Contacts of the helix formed by residues 123 - 134 (chain A) in PDB entry 2ZA6
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ASN* 3.3 22.7 + - - +
9A TYR* 3.7 13.3 - - - -
10A SER 4.7 0.5 + - - -
13A VAL* 4.3 9.2 - - + +
73A ARG* 2.8 33.2 + - - -
118A GLY* 2.8 25.6 + - - +
119A SER* 5.0 0.2 - - - +
121A GLN* 4.5 8.1 - - + +
122A ALA* 1.3 72.4 - - - +
124A PRO* 1.3 62.6 - - - +
125A HIS* 3.6 2.6 + - - +
126A LEU* 3.2 15.5 + - + +
127A CYS* 3.2 24.2 + - - -
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Residues in contact with PRO 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASN* 3.9 9.0 - - - +
122A ALA* 3.2 14.4 - - + +
123A ASP* 1.3 82.0 - - - +
125A HIS* 1.3 61.2 + - - +
127A CYS* 3.8 8.8 - - + +
128A ASP* 2.9 30.7 + - - +
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Residues in contact with HIS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A MET* 4.4 17.8 - - + +
72A GLN* 5.1 9.0 - - + -
73A ARG* 3.6 41.4 + - + +
123A ASP* 3.2 1.5 - - - +
124A PRO* 1.3 83.3 - - - +
126A LEU* 1.3 58.8 + - - +
128A ASP* 3.5 11.8 + - - +
129A PHE* 2.9 35.4 + + + +
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 5.2 0.4 - - + -
13A VAL* 3.5 42.2 - - + -
17A VAL* 4.4 0.2 - - + -
69A MET* 3.8 30.3 - - + -
73A ARG* 3.9 3.6 - - - +
114A LEU* 3.8 31.6 - - + +
118A GLY* 3.8 17.7 - - - -
123A ASP* 3.2 23.8 + - - +
125A HIS* 1.3 82.4 + - - +
127A CYS* 1.3 62.9 + - - +
129A PHE* 3.1 6.9 + - + +
130A LEU* 3.0 33.2 + - + +
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Residues in contact with CYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A HIS* 3.5 39.3 - - + +
118A GLY* 3.7 5.6 - - - -
119A SER* 3.5 32.3 - - - -
123A ASP 3.2 18.5 + - - +
124A PRO* 3.8 8.1 - - + +
125A HIS 3.3 0.2 - - - -
126A LEU* 1.3 79.7 - - - +
128A ASP* 1.3 56.4 + - - +
130A LEU* 3.4 0.8 + - - -
131A GLU* 3.0 39.0 + - - +
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Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PRO 2.9 18.3 + - - +
125A HIS* 3.8 12.5 + - - +
127A CYS* 1.3 72.1 - - - +
129A PHE* 1.3 64.4 + - - +
131A GLU* 4.3 10.5 - - - +
132A SER* 2.8 53.3 + - - -
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Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 3.7 29.6 - - + -
66A LEU* 3.7 18.6 - - + -
69A MET* 3.6 44.9 - - + -
72A GLN* 5.4 2.7 - - - -
125A HIS* 2.9 30.4 + + + +
126A LEU* 3.1 7.4 + - + +
128A ASP* 1.3 80.9 + - - +
130A LEU* 1.3 67.3 + - + +
132A SER* 4.8 0.4 - - - -
133A HIS* 3.0 51.8 + + - +
134A PHE* 3.4 30.1 - + - -
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.6 3.6 - - + -
66A LEU* 4.6 1.6 - - + -
111A LEU* 3.9 28.9 - - + +
114A LEU* 3.8 28.0 - - + -
115A HIS* 3.6 42.0 - - + +
126A LEU* 3.0 27.1 + - + +
127A CYS 3.8 3.1 - - - +
129A PHE* 1.3 93.0 - - + +
131A GLU* 1.3 62.2 + - - +
134A PHE* 2.9 31.4 + - + +
135A LEU* 2.9 21.2 + - + -
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A HIS* 2.6 32.0 + - - +
127A CYS* 3.0 25.6 + - - +
128A ASP* 3.8 9.0 - - - +
130A LEU* 1.3 77.0 - - - +
132A SER* 1.3 62.8 + - - +
133A HIS 3.5 0.2 + - - -
134A PHE 4.2 0.2 + - - -
135A LEU* 3.7 28.4 + - + +
136A ASP* 4.1 13.0 + - - +
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASP* 2.8 38.5 + - - -
129A PHE* 4.0 2.2 - - - -
131A GLU* 1.3 79.8 - - - +
133A HIS* 1.3 78.4 + - - +
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Residues in contact with HIS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 3.4 44.9 + - - +
129A PHE* 3.0 48.3 + + - +
132A SER* 1.3 93.5 + - - +
134A PHE* 1.3 72.0 + - + +
137A GLU* 4.0 20.8 - - - +
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Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.2 40.2 - + - -
62A GLY* 3.5 32.1 - - - -
65A ARG* 4.1 9.9 - - + -
66A LEU* 3.7 15.0 - - + -
111A LEU* 3.6 24.2 - - + -
129A PHE* 3.4 38.6 - + - -
130A LEU* 2.9 15.9 + - + +
131A GLU 4.2 0.2 + - - -
132A SER 3.8 0.6 - - - -
133A HIS* 1.3 95.7 - - + +
135A LEU* 1.3 65.6 + - - +
136A ASP 3.4 1.8 - - - -
137A GLU* 3.2 12.4 + - - +
138A GLU* 2.9 27.0 + - - +
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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