Contacts of the helix formed by residues 138 - 155 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A GLU* 3.4 21.7 + - - +
135A ASN 2.9 10.7 + - - +
137A ASP* 1.3 81.9 - - + +
139A ALA* 1.3 63.2 + - - +
140A GLU 3.3 2.5 - - - -
141A VAL* 3.0 35.0 + - + +
142A ALA 3.1 7.1 + - - -
135B ASN* 3.7 25.6 - - - +
138B LEU* 3.6 39.0 - - + +
139B ALA* 4.3 11.0 - - + +
142B ALA* 5.5 4.7 - - + -
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Residues in contact with ALA 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 ASN* 3.5 5.2 + - - +
136A LYS* 3.0 27.4 + - + +
137A ASP 3.5 1.0 - - - -
138A LEU* 1.3 75.7 - - - +
140A GLU* 1.3 66.2 + - + +
142A ALA* 2.8 22.3 + - - +
143A GLU* 2.9 21.1 + - - +
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Residues in contact with GLU 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 LYS 5.9 0.4 - - - +
137A ASP 5.2 6.2 - - - +
139A ALA* 1.3 77.0 - - + +
141A VAL* 1.3 61.3 + - + +
143A GLU* 2.8 35.6 + - - +
144A HIS* 3.2 5.4 + - - +
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Residues in contact with VAL 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 ASP 5.1 0.7 - - - +
138A LEU* 3.0 37.0 - - + +
140A GLU* 1.3 76.2 - - + +
142A ALA* 1.3 62.0 + - - +
144A HIS* 3.2 18.7 + - + +
145A VAL* 3.2 16.5 + - - +
138B LEU* 3.8 39.9 - - + +
141B VAL* 4.0 13.6 - - + +
142B ALA* 4.4 13.0 - - + +
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Residues in contact with ALA 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 3.1 7.1 + - - +
139A ALA* 2.8 20.7 + - - +
141A VAL* 1.3 76.5 - - - +
143A GLU* 1.3 57.9 + - - +
145A VAL* 2.9 32.1 + - + +
146A GLN* 3.2 15.6 + - - +
138B LEU* 4.1 15.5 - - + +
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Residues in contact with GLU 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 ALA* 2.9 23.5 + - - +
140A GLU* 2.8 19.0 + - - +
142A ALA* 1.3 72.8 - - - +
144A HIS* 1.3 65.4 + - - +
145A VAL 2.9 1.1 - - - -
146A GLN* 2.8 35.7 + - - +
147A TYR* 3.1 11.2 + - - +
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Residues in contact with HIS 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 GLU 3.2 4.2 + - - +
141A VAL* 3.2 16.3 + - - +
143A GLU* 1.3 76.6 - - - +
145A VAL* 1.3 57.3 + - - +
147A TYR* 3.5 16.2 + + - +
148A MSE 2.9 62.3 + - + +
141B VAL* 4.2 14.4 - - + -
145B VAL* 3.8 30.0 - - + +
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Residues in contact with VAL 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 VAL 3.2 16.6 - - - +
142A ALA* 2.9 19.7 - - + +
143A GLU 2.8 4.4 + - - -
144A HIS* 1.3 74.7 - - - +
146A GLN* 1.3 56.4 + - + +
148A MSE 3.6 6.8 + - - +
149A ALA* 3.0 26.1 + - + +
138B LEU* 3.8 19.3 - - + -
141B VAL* 4.3 18.2 - - + -
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Residues in contact with GLN 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 ALA* 3.2 13.7 + - - +
143A GLU* 2.8 31.6 + - - +
145A VAL* 1.3 73.8 - - + +
147A TYR* 1.3 55.3 - - - +
149A ALA* 2.8 10.2 + - + +
150A GLU* 2.7 37.4 + - - +
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Residues in contact with TYR 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 GLU 3.1 10.6 + - - +
144A HIS* 3.6 22.4 - + - +
146A GLN* 1.3 76.5 - - - +
148A MSE 1.3 84.3 + - - +
150A GLU* 3.0 21.7 - - - +
151A VAL* 2.8 42.0 + - + +
154A ARG* 5.3 7.0 - - - -
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Residues in contact with MSE 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 HIS* 2.9 50.4 + - + +
145A VAL* 3.7 6.5 - - - +
147A TYR* 1.3 97.1 - - - +
149A ALA* 1.3 53.3 + - - +
151A VAL* 3.5 14.8 - - + +
152A ILE* 2.8 56.1 + - + +
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Residues in contact with ALA 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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145A VAL* 3.0 17.3 + - + +
146A GLN* 2.8 17.3 + - + +
148A MSE 1.3 72.9 - - - +
150A GLU* 1.3 55.2 + - - +
152A ILE* 3.2 10.9 + - - +
153A GLU* 2.8 38.6 + - - +
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Residues in contact with GLU 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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146A GLN 2.7 11.7 + - - +
147A TYR* 3.0 24.4 - - - +
149A ALA* 1.3 72.2 - - - +
151A VAL* 1.3 58.8 + - - +
153A GLU* 2.8 26.8 + - - +
154A ARG* 3.1 39.4 + - - +
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Residues in contact with VAL 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 TYR* 2.8 53.3 + - + +
148A MSE 3.5 20.2 - - + +
150A GLU* 1.3 72.4 + - + +
152A ILE* 1.3 62.7 + - + +
154A ARG* 2.8 42.0 + - - +
155A LEU* 3.1 27.9 + - + +
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Residues in contact with ILE 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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148A MSE 2.8 43.6 + - + +
149A ALA* 3.7 7.2 - - - +
151A VAL* 1.3 74.6 - - + +
153A GLU* 1.3 61.7 + - - +
155A LEU* 3.0 35.6 + - + +
156A SER* 4.1 4.3 + - - -
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Residues in contact with GLU 153 (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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149A ALA 2.8 13.9 + - - +
150A GLU* 2.8 16.4 + - - +
152A ILE* 1.3 81.7 - - - +
154A ARG* 1.3 60.2 + - - +
156A SER* 3.9 14.2 + - - +
157A ASN 3.5 15.4 - - - +
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Residues in contact with ARG 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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147A TYR* 5.3 8.1 - - - -
150A GLU* 3.1 34.9 + - + +
151A VAL* 2.8 36.7 + - - +
153A GLU* 1.3 74.2 - - - +
155A LEU* 1.3 59.7 + - + +
156A SER 2.9 12.2 + - - -
157A ASN* 3.6 15.6 + - - -
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Residues in contact with LEU 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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151A VAL* 3.1 40.2 + - + +
152A ILE* 3.0 25.7 + - + +
154A ARG* 1.3 76.7 - - + +
156A SER* 1.3 62.8 + - - +
157A ASN 4.0 0.7 - - - -
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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