Contacts of the helix formed by residues 134 - 148 (chain A) in PDB entry 2ZB8
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A TYR 3.7 0.2 + - - -
129A PHE 3.3 17.9 - - - -
131A GLY 3.0 9.6 + - - -
132A ALA 3.3 0.4 + - - -
133A ILE* 1.3 80.5 - - - +
135A MET* 1.3 55.5 + - - -
137A GLY 3.1 1.9 + - - -
138A LEU* 2.7 41.1 + - - +
300A ILE* 3.8 7.3 - - - +
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Residues in contact with MET 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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49A ASP* 4.0 21.1 - - - +
51A TYR* 4.4 16.4 - - + -
99A PHE* 5.3 17.5 - - + -
129A PHE 4.4 2.8 + - - -
130A LEU* 5.0 0.6 - - - +
134A GLY* 1.3 69.2 - - - -
136A PRO* 1.4 69.6 - - + +
138A LEU* 3.1 13.0 + - + +
139A THR* 2.7 36.1 + - - -
289A VAL* 4.1 14.1 - - + -
290A LEU* 5.6 3.1 - - + -
296A PHE* 6.4 1.1 - - + -
700A NAP 3.4 35.9 - - + -
800A IMN 4.0 24.5 - - + +
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Residues in contact with PRO 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASP* 4.6 5.2 - - - +
130A LEU 3.4 23.3 - - - +
131A GLY* 3.3 17.7 - - - +
135A MET* 1.4 100.6 - - + +
137A GLY* 1.3 60.2 - - - +
139A THR* 3.1 5.0 + - - +
140A SER* 3.0 25.5 + - - -
166A ALA* 3.8 25.8 - - + +
167A CYS* 3.7 28.1 - - - +
340A LYS* 4.2 9.0 - - - +
700A NAP 4.8 3.1 - - + +
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Residues in contact with GLY 137 (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 GLY 2.9 13.1 + - - -
132A ALA* 3.5 24.9 - - - -
134A GLY 3.1 0.4 + - - -
136A PRO* 1.3 77.1 - - - +
138A LEU* 1.3 61.4 + - - +
140A SER* 3.3 2.6 + - - -
141A LEU* 3.0 24.8 + - - +
166A ALA 5.4 0.2 + - - -
170A VAL* 4.2 15.0 - - - +
303A LEU* 3.6 11.5 - - - +
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Residues in contact with LEU 138 (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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134A GLY 2.7 22.6 + - - +
135A MET* 3.4 12.6 - - + +
137A GLY* 1.3 70.6 - - - -
139A THR* 1.3 64.7 + - - +
141A LEU* 4.6 1.6 - - + +
142A ILE* 2.9 41.9 + - + +
289A VAL* 4.0 10.1 - - + -
296A PHE* 3.6 45.8 - - + +
299A GLY* 3.8 15.0 - - - -
300A ILE* 3.7 42.8 - - + +
303A LEU* 3.7 3.7 - - + +
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Residues in contact with THR 139 (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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135A MET* 2.7 28.1 + - - -
136A PRO 3.1 6.5 + - - -
138A LEU* 1.3 73.8 - - - +
140A SER* 1.3 59.1 + - - +
143A GLY* 2.9 23.9 + - - -
167A CYS* 4.2 3.4 - - - -
229A PHE* 4.4 2.0 - - + -
253A CYS* 3.5 25.4 - - - -
287A PHE* 3.4 18.5 - - + -
289A VAL* 3.4 19.5 - - + +
700A NAP 3.2 39.9 - - + -
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Residues in contact with SER 140 (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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136A PRO 3.0 6.8 + - - -
137A GLY 3.8 6.5 - - - -
138A LEU 3.2 0.2 - - - -
139A THR* 1.3 77.9 - - - +
141A LEU* 1.3 62.9 + - - +
144A ILE* 3.0 32.0 + - - +
167A CYS* 2.7 43.2 + - - +
170A VAL* 4.0 8.9 - - - +
171A ALA* 3.8 19.3 - - - -
174A ILE* 4.4 0.7 - - - -
229A PHE* 3.7 12.5 - - - -
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Residues in contact with LEU 141 (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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137A GLY 3.0 16.6 + - - +
138A LEU* 4.0 4.0 - - + +
140A SER* 1.3 76.3 - - - +
142A ILE* 1.3 63.1 + - + +
144A ILE* 3.3 1.4 + - - +
145A GLN* 2.9 56.0 + - + +
174A ILE* 3.8 21.2 - - + +
178A LEU* 4.6 0.9 - - + -
299A GLY* 3.5 40.2 - - - +
302A GLN* 4.1 15.3 - - + -
303A LEU* 4.0 10.1 - - + -
306A TRP* 3.8 25.1 - - + -
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Residues in contact with ILE 142 (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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138A LEU* 2.9 37.6 + - + +
141A LEU* 1.3 76.3 - - + +
143A GLY* 1.3 56.9 + - - +
145A GLN* 4.3 5.2 - - + -
146A GLU* 2.6 54.3 + - + +
287A PHE* 3.9 11.2 - - + -
289A VAL* 4.1 4.9 - - + -
292A TYR* 3.8 23.3 - - + +
295A LYS* 4.2 25.8 - - + +
296A PHE* 4.0 32.1 - - + -
299A GLY* 5.5 0.9 - - - -
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Residues in contact with GLY 143 (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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139A THR 2.9 20.5 + - - -
140A SER 4.0 0.7 - - - -
142A ILE* 1.3 77.1 - - - +
144A ILE* 1.3 56.7 + - - +
147A LYS* 2.8 29.8 + - - +
148A GLY 3.4 3.3 + - - -
251A ILE* 3.8 18.2 - - - +
287A PHE* 3.3 23.3 - - - -
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Residues in contact with ILE 144 (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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140A SER 3.0 23.5 + - - +
141A LEU 3.9 2.0 - - - +
143A GLY* 1.3 76.4 - - - +
145A GLN* 1.3 61.0 + - - +
148A GLY* 2.8 29.0 + - - -
149A HIS 3.9 0.9 + - - -
150A ILE* 3.1 37.0 + - + +
158A MET* 3.9 12.3 - - + -
171A ALA* 3.4 37.7 - - + +
174A ILE* 3.6 17.0 - - + -
175A GLY* 4.3 0.9 - - - +
178A LEU* 4.1 13.5 - - + -
229A PHE* 3.9 4.7 - - + -
251A ILE* 3.7 21.5 - - + -
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Residues in contact with GLN 145 (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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141A LEU* 2.9 39.3 + - + +
142A ILE* 3.7 6.3 - - + +
144A ILE* 1.3 79.5 - - - +
146A GLU* 1.3 68.6 + - - +
148A GLY 4.6 0.5 + - - -
149A HIS 5.0 3.6 + - - -
178A LEU* 3.8 29.1 - - + +
295A LYS* 6.4 0.9 - - + -
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Residues in contact with GLU 146 (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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142A ILE* 2.6 36.1 + - + +
145A GLN* 1.3 81.6 - - + +
147A LYS* 1.3 69.2 + - + +
149A HIS* 4.2 10.5 + - - -
287A PHE* 4.8 1.3 - - + -
292A TYR* 3.6 39.6 + - + +
295A LYS* 3.1 30.3 - - - +
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Residues in contact with LYS 147 (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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143A GLY 2.8 17.6 + - - +
146A GLU* 1.3 81.6 - - + +
148A GLY* 1.3 60.5 + - - +
149A HIS* 3.2 22.4 - - - +
249A HIS* 3.6 15.5 - - + +
250A ILE 5.0 3.8 - - - +
251A ILE* 4.0 20.3 - - + +
252A LEU 5.9 0.2 - - - +
283A THR* 6.1 1.1 - - + -
285A GLU* 2.4 49.3 + - + +
286A ARG* 3.8 22.0 + - - +
287A PHE* 4.3 21.5 - - + -
292A TYR* 4.0 21.2 + - - -
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Residues in contact with GLY 148 (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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143A GLY 3.4 2.6 + - - -
144A ILE* 2.8 22.2 + - - -
146A GLU 3.8 0.2 - - - -
147A LYS* 1.3 78.2 - - - +
149A HIS* 1.3 71.3 + - - +
150A ILE* 3.2 4.7 + - - -
227A VAL* 3.9 23.9 - - - +
249A HIS* 4.2 5.2 + - - +
251A ILE* 3.9 19.5 - - - -
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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