Contacts of the helix formed by residues 121 - 136 (chain A) in PDB entry 1Z83
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ALA* 1.3 75.4 - - - +
122A PRO* 1.3 75.3 - - - +
123A GLU* 3.3 4.9 - - - -
124A THR* 3.2 4.9 + - - -
125A MET* 3.1 21.9 + - - +
176A GLU* 3.2 22.1 + - - -
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Residues in contact with PRO 122 (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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121A GLY* 1.3 84.0 - - - +
123A GLU* 1.3 58.9 + - + +
125A MET* 3.6 13.2 + - + +
126A THR* 2.9 32.8 + - - -
150A LEU* 4.2 14.3 - - + +
154A TYR* 3.7 25.8 - - + +
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Residues in contact with GLU 123 (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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121A GLY* 5.1 1.8 - - - -
122A PRO* 1.3 80.8 - - + +
124A THR* 1.3 71.9 + - - +
126A THR* 3.9 5.2 - - - -
127A GLN* 2.8 36.5 + - + +
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Residues in contact with THR 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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120A ALA* 4.5 1.8 - - + -
121A GLY 3.2 9.6 + - - -
123A GLU* 1.3 86.4 - - - +
125A MET* 1.3 61.0 + - - +
127A GLN* 3.5 5.3 + - - +
128A ARG* 3.1 62.0 + - + +
176A GLU* 3.0 41.4 + - + +
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Residues in contact with MET 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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16A GLY* 3.5 29.8 - - - +
17A PRO* 3.2 26.9 - - + +
18A GLY 4.2 12.1 - - - +
19A SER* 4.1 8.1 - - - -
120A ALA* 3.6 29.2 - - + +
121A GLY 3.1 12.3 + - - +
122A PRO* 3.7 4.9 - - + +
124A THR* 1.3 72.6 - - - +
126A THR* 1.3 67.0 + - - +
128A ARG* 3.4 2.8 + - - +
129A LEU* 3.1 29.8 + - + +
146A ILE* 5.3 0.4 - - + -
150A LEU* 3.5 21.8 - - + -
153A TYR* 5.1 1.8 - - + -
154A TYR* 3.4 27.8 - - + +
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Residues in contact with THR 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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122A PRO 2.9 22.9 + - - -
123A GLU* 3.9 6.1 - - - -
124A THR 3.4 0.2 - - - -
125A MET* 1.3 76.1 - - - +
127A GLN* 1.3 58.6 + - + +
129A LEU* 3.3 1.9 + - - +
130A LEU* 2.9 49.9 + - + +
143A GLU* 6.5 0.7 - - - -
146A ILE* 3.9 18.6 - - + +
147A LYS* 6.2 1.8 - - - +
150A LEU* 3.5 19.6 - - - +
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Residues in contact with GLN 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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123A GLU* 2.8 29.0 + - + +
124A THR* 3.9 5.6 - - - +
126A THR* 1.3 77.4 - - + +
128A ARG* 1.3 58.7 + - + +
130A LEU* 3.5 8.5 + - - +
131A LYS* 3.0 30.7 + - - +
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Residues in contact with ARG 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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18A GLY 3.3 19.0 + - - +
19A SER* 3.0 30.5 + - - +
120A ALA* 4.6 1.6 - - - +
124A THR* 3.1 44.1 + - + +
125A MET 3.7 3.4 - - - +
126A THR 3.3 0.2 - - - -
127A GLN* 1.3 76.0 - - + +
129A LEU* 1.3 60.0 + - + +
131A LYS* 3.6 8.0 + - - +
132A ARG* 3.1 25.1 + - - +
175A ALA 3.0 23.6 + - - -
176A GLU* 4.1 2.8 - - - +
177A GLY 4.1 4.9 + - - +
631A AP5 3.4 78.2 + - + +
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Residues in contact with LEU 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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17A PRO* 3.5 29.6 - - + +
18A GLY* 3.7 20.4 - - - -
125A MET 3.1 15.4 + - - +
128A ARG* 1.3 73.4 - - - +
130A LEU* 1.3 61.3 + - - +
131A LYS 3.2 0.2 - - - -
132A ARG* 3.3 39.8 + - - +
133A GLY* 2.9 27.5 + - - -
141A ASP* 3.9 10.3 - - - +
146A ILE* 3.6 33.0 - - + -
149A ARG* 3.9 17.9 - - - +
631A AP5 3.7 7.2 - - - +
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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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126A THR* 2.9 37.1 + - + +
127A GLN* 3.8 7.2 - - - +
129A LEU* 1.3 76.1 - - - +
131A LYS* 1.3 60.6 + - - +
133A GLY* 3.3 9.5 + - - -
134A GLU* 3.4 17.4 + - - +
141A ASP 4.1 8.7 - - - +
143A GLU* 4.2 23.6 - - + +
146A ILE* 3.8 19.0 - - + +
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Residues in contact with LYS 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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127A GLN 3.0 18.7 + - - +
128A ARG* 3.7 8.1 - - - +
129A LEU 3.2 0.2 - - - -
130A LEU* 1.3 72.4 - - - +
132A ARG* 1.3 67.5 + - - +
134A GLU* 3.3 36.3 + - - +
135A THR* 4.0 5.0 + - - +
631A AP5 6.1 0.2 - - - +
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Residues in contact with ARG 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 ARG 3.1 16.7 + - - +
129A LEU* 3.3 15.2 + - - +
131A LYS* 1.3 79.3 - - - +
133A GLY* 1.3 54.2 + - - +
134A GLU 3.1 0.7 + - - -
135A THR* 3.1 10.3 + - + +
136A SER* 2.8 53.3 + - - +
138A ARG* 3.3 30.4 - - - +
141A ASP* 2.8 33.5 + - - +
149A ARG* 4.0 0.2 - - - +
631A AP5 2.8 78.4 + - - +
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Residues in contact with GLY 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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129A LEU 2.9 16.5 + - - -
130A LEU 3.3 4.5 + - - -
131A LYS 3.3 0.6 - - - -
132A ARG* 1.3 75.0 - - - +
134A GLU* 1.3 61.0 + - - +
135A THR 3.4 0.2 - - - -
136A SER* 4.0 16.0 - - - +
138A ARG 5.8 0.7 - - - -
141A ASP* 4.0 19.2 + - - -
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Residues in contact with GLU 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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130A LEU 3.4 12.0 + - - +
131A LYS* 3.4 30.1 + - - +
132A ARG 3.1 0.6 + - - -
133A GLY* 1.3 78.4 - - - +
135A THR* 1.3 62.5 + - - +
136A SER 5.1 0.2 - - - +
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Residues in contact with THR 135 (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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131A LYS 4.4 3.8 - - - +
132A ARG* 3.1 19.3 + - + +
134A GLU* 1.3 82.4 - - - +
136A SER* 1.3 79.6 + - - +
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Residues in contact with SER 136 (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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132A ARG* 2.8 47.4 + - - +
133A GLY* 4.0 11.3 - - - +
134A GLU 5.0 0.3 - - - -
135A THR* 1.3 81.8 - - - +
137A GLY* 1.3 60.0 + - - +
138A ARG* 3.5 15.4 + - - +
141A ASP* 3.7 7.3 + - - -
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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