Contacts of the helix formed by residues 132 - 146 (chain A) in PDB entry 6A08
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 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A LEU 3.0 5.0 + - - -
131A ARG* 1.3 88.1 - - + +
133A GLU* 1.3 67.2 + - - +
134A LYS* 3.1 32.8 + - + +
135A ARG* 3.2 38.5 + - - +
136A SER* 3.3 12.1 + - - -
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Residues in contact with GLU 133 (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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129A TRP* 3.9 28.2 - - + +
130A LEU 4.5 0.2 + - - -
132A ASP* 1.3 72.3 - - - +
134A LYS* 1.3 62.7 + - - +
136A SER* 3.2 2.4 + - - -
137A LEU* 2.9 44.6 + - + +
212A GLU 5.4 0.7 - - - +
213A SER* 5.9 0.2 - - - -
216A ALA* 3.7 24.0 - - - +
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Residues in contact with LYS 134 (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 ASP* 3.1 21.7 + - - +
133A GLU* 1.3 79.7 - - - +
135A ARG* 1.3 73.6 + - + +
137A LEU* 3.4 6.5 + - - +
138A ASP* 2.9 48.1 + - - +
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Residues in contact with ARG 135 (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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130A LEU* 3.7 27.7 - - + +
131A ARG* 3.5 32.0 - - - +
132A ASP* 3.2 29.6 + - - +
134A LYS* 1.3 96.2 - - + +
136A SER* 1.3 65.7 - - - +
138A ASP* 3.2 8.9 + - - +
139A LEU* 3.1 18.5 + - - +
182A PHE* 3.7 33.9 - - - -
205A GLU* 5.0 5.9 + - - +
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Residues in contact with SER 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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127A LEU* 4.0 7.4 - - - +
129A TRP* 3.4 33.4 - - - -
130A LEU* 2.8 47.3 + - - +
132A ASP 3.3 2.9 + - - -
133A GLU 3.2 7.1 + - - -
135A ARG* 1.3 78.1 - - - +
137A LEU* 1.3 62.3 + - - +
139A LEU* 3.2 7.2 + - - +
140A VAL* 3.1 25.2 + - - +
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Residues in contact with LEU 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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129A TRP* 4.7 3.6 - - + -
133A GLU* 2.9 45.7 + - + +
134A LYS* 3.9 6.7 - - - +
136A SER* 1.3 75.0 - - - +
138A ASP* 1.3 60.8 + - - +
140A VAL* 3.3 5.2 + - + +
141A ARG* 2.9 23.6 + - - +
216A ALA* 3.8 25.6 - - + +
217A VAL* 4.0 21.8 - - + -
220A HIS* 3.4 48.9 + - + +
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Residues in contact with ASP 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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134A LYS* 2.9 42.6 + - - +
135A ARG* 3.2 10.9 + - - +
137A LEU* 1.3 78.9 - - - +
139A LEU* 1.3 59.3 + - - +
141A ARG* 3.8 7.8 - - - +
142A ARG* 3.0 35.6 + - + +
220A HIS* 5.4 2.6 + - - -
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Residues in contact with LEU 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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107A THR* 3.8 34.5 - - + +
113A LEU* 4.0 16.9 - - + +
125A PHE* 3.6 15.6 - - + -
127A LEU* 4.1 12.3 - - + -
130A LEU* 4.1 19.7 - - + -
135A ARG 3.1 11.2 + - - +
136A SER 3.2 9.4 + - - +
138A ASP* 1.3 74.3 - - - +
140A VAL* 1.3 68.2 + - - +
142A ARG* 3.3 28.3 + - - +
143A ALA* 3.0 23.7 + - - +
181A ASN* 4.5 10.8 - - + +
182A PHE* 4.3 7.0 - - + -
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Residues in contact with VAL 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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125A PHE* 5.0 1.8 - - + -
127A LEU* 3.8 28.7 - - + -
136A SER 3.1 14.2 + - - +
137A LEU* 3.3 11.4 + - + +
139A LEU* 1.3 78.3 - - - +
141A ARG* 1.3 57.3 + - - +
143A ALA* 3.2 7.1 + - - +
144A GLU* 3.0 27.6 + - - +
151A ILE* 4.1 24.9 - - + +
217A VAL* 4.4 15.3 - - + +
220A HIS* 4.4 10.3 - - + -
221A THR* 4.1 26.7 - - + +
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Residues in contact with ARG 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 LEU 2.9 16.9 + - - +
138A ASP* 3.8 9.6 - - - +
139A LEU 3.2 0.2 - - - -
140A VAL* 1.3 75.0 - - - +
142A ARG* 1.3 60.0 + - - +
144A GLU* 3.3 14.2 + - - +
145A ASP* 2.8 58.0 + - - +
220A HIS* 3.1 54.2 + - - +
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Residues in contact with ARG 142 (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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112A SER* 4.7 3.6 - - - -
113A LEU* 3.8 15.0 - - + +
114A GLU* 2.8 44.1 + - - +
138A ASP* 3.0 21.5 + - + +
139A LEU* 3.5 24.6 - - - +
141A ARG* 1.3 76.9 - - - +
143A ALA* 1.3 63.2 + - - +
145A ASP* 3.4 7.5 + - - +
146A ALA* 3.0 25.1 + - - +
180A ALA 5.1 0.4 + - - -
181A ASN* 3.0 43.9 + - - +
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Residues in contact with ALA 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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113A LEU* 3.9 11.2 - - + +
125A PHE* 3.5 44.2 - - + -
139A LEU 3.0 11.8 + - - +
140A VAL 3.2 7.8 + - - +
142A ARG* 1.3 75.8 - - - +
144A GLU* 1.3 62.1 + - - +
146A ALA* 3.2 7.1 + - - -
147A GLY 3.3 0.2 + - - -
148A CYS* 3.0 34.6 + - + +
151A ILE* 4.2 4.9 - - + -
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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 VAL* 3.0 17.6 + - - +
141A ARG* 3.8 14.3 + - - +
143A ALA* 1.3 75.1 - - - +
145A ASP* 1.3 66.4 + - - +
147A GLY* 3.1 14.0 + - - -
148A CYS 4.4 3.0 - - - +
220A HIS 4.2 3.8 - - - +
221A THR* 2.7 35.2 + - - -
222A ASP* 3.7 20.2 + - - +
223A LEU* 3.9 31.1 - - + +
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Residues in contact with ASP 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 ARG* 2.8 44.2 + - - +
142A ARG* 3.7 7.4 - - - +
144A GLU* 1.3 78.9 - - - +
146A ALA* 1.3 59.8 + - - +
147A GLY 3.2 1.1 + - - -
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Residues in contact with ALA 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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113A LEU* 4.0 15.0 - - + -
114A GLU* 4.3 14.8 - - + +
117A ALA* 3.4 34.4 - - + +
142A ARG 3.0 17.1 + - - +
143A ALA 3.7 4.7 - - - +
144A GLU 3.2 0.6 - - - -
145A ASP* 1.3 75.6 - - - +
147A GLY* 1.3 57.2 + - - +
148A CYS* 3.6 0.9 - - - -
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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