Contacts of the helix formed by residues 121 - 136 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B ALA* 1.3 73.8 - - - +
122B PRO* 1.3 77.1 - - - +
123B GLU 3.3 2.5 - - - -
124B THR* 3.2 6.0 + - - -
125B MET* 3.1 22.8 + - - +
176B GLU* 3.0 20.5 + - - -
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Residues in contact with PRO 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA 4.6 0.2 - - - +
121B GLY* 1.3 82.9 - - - +
123B GLU* 1.3 57.4 + - + +
125B MET* 3.3 12.8 + - + +
126B THR* 2.9 34.5 + - - -
150B LEU* 4.5 15.2 - - + +
154B TYR* 3.5 25.5 - - + +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B GLY 3.3 1.0 + - - -
122B PRO* 1.3 81.5 - - + +
124B THR* 1.3 63.0 + - - +
126B THR* 4.0 5.2 - - - -
127B GLN* 3.1 25.8 + - - +
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA* 4.6 3.1 - - + -
121B GLY 3.2 6.5 + - - -
123B GLU* 1.3 76.4 - - - +
125B MET* 1.3 66.5 + - - +
127B GLN* 3.5 4.0 + - - +
128B ARG* 3.1 62.9 + - + +
176B GLU* 2.6 39.8 + - + +
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Residues in contact with MET 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLY* 3.5 31.2 - - - +
17B PRO 3.0 26.5 - - - +
18B GLY 4.2 7.0 - - - -
19B SER* 4.1 11.9 - - - +
120B ALA* 3.8 26.2 - - + +
121B GLY 3.1 7.2 + - - +
122B PRO* 3.7 11.9 - - + +
124B THR* 1.3 74.6 - - - +
126B THR* 1.3 64.0 + - - +
128B ARG* 3.3 3.1 + - - +
129B LEU* 3.1 30.1 + - + +
146B ILE* 6.3 0.2 - - + -
150B LEU* 3.4 26.7 - - + -
153B TYR* 5.2 1.6 - - + -
154B TYR* 3.3 29.4 - - + +
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PRO 2.9 18.3 + - - -
123B GLU* 4.0 5.8 - - - -
125B MET* 1.3 75.9 - - - +
127B GLN* 1.3 62.0 + - - +
129B LEU* 3.4 1.7 + - - +
130B LEU* 3.0 41.8 + - + +
143B GLU* 6.5 0.7 - - + -
146B ILE* 3.9 21.2 - - + +
147B LYS* 6.5 1.3 - - + -
150B LEU* 3.5 21.0 - - - +
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLU 3.1 18.8 + - - +
124B THR* 3.9 4.9 - - - +
125B MET 3.3 0.2 - - - -
126B THR* 1.3 77.2 - - - +
128B ARG* 1.3 63.4 + - + +
130B LEU* 3.6 7.8 + - - +
131B LYS* 3.1 23.2 + - + +
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLY* 3.2 21.2 + - - +
19B SER* 3.0 30.7 + - - +
20B GLY 4.1 0.4 - - - +
120B ALA* 4.7 0.8 - - - +
124B THR* 3.1 45.2 + - + +
125B MET 3.3 3.6 + - - +
127B GLN* 1.3 77.4 - - + +
129B LEU* 1.3 59.1 + - - +
131B LYS* 3.4 6.6 + - - +
132B ARG* 3.0 26.9 + - - +
175B ALA 2.9 23.6 + - - -
176B GLU* 3.8 6.9 - - - +
177B GLY 4.3 2.4 + - - +
632B AP5 3.4 76.3 + - + +
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PRO* 3.4 35.2 - - + +
18B GLY* 3.8 14.1 - - - -
125B MET* 3.1 17.7 + - + +
126B THR 4.0 0.2 - - - +
128B ARG* 1.3 75.6 - - - +
130B LEU* 1.3 60.4 + - - +
132B ARG* 3.2 39.0 + - - +
133B GLY* 2.8 26.0 + - - -
141B ASP* 3.7 12.9 - - - +
146B ILE* 3.6 36.1 - - + -
149B ARG* 4.0 10.5 - - - +
632B AP5 3.7 11.9 - - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B THR* 3.0 37.1 + - + +
127B GLN* 3.9 6.7 - - - +
129B LEU* 1.3 77.9 - - - +
131B LYS* 1.3 61.7 + - - +
133B GLY* 3.1 10.9 + - - -
134B GLU* 3.2 18.1 + - - +
141B ASP 4.3 3.4 - - - +
143B GLU* 4.0 31.2 - - + +
146B ILE* 3.6 20.0 - - + -
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLN* 3.1 20.3 + - + +
128B ARG* 3.6 6.3 - - - +
129B LEU 3.3 0.2 - - - -
130B LEU* 1.3 74.1 - - - +
132B ARG* 1.3 65.8 + - - +
134B GLU* 3.4 36.4 - - - +
135B THR* 4.2 4.5 + - - +
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ARG 3.0 15.8 + - - +
129B LEU* 3.2 15.7 - - - +
131B LYS* 1.3 75.3 - - - +
133B GLY* 1.3 60.2 + - - +
135B THR* 3.1 10.5 + - + +
136B SER* 2.8 46.5 + - - +
138B ARG* 3.4 24.9 - - - +
141B ASP* 2.8 34.5 + - - +
632B AP5 2.7 81.8 + - - +
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU 2.8 17.0 + - - -
130B LEU 3.1 6.6 + - - -
132B ARG* 1.3 74.9 - - - +
134B GLU* 1.3 64.5 + - - +
135B THR 3.2 0.9 + - - -
136B SER* 4.0 15.9 + - - +
141B ASP* 4.0 17.9 + - - -
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LEU* 3.2 11.0 + - - +
131B LYS* 3.4 33.4 + - - +
132B ARG 3.2 0.2 - - - -
133B GLY* 1.3 77.0 - - - +
135B THR* 1.3 59.0 + - - +
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LYS 4.6 3.8 - - - +
132B ARG* 3.1 15.9 + - + +
134B GLU* 1.3 82.1 - - - +
136B SER* 1.3 75.1 + - - +
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG* 2.8 39.5 + - - -
133B GLY* 4.0 9.9 + - - +
134B GLU 3.9 0.4 - - - +
135B THR* 1.3 83.0 - - - +
137B GLY* 1.3 59.3 + - - +
138B ARG* 3.5 12.2 + - - +
141B ASP* 3.3 19.8 + - - -
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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