by residues 122 - 133 (chain X) in PDB entry 2ZG8
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 ASP 122 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7X ASN* 3.3 23.1 - - - +
8X TYR* 3.7 11.1 - - - -
9X SER 4.8 0.7 + - - -
12X VAL* 4.3 8.4 - - + +
72X ARG* 2.9 34.5 + - - -
117X GLY* 2.9 22.8 + - - +
118X SER* 5.1 0.2 - - - +
120X GLN* 4.3 9.6 - - + +
121X ALA* 1.3 73.0 - - - +
123X PRO* 1.3 61.7 - - - +
124X HIS* 3.6 3.5 + - - +
125X LEU* 3.3 18.8 + - + +
126X CYS* 3.2 20.5 + - - +
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Residues in contact with PRO 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X ASN* 4.0 6.1 - - - +
121X ALA* 3.3 12.6 - - + +
122X ASP* 1.3 83.1 - - - +
124X HIS* 1.3 64.9 + - - +
126X CYS* 3.7 12.9 - - - -
127X ASP* 3.1 26.0 + - - +
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Residues in contact with HIS 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X MET* 4.5 13.1 - - + +
71X GLN* 5.0 9.6 + - + -
72X ARG* 3.8 38.7 + - + +
122X ASP* 3.3 2.7 + - - +
123X PRO* 1.3 83.4 - - - +
125X LEU* 1.3 60.5 + - - +
127X ASP* 3.9 5.3 - - - +
128X PHE* 3.0 39.8 + + + +
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Residues in contact with LEU 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X TYR* 5.2 0.7 - - + -
12X VAL* 3.8 23.3 - - + -
16X VAL* 4.4 6.1 - - + -
68X MET* 3.9 29.6 - - + -
72X ARG* 3.9 4.0 - - - +
113X LEU* 3.7 25.8 - - + +
114X HIS* 4.8 0.2 - - - -
117X GLY* 3.8 15.5 - - - -
122X ASP* 3.3 24.3 + - - +
124X HIS* 1.3 79.5 + - - +
126X CYS* 1.3 68.3 + - - +
128X PHE* 3.2 6.4 + - + +
129X LEU* 3.0 55.8 + - + +
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Residues in contact with CYS 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X HIS* 3.2 57.9 + - + +
117X GLY 5.2 0.2 - - - -
118X SER* 5.2 5.8 - - - +
122X ASP 3.2 11.5 + - - +
123X PRO* 3.7 15.7 - - + -
124X HIS 3.4 0.2 - - - -
125X LEU* 1.3 85.2 - - + +
127X ASP* 1.3 64.1 + - - +
129X LEU* 3.5 1.6 + - - +
130X GLU* 3.3 14.6 + - - +
182X PLL 3.7 15.7 - - - -
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Residues in contact with ASP 127 (chain X).
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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123X PRO 3.1 14.6 + - - +
124X HIS* 4.0 5.9 - - - +
126X CYS* 1.3 79.8 - - - +
128X PHE* 1.3 67.0 + - - +
129X LEU 3.2 0.4 - - - -
130X GLU* 3.3 2.1 + - - +
131X SER* 3.1 28.8 + - - -
182X PLL 3.9 21.2 - - + +
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Residues in contact with PHE 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64X ARG* 3.6 23.3 - - + -
65X LEU* 3.7 18.2 - - + -
68X MET* 3.5 47.3 - - + -
71X GLN* 5.4 2.7 - - - -
124X HIS* 3.0 30.4 + + + +
125X LEU* 3.4 6.1 - - - +
127X ASP* 1.3 78.7 + - - +
129X LEU* 1.3 72.5 + - + +
131X SER* 4.9 0.4 - - - -
132X HIS* 3.2 55.3 + + - +
133X PHE* 3.6 28.7 - + - -
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Residues in contact with LEU 129 (chain X).
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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19X LEU* 4.3 4.9 - - + -
65X LEU* 4.4 3.4 - - + -
110X LEU* 4.0 24.5 - - + +
113X LEU* 3.5 42.6 - - + -
114X HIS* 3.8 18.6 - - + +
125X LEU* 3.0 35.7 + - + +
126X CYS 3.7 4.7 - - - +
128X PHE* 1.3 92.7 - - + +
130X GLU* 1.3 60.6 + - - +
133X PHE* 3.0 14.4 + - + +
134X LEU* 2.8 35.4 + - + +
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Residues in contact with GLU 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X HIS* 4.7 0.2 - - - -
126X CYS 3.3 4.9 + - - +
127X ASP* 3.3 6.5 + - - +
129X LEU* 1.3 80.3 - - - +
131X SER* 1.3 64.0 + - - +
134X LEU* 3.1 39.7 + - + +
135X ASP* 3.2 41.5 + - + +
182X PLL 3.2 39.7 - - + +
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Residues in contact with SER 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127X ASP* 3.1 21.2 + - - -
128X PHE* 4.1 2.5 - - - -
130X GLU* 1.3 83.3 - - - +
132X HIS* 1.3 80.2 + - - +
135X ASP* 5.1 5.4 - - - +
136X GLU* 4.7 7.3 - - - +
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Residues in contact with HIS 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64X ARG* 3.2 47.8 + - + +
128X PHE* 3.2 43.5 + + - -
131X SER* 1.3 95.7 + - - +
133X PHE* 1.3 76.7 + - + +
136X GLU* 3.6 18.3 - - - +
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Residues in contact with PHE 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X TYR* 3.2 31.2 - + - -
61X GLY* 3.4 41.1 - - - -
64X ARG* 3.9 8.7 - - + -
65X LEU* 3.6 16.8 - - + -
110X LEU* 3.6 25.1 - - + -
128X PHE* 3.6 30.7 - + - -
129X LEU* 3.0 19.2 + - + +
131X SER 3.5 1.2 - - - -
132X HIS* 1.3 102.8 - - + +
134X LEU* 1.3 60.2 + - - +
135X ASP 3.4 1.3 - - - -
136X GLU* 3.3 5.7 + - - +
137X GLU* 2.9 34.1 + - - +
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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