Contacts of the helix formed by residues 135 - 149 (chain A) in PDB entry 1XTD
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A PRO* 3.2 4.4 - - + +
134A PRO* 1.3 77.6 - - + +
136A ALA* 1.3 67.8 + - - +
137A ALA* 3.3 9.9 + - - +
138A LEU* 3.1 42.5 + - + +
139A ALA* 3.1 22.9 + - - +
164A GLN* 5.5 2.0 - - - +
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Residues in contact with ALA 136 (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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134A PRO 3.3 6.8 + - - +
135A ASP* 1.3 72.0 + - - +
137A ALA* 1.3 60.4 + - - +
139A ALA* 3.0 8.1 + - - +
140A THR* 3.0 32.1 + - - +
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Residues in contact with ALA 137 (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 ASP* 3.3 8.1 + - - +
136A ALA* 1.3 78.3 - - - +
138A LEU* 1.3 61.8 + - - +
140A THR* 4.0 6.9 - - - -
141A GLN* 3.2 27.5 + - - +
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Residues in contact with LEU 138 (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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133A PRO* 3.7 16.2 - - + -
135A ASP* 3.1 32.4 + - + +
137A ALA* 1.3 75.2 - - - +
139A ALA* 1.3 62.3 + - - +
141A GLN* 3.4 4.7 + - + +
142A ILE* 3.1 34.1 + - + +
165A VAL* 3.5 31.9 - - + +
166A LEU* 4.0 20.6 - - + +
167A GLN* 4.3 0.9 - - - -
168A THR* 4.1 33.4 - - + +
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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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132A MSE 4.0 31.8 - - + +
133A PRO* 4.2 16.5 - - + +
135A ASP 3.1 17.2 + - - +
136A ALA* 3.0 6.4 + - - +
138A LEU* 1.3 73.0 - - - +
140A THR* 1.3 62.8 + - - +
142A ILE 3.6 0.3 + - - -
143A LYS* 3.2 23.2 + - - +
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Residues in contact with THR 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 ALA 3.0 17.8 + - - -
137A ALA* 4.0 7.9 - - - -
139A ALA* 1.3 73.0 - - - +
141A GLN* 1.3 61.5 + - - +
143A LYS* 3.4 5.2 + - + +
144A GLU* 2.8 56.4 + - - +
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Residues in contact with GLN 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 ALA 3.2 18.3 + - - +
138A LEU* 3.7 7.6 - - + +
139A ALA 3.4 0.2 - - - -
140A THR* 1.3 79.0 - - - +
142A ILE* 1.3 62.4 + - - +
144A GLU* 3.5 14.6 + - - +
145A GLN* 3.0 47.3 + - - +
168A THR* 4.4 17.7 - - + +
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Residues in contact with ILE 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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102A VAL* 4.6 7.0 - - + -
105A ILE* 4.5 12.1 - - + -
117A LEU* 4.8 1.8 - - + -
132A MSE 3.3 34.5 - - + -
133A PRO* 4.5 2.2 - - + -
138A LEU* 3.1 24.6 + - + +
139A ALA 4.0 0.4 - - - +
140A THR 3.2 0.2 - - - -
141A GLN* 1.3 76.3 - - - +
143A LYS* 1.3 62.9 + - - +
145A GLN* 3.2 2.6 + - - +
146A PHE* 3.0 22.9 + - - +
152A VAL* 4.0 21.2 - - + +
154A VAL* 3.9 23.6 - - + -
165A VAL* 4.0 17.9 - - + -
168A THR* 4.1 19.7 - - + -
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Residues in contact with LYS 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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105A ILE* 4.3 33.5 - - + +
132A MSE 5.1 3.7 - - - +
139A ALA 3.2 15.4 + - - +
140A THR* 3.8 6.3 - - - +
142A ILE* 1.3 78.9 - - - +
144A GLU* 1.3 61.9 + - - +
146A PHE* 3.9 0.2 - - - +
147A ASP* 3.0 57.1 + - - +
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Residues in contact with GLU 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 THR* 2.8 46.4 + - - +
141A GLN* 3.9 17.9 + - - +
143A LYS* 1.3 73.4 - - - +
145A GLN* 1.3 64.2 + - - +
147A ASP* 3.4 6.9 + - - +
148A SER* 3.0 28.6 + - - -
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Residues in contact with GLN 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 GLN* 3.0 37.0 + - - +
142A ILE 3.2 1.1 + - - +
144A GLU* 1.3 81.0 + - - +
146A PHE* 1.3 62.9 + - - +
148A SER* 2.8 30.2 + - - -
149A GLY 3.4 4.7 + - - -
150A LYS* 3.6 23.4 + - + +
152A VAL* 3.5 21.3 - - + -
168A THR* 5.6 4.7 - - + +
170A ASN* 2.8 31.5 - - - +
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Residues in contact with PHE 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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102A VAL* 3.6 37.2 - - + -
103A LEU 3.6 22.2 - - - -
104A ASP* 3.7 15.3 - - - -
105A ILE* 3.6 29.6 - - + -
142A ILE* 3.0 16.9 + - + +
143A LYS 3.9 1.3 - - - +
145A GLN* 1.3 74.8 - - - +
147A ASP* 1.3 76.6 + - - +
149A GLY* 3.1 15.4 + - - -
150A LYS 4.3 5.5 - - - +
152A VAL* 3.3 15.8 - - + +
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Residues in contact with ASP 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 LYS* 3.0 50.3 + - - +
144A GLU* 3.7 6.5 - - - +
146A PHE* 1.3 92.1 - - - +
148A SER* 1.3 59.4 + - - +
149A GLY* 3.4 0.7 + - - -
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Residues in contact with SER 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 GLU 3.0 13.5 + - - -
145A GLN* 2.8 25.9 + - - -
147A ASP* 1.3 77.8 - - - +
149A GLY* 1.3 58.6 + - - +
150A LYS* 3.5 24.3 + - - -
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Residues in contact with GLY 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 GLN 3.4 0.4 + - - -
146A PHE 3.1 13.3 + - - -
147A ASP 3.2 1.1 - - - -
148A SER* 1.3 80.9 - - - +
150A LYS* 1.3 66.3 + - - +
151A GLU 3.9 0.3 + - - -
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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