Contacts of the helix formed by residues 142 - 155 (chain A) in PDB entry 2WZD
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A VAL* 4.1 21.7 - - + +
126A GLU* 4.6 0.5 - - - +
129A GLY* 2.8 36.3 - - - +
130A LYS* 4.2 6.4 - - - +
143A PRO* 1.4 83.5 - - + +
144A ALA* 3.3 2.5 - - - -
145A LYS* 3.1 18.6 + - + +
146A ILE* 2.9 40.7 + - + +
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Residues in contact with PRO 143 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A GLU* 1.4 93.2 - - + +
144A ALA* 1.3 56.0 + - - +
146A ILE* 3.2 13.1 + - + +
147A GLU* 2.9 28.6 + - - +
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Residues in contact with ALA 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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142A GLU 3.3 1.0 - - - -
143A PRO* 1.3 79.0 - - - +
145A LYS* 1.3 61.1 + - + +
147A GLU* 3.1 22.2 + - - +
148A ALA* 2.9 27.3 + - - +
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Residues in contact with LYS 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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126A GLU* 3.3 33.6 - - + +
142A GLU* 3.1 20.2 + - + +
144A ALA* 1.3 77.4 - - + +
146A ILE* 1.3 58.5 + - - +
148A ALA* 3.3 7.2 + - + +
149A PHE* 2.9 24.4 + - - +
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Residues in contact with ILE 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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126A GLU* 3.9 19.5 - - + +
129A GLY* 4.4 11.4 - - - +
142A GLU* 2.9 48.5 + - + +
143A PRO* 3.5 11.4 - - + +
145A LYS* 1.3 75.9 - - - +
147A GLU* 1.3 62.8 + - - +
149A PHE* 3.2 2.9 + - - +
150A ARG* 3.0 56.7 + - - +
173A SER* 4.0 7.0 - - - +
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Residues in contact with GLU 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 PRO 2.9 13.1 + - - +
144A ALA* 3.1 28.4 - - - +
146A ILE* 1.3 78.0 - - - +
148A ALA* 1.3 73.8 + - - +
150A ARG* 3.3 8.4 + - - +
151A ALA* 2.9 34.3 + - + +
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Residues in contact with ALA 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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144A ALA 2.9 18.2 + - - +
145A LYS* 3.8 9.9 - - + +
147A GLU* 1.3 86.3 - - - +
149A PHE* 1.3 61.8 + - - +
151A ALA* 3.4 6.0 + - - +
152A SER* 3.0 23.4 + - - -
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Residues in contact with PHE 149 (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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98A CYS* 4.0 4.5 - - - -
99A VAL* 3.6 32.3 - - + +
121A LEU* 4.1 25.4 - - + -
124A HIS* 3.6 33.9 - + + -
126A GLU* 3.5 24.7 - - + -
127A GLU* 3.8 22.9 - - + -
145A LYS 2.9 17.0 + - - +
146A ILE 3.2 5.4 + - - +
148A ALA* 1.3 77.6 - - - +
150A ARG* 1.3 61.1 + - - +
152A SER* 3.3 6.8 + - - -
153A LEU* 3.2 40.1 + - + +
173A SER* 3.8 17.9 - - - -
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Residues in contact with ARG 150 (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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127A GLU 5.5 0.2 + - - -
146A ILE* 3.0 37.0 + - - +
147A GLU* 3.7 7.2 - - - +
149A PHE* 1.3 76.7 - - - +
151A ALA* 1.3 53.5 + - - +
153A LEU* 3.4 8.6 + - - +
154A SER* 2.8 37.2 + - - -
171A ALA 4.7 4.0 + - - -
172A HIS* 4.5 0.6 - - - +
173A SER* 3.0 48.0 + - - +
176A VAL* 4.4 14.1 + - - +
177A GLY* 3.4 37.5 - - - +
178A VAL* 4.9 0.6 - - - +
179A ASN* 6.4 0.2 - - - -
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Residues in contact with ALA 151 (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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147A GLU* 2.9 24.4 + - + +
148A ALA* 3.6 8.7 - - - +
150A ARG* 1.3 76.3 - - - +
152A SER* 1.3 60.9 + - - +
154A SER* 3.2 6.4 + - - -
155A LYS* 2.9 45.9 + - + +
179A ASN* 6.5 0.2 - - - -
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Residues in contact with SER 152 (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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99A VAL* 3.4 29.2 - - - +
100A GLY* 3.5 9.7 - - - -
104A GLU* 2.7 29.1 + - - +
148A ALA 3.0 13.4 + - - -
149A PHE* 3.3 8.9 + - - -
151A ALA* 1.3 74.0 - - - +
153A LEU* 1.3 64.9 + - - +
155A LYS* 3.1 16.1 + - - +
156A LEU* 3.4 14.8 - - - +
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A VAL* 4.2 10.7 - - - +
60A MET* 4.0 15.9 - - - -
98A CYS 3.5 22.9 - - - +
99A VAL* 3.7 8.3 - - + -
118A LEU* 4.5 1.8 - - + -
121A LEU* 4.0 17.7 - - + -
149A PHE* 3.2 35.2 + - + +
150A ARG* 3.8 9.6 - - - +
152A SER* 1.3 77.4 - - - +
154A SER* 1.3 62.9 + - - +
156A LEU* 3.2 26.7 + - + +
157A GLY 4.4 0.3 + - - -
173A SER 4.6 2.0 - - - -
174A SER* 3.9 33.0 - - - +
178A VAL* 4.5 13.2 - - + -
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Residues in contact with SER 154 (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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150A ARG 2.8 23.0 + - - -
151A ALA* 3.5 7.4 - - - -
152A SER 3.1 0.6 - - - -
153A LEU* 1.3 78.4 - - - +
155A LYS* 1.3 74.1 + - - +
156A LEU 3.3 0.2 + - - -
157A GLY 3.2 16.6 + - - +
178A VAL* 3.6 13.3 - - - -
179A ASN* 2.9 46.7 + - - +
180A LEU* 3.4 12.9 - - - +
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Residues in contact with LYS 155 (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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17A ARG* 2.9 27.5 + - - +
104A GLU* 4.4 23.7 - - + +
108A ALA* 5.5 0.5 - - - -
151A ALA* 2.9 48.4 + - + +
152A SER* 3.1 12.5 + - - +
154A SER* 1.3 88.8 - - - +
156A LEU* 1.3 56.2 + - - +
157A GLY 3.3 1.6 - - - -
179A ASN* 5.6 1.4 + - - +
180A LEU* 6.2 0.4 - - - -
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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