Contacts of the helix formed by residues 134 - 150 (chain B) in PDB entry 3ASZ
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 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ARG* 2.9 40.2 + - - +
133B ALA* 1.3 75.5 - - - +
135B ALA* 1.3 66.3 + - - +
136B ASP* 3.3 20.2 - - - +
137B GLU* 3.1 18.4 + - - +
138B ARG* 3.0 19.5 + - - +
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Residues in contact with ALA 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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133B ALA 3.6 2.4 + - - -
134B ASP* 1.3 72.4 - - - +
136B ASP* 1.3 57.4 + - - +
138B ARG* 3.3 22.9 + - - +
139B PHE* 2.9 30.9 + - - +
161B TYR* 3.9 19.5 + - - +
166B LYS* 6.1 4.0 - - - -
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Residues in contact with ASP 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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134B ASP* 3.3 21.8 - - - +
135B ALA* 1.3 74.5 - - - +
137B GLU* 1.3 85.6 + - - +
139B PHE* 3.4 7.1 + - - +
140B ILE* 3.2 32.0 + - + +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ARG* 4.2 17.6 + - - -
133B ALA* 5.3 2.6 - - + +
134B ASP* 3.1 21.2 + - + +
136B ASP* 1.3 90.6 + - - +
138B ARG* 1.3 65.1 + - - +
140B ILE* 3.4 16.6 + - + +
141B ARG* 3.4 44.2 + - - +
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Residues in contact with ARG 138 (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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14B GLY* 3.8 3.2 - - - +
15B THR* 3.0 45.0 + - - +
16B ALA* 3.3 27.1 - - - +
17B SER* 3.6 21.1 - - - +
133B ALA* 3.3 32.6 + - + +
134B ASP 3.0 15.3 + - - +
135B ALA* 3.8 23.5 - - - +
137B GLU* 1.3 76.0 - - - +
139B PHE* 1.3 59.6 + - - +
141B ARG* 3.3 1.8 + - - +
142B ARG* 2.8 27.1 + - - +
161B TYR* 4.7 11.1 + - - -
165B VAL* 5.8 0.4 - - - +
169B HIS* 3.4 41.9 + - - +
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Residues in contact with PHE 139 (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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135B ALA 2.9 18.0 + - - +
136B ASP* 3.7 7.9 - - - +
138B ARG* 1.3 77.4 - - - +
140B ILE* 1.3 59.9 + - + +
142B ARG* 3.5 7.1 - - + +
143B LEU* 2.7 53.6 + - + +
154B LEU* 4.9 1.1 - - + -
157B VAL* 3.9 27.1 - - + -
158B VAL* 4.1 25.4 - - + -
161B TYR* 3.7 50.0 - + + -
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Residues in contact with ILE 140 (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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136B ASP* 3.2 19.0 + - + +
137B GLU* 3.5 19.1 - - + +
138B ARG 3.2 0.2 - - - -
139B PHE* 1.3 85.7 - - + +
141B ARG* 1.3 65.7 + - + +
143B LEU* 3.3 7.3 + - + +
144B LYS* 3.0 45.1 + - + +
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Residues in contact with ARG 141 (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 ALA* 3.0 38.1 + - + +
17B SER 3.7 15.8 + - - -
18B GLY* 5.0 2.9 - - - +
133B ALA* 3.9 17.4 - - - +
137B GLU* 3.4 28.8 + - - +
138B ARG* 3.3 10.9 + - - +
140B ILE* 1.3 79.5 - - + +
142B ARG* 1.3 59.8 - - - +
144B LYS* 3.3 13.2 + - + +
145B ARG* 2.9 32.2 + - - +
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Residues in contact with ARG 142 (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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15B THR* 3.1 28.1 + - + +
16B ALA* 3.6 10.7 - - + +
138B ARG 2.8 18.4 + - - +
139B PHE* 3.5 9.2 - - + +
141B ARG* 1.3 75.1 - - - +
143B LEU* 1.3 59.5 + - - +
145B ARG* 3.4 24.5 + - - +
146B ASP* 2.8 57.5 + - - +
157B VAL* 4.5 10.0 - - + +
160B GLN* 3.0 29.7 + - - -
161B TYR* 5.2 10.5 - - + -
165B VAL* 3.7 11.8 - - - +
212B C5P 2.9 54.8 + - - -
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE* 2.7 39.7 + - + +
140B ILE* 3.5 8.1 - - - +
142B ARG* 1.3 73.8 - - - +
144B LYS* 1.3 65.0 + - + +
146B ASP* 3.9 0.7 - - - +
147B VAL* 3.1 46.2 + - + +
154B LEU* 3.4 38.8 - - + -
157B VAL* 4.0 25.3 - - + +
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Residues in contact with LYS 144 (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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140B ILE* 3.0 36.0 + - + +
141B ARG* 3.7 14.1 - - + +
142B ARG 3.3 0.2 - - - -
143B LEU* 1.3 80.3 - - + +
145B ARG* 1.3 58.2 + - - +
147B VAL* 3.9 1.9 - - - +
148B LEU* 2.9 48.6 + - + +
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Residues in contact with ARG 145 (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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15B THR* 3.4 9.5 + - - -
16B ALA* 4.3 10.8 - - + +
20B THR* 5.6 1.4 + - - -
141B ARG 2.9 21.1 + - - +
142B ARG* 3.4 32.8 - - - +
144B LYS* 1.3 73.6 - - - +
146B ASP* 1.3 74.7 + - - +
148B LEU* 5.0 0.9 - - - -
149B GLU* 2.9 57.1 + - - +
150B ARG* 2.9 41.3 + - - +
212B C5P 2.4 41.2 + - - -
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Residues in contact with ASP 146 (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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142B ARG* 2.8 55.6 + - - +
143B LEU 3.9 0.2 - - - +
145B ARG* 1.3 95.0 + - - +
147B VAL* 1.3 57.8 + - - +
150B ARG* 3.0 32.8 + - - -
152B ARG* 3.2 31.4 + - + +
157B VAL* 3.5 29.8 - - + +
160B GLN* 4.3 4.2 - - - +
212B C5P 5.1 0.2 - - - +
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Residues in contact with VAL 147 (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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91B ARG* 5.7 0.2 + - - -
143B LEU* 3.1 36.5 + - + +
144B LYS* 4.0 3.1 - - - +
146B ASP* 1.3 77.5 - - - +
148B LEU* 1.3 70.8 + - + +
151B GLY* 4.3 8.1 + - - -
152B ARG 3.5 23.4 - - - +
153B SER* 4.4 2.0 - - - -
154B LEU* 4.3 12.1 - - + +
157B VAL* 4.6 2.0 - - + -
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Residues in contact with LEU 148 (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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91B ARG* 4.1 9.8 + - - -
144B LYS* 2.9 33.4 + - + +
145B ARG* 5.0 0.4 - - - -
147B VAL* 1.3 88.5 - - + +
149B GLU* 1.3 68.1 + - + +
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Residues in contact with GLU 149 (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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90B PHE* 5.7 0.3 - - - +
91B ARG* 3.3 25.4 + - - +
145B ARG* 2.9 37.0 + - - +
148B LEU* 1.3 84.4 - - + +
150B ARG* 1.3 72.5 + - + +
151B GLY 3.5 2.2 - - - -
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Residues in contact with ARG 150 (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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90B PHE* 3.5 55.5 - - + -
91B ARG* 3.8 23.2 - - - +
145B ARG* 2.9 41.9 - - - +
146B ASP* 3.0 25.3 + - - +
149B GLU* 1.3 86.6 + - + +
151B GLY* 1.3 64.5 + - - +
152B ARG* 3.1 32.8 + - + +
212B C5P 2.6 49.5 + - - -
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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