Contacts of the helix formed by residues 136 - 145 (chain B) in PDB entry 2WZJ
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 GLU 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLY 4.8 1.0 - - - +
135B GLY* 1.3 72.2 - - - -
137B VAL* 1.3 65.3 + - - +
138B PHE* 3.7 15.9 - - - +
139B ASP* 3.1 26.8 + - - +
140B TYR* 3.0 22.0 + - - +
178B ALA 4.2 3.1 - - - +
179B GLU* 3.1 50.5 - - - +
181B LEU 3.7 4.0 - - - -
182B LEU* 4.0 9.2 - - + -
183B LEU* 4.3 2.8 - - - +
208C GLU* 5.1 0.2 - - - +
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLY 3.9 0.4 + - - -
136B GLU* 1.3 72.0 - - - +
138B PHE* 1.3 52.2 + - - +
140B TYR* 3.2 2.7 + - - +
141B LEU* 2.7 42.3 + - + +
147B MET* 5.1 7.2 - - + -
155B LYS* 5.9 0.4 - - + -
159B ILE* 5.9 0.2 - - + -
178B ALA* 3.6 16.6 - - + +
181B LEU* 2.8 44.4 + - + +
183B LEU* 3.9 21.1 - - + -
189B ILE* 3.8 19.7 - - + -
243B LEU* 3.8 28.9 - - + -
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Residues in contact with PHE 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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136B GLU* 3.0 10.1 - - - +
137B VAL* 1.3 75.1 - - - +
139B ASP* 1.3 83.3 + - - +
141B LEU* 3.5 5.1 + - - +
142B VAL* 3.1 38.6 + - + +
178B ALA* 2.9 29.4 + - + +
179B GLU* 3.7 24.2 - - + -
215B TYR* 5.6 1.1 - - - -
206C LEU* 3.6 40.2 - - + -
208C GLU* 3.4 36.6 - - + -
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Residues in contact with ASP 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 GLY* 5.8 0.4 - - - -
136B GLU* 3.1 31.6 + - + +
138B PHE* 1.3 98.7 - - - +
140B TYR* 1.3 57.9 + - - +
142B VAL* 3.3 8.1 + - - +
143B ALA* 3.0 31.2 + - - +
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Residues in contact with TYR 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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134B GLY 5.8 1.1 - - - -
136B GLU 3.0 12.1 + - - +
137B VAL* 3.5 11.4 - - - +
139B ASP* 1.3 75.1 - - - +
141B LEU* 1.3 68.0 + - + +
143B ALA* 4.6 1.1 - - - -
144B HIS* 3.0 59.8 + + + +
145B GLY 5.1 2.0 - - - -
147B MET* 3.6 37.9 - - + -
151B GLU* 3.3 23.8 + - - -
183B LEU* 4.1 17.0 - - + -
187B MET* 4.2 22.2 - - + -
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Residues in contact with LEU 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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137B VAL* 2.7 34.9 + - + +
138B PHE* 3.8 4.3 - - - +
140B TYR* 1.3 74.9 - - + +
142B VAL* 1.3 57.2 + - - +
145B GLY* 2.8 51.9 + - - +
146B ARG* 4.6 0.2 - - - -
147B MET* 4.5 15.5 - - + -
178B ALA* 4.8 6.5 - - + -
242B THR* 3.3 47.6 - - - +
243B LEU* 4.3 18.8 - - + +
246B GLY* 5.0 4.5 - - - +
206C LEU* 3.9 20.1 - - + +
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Residues in contact with VAL 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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138B PHE* 3.1 41.7 + - + +
139B ASP* 3.6 9.2 - - - +
141B LEU* 1.3 76.9 - - - +
143B ALA* 1.3 63.5 + - + +
145B GLY 4.6 1.0 + - - -
206C LEU* 3.8 21.8 - - + -
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Residues in contact with ALA 143 (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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139B ASP 3.0 16.4 + - - +
140B TYR* 4.0 2.9 - - - +
141B LEU 3.2 0.2 - - - -
142B VAL* 1.3 82.6 - - + +
144B HIS* 1.3 79.0 + - + +
145B GLY 3.8 0.2 - - - -
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Residues in contact with HIS 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 TYR* 3.0 60.9 + + + +
143B ALA* 1.3 93.3 + - + +
145B GLY* 1.3 65.6 + - - +
146B ARG 4.1 4.7 - - - +
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Residues in contact with GLY 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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140B TYR* 4.6 1.7 - - - +
141B LEU* 2.8 33.0 + - - +
142B VAL 4.5 1.4 + - - -
143B ALA 3.8 0.6 - - - -
144B HIS* 1.3 81.9 - - - +
146B ARG* 1.3 69.6 + - - +
147B MET* 3.5 2.9 + - - +
246B GLY* 4.8 4.3 - - - -
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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