Contacts of the helix formed by residues 138 - 154 (chain D) in PDB entry 2ZXX
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 LEU 138 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134D GLU* 3.8 23.3 - - + +
135D ASN* 2.8 7.9 + - - +
137D ASP* 1.3 89.1 - - + +
139D ALA* 1.3 65.2 + - - +
140D GLU* 2.7 9.9 + - - +
141D VAL* 2.8 29.8 + - + +
142D ALA 3.2 6.6 + - - -
135E ASN* 5.0 3.8 - - - +
138E LEU* 3.6 41.5 - - + +
139E ALA* 4.2 17.9 - - + +
142E ALA* 5.6 5.6 - - + -
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ASN* 3.0 10.3 + - - +
136D LYS* 2.9 30.7 + - + +
137D ASP 3.7 0.2 - - - -
138D LEU* 1.3 75.9 - - - +
140D GLU* 1.3 62.2 + - + +
142D ALA* 3.0 26.1 - - - +
143D GLU* 3.4 6.4 + - - +
138E LEU* 5.5 0.2 - - - -
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Residues in contact with GLU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D LYS 5.3 1.6 - - - +
137D ASP 4.9 7.2 - - - +
138D LEU* 2.7 6.4 + - - +
139D ALA* 1.3 77.6 - - + +
141D VAL* 1.3 60.8 + - - +
142D ALA 3.0 5.8 + - - -
143D GLU* 3.2 30.8 + - - +
144D HIS* 3.6 3.8 + - - +
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU* 2.8 28.6 + - + +
140D GLU* 1.3 75.2 - - - +
142D ALA* 1.3 58.5 + - - +
144D HIS* 3.5 14.4 + - + +
145D VAL* 3.0 20.3 + - - +
138E LEU* 3.5 39.7 - - + +
141E VAL* 3.7 24.5 - - + +
142E ALA* 3.8 24.7 - - + +
145E VAL* 5.5 2.7 - - + -
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU 3.2 6.1 + - - +
139D ALA* 3.0 22.2 - - - +
140D GLU 3.0 0.2 - - - -
141D VAL* 1.3 76.6 - - - +
143D GLU* 1.3 65.8 + - - +
144D HIS 3.1 1.3 - - - -
145D VAL* 2.7 23.5 + - - +
146D GLN* 3.0 11.2 + - - +
138E LEU* 4.6 11.9 - - + -
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Residues in contact with GLU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D ALA 3.4 5.0 + - - +
140D GLU* 3.2 21.7 + - - +
142D ALA* 1.3 77.9 - - - +
144D HIS* 1.3 61.8 + - + +
146D GLN* 3.2 10.4 + - - +
147D TYR* 2.8 32.5 + - + +
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Residues in contact with HIS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D GLU 3.6 2.5 + - - +
141D VAL* 3.5 16.3 + - + +
142D ALA 3.1 1.2 - - - -
143D GLU* 1.3 83.1 - - + +
145D VAL* 1.3 57.8 + - + +
147D TYR* 3.9 13.0 - + - +
148D MSE 3.0 54.5 + - + +
141E VAL* 4.2 16.2 - - + -
145E VAL* 4.0 28.2 - - + +
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Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D VAL 3.0 21.3 - - - +
142D ALA* 2.7 18.9 + - - +
144D HIS* 1.3 71.5 - - + +
146D GLN* 1.3 63.9 + - - +
148D MSE 3.2 7.0 + - + +
149D ALA* 2.9 22.5 + - - +
137E ASP* 6.6 0.4 - - + -
138E LEU* 4.6 13.7 - - + -
141E VAL* 5.2 18.4 - - + -
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Residues in contact with GLN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ALA 3.0 9.4 + - - +
143D GLU* 3.5 12.2 + - - +
145D VAL* 1.3 74.7 - - - +
147D TYR* 1.3 69.6 + - - +
149D ALA* 3.1 20.0 + - + +
150D GLU* 3.1 22.7 + - - +
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Residues in contact with TYR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D GLU* 2.8 25.2 + - + +
144D HIS* 3.9 16.8 - + - +
146D GLN* 1.3 83.1 - - - +
148D MSE 1.3 103.7 + - + +
150D GLU* 3.3 23.7 - - + +
151D VAL* 3.1 35.7 - - + +
154D ARG* 5.3 3.8 + - - -
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Residues in contact with MSE 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D HIS* 3.0 42.1 + - + +
145D VAL* 3.2 9.4 + - + +
147D TYR* 1.3 123.9 - - + +
149D ALA* 1.3 58.4 + - - +
151D VAL* 2.9 18.9 + - + +
152D ILE* 2.7 50.7 + - + +
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D VAL 2.9 13.0 + - - +
146D GLN* 3.2 15.9 - - + +
148D MSE 1.3 77.0 - - - +
150D GLU* 1.3 64.2 - - - +
151D VAL 3.0 0.3 + - - -
152D ILE* 3.1 5.4 + - - +
153D GLU* 3.1 24.1 + - - +
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D GLN* 3.1 18.1 + - - +
147D TYR* 3.3 26.3 - - + +
148D MSE 3.2 0.2 - - - -
149D ALA* 1.3 78.7 - - - +
151D VAL* 1.3 62.7 + - + +
153D GLU* 4.0 7.3 - - - +
154D ARG* 2.7 61.3 + - - +
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D TYR* 3.1 47.6 - - + +
148D MSE 2.9 20.1 + - + +
150D GLU* 1.3 75.8 - - + +
152D ILE* 1.3 69.5 + - + +
153D GLU 3.2 1.8 - - - -
154D ARG* 3.0 34.0 + - - +
155D LEU* 2.8 37.8 + - + +
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Residues in contact with ILE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D MSE 2.7 35.1 + - + +
149D ALA* 3.8 6.1 - - - +
151D VAL* 1.3 78.4 - - + +
153D GLU* 1.3 62.1 + - - +
155D LEU* 3.4 19.2 - - - +
156D SER* 4.4 3.6 + - - -
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Residues in contact with GLU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ALA 3.1 14.5 + - - +
150D GLU* 4.0 6.2 - - - +
152D ILE* 1.3 75.0 - - - +
154D ARG* 1.3 63.5 + - - +
155D LEU 2.8 11.9 + - - -
156D SER* 3.0 17.5 + - - -
157D ASN* 3.7 24.1 + - - +
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Residues in contact with ARG 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D TYR* 5.3 4.0 + - - -
150D GLU* 2.7 69.7 + - - +
151D VAL* 3.0 32.3 + - - +
153D GLU* 1.3 77.2 - - - +
155D LEU* 1.3 56.9 + - - +
156D SER 3.3 2.7 - - - -
157D ASN* 3.2 39.1 - - - +
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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