Contacts of the helix formed by residues 130 - 146 (chain A) in PDB entry 3ROT
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ARG* 5.5 10.4 + - - +
126A PHE* 5.5 1.6 - - - -
129A SER* 1.3 70.2 - - - +
131A ASN* 1.3 58.4 + - - +
132A LEU* 3.2 11.1 + - - +
133A LEU* 3.1 35.7 + - + +
134A ALA* 2.8 29.4 + - - +
291A ASN* 3.9 20.2 - - - +
293A ALA* 5.6 0.2 - - - +
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Residues in contact with ASN 131 (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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112A ASP 4.1 14.7 + - - +
113A THR* 4.9 3.1 + - - +
126A PHE* 5.7 0.9 - - - -
129A SER* 3.2 17.1 + - - +
130A ASP* 1.3 71.8 + - - +
132A LEU* 1.3 63.2 + - - +
134A ALA* 3.3 6.2 + - - +
135A GLY 2.9 18.9 + - - -
161A HIS* 5.3 0.3 - - - -
163A GLY* 3.3 37.9 - - - +
166A LYS* 3.6 11.4 - - + -
167A ARG* 2.8 50.2 + - + +
264A GLN* 4.5 1.0 + - - -
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Residues in contact with LEU 132 (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 ASP* 3.2 9.0 + - - +
131A ASN* 1.3 77.2 - - - +
133A LEU* 1.3 63.9 + - - +
135A GLY* 3.1 4.2 + - - -
136A LYS* 3.0 43.9 + - - +
166A LYS* 3.6 39.6 - - + +
169A TYR* 3.6 32.8 - - + -
170A GLY* 3.7 10.5 - - - +
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Residues in contact with LEU 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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130A ASP* 3.1 31.7 + - + +
132A LEU* 1.3 78.3 - - - +
134A ALA* 1.3 58.6 + - - +
136A LYS* 3.2 19.7 + - + +
137A LYS* 2.9 34.4 + - + +
140A GLU* 6.2 0.2 - - - +
291A ASN* 5.5 5.2 - - - +
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Residues in contact with ALA 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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129A SER* 4.8 12.1 - - - +
130A ASP 2.8 18.0 + - - +
131A ASN* 3.6 9.4 - - - +
133A LEU* 1.3 76.0 - - - +
135A GLY* 1.3 58.7 + - - +
137A LYS* 3.3 2.8 + - - +
138A LEU* 2.9 29.3 + - - +
243A PHE* 3.9 21.4 - - + -
262A MSE 3.7 21.0 - - + +
264A GLN* 6.5 0.4 - - + -
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Residues in contact with GLY 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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131A ASN 2.9 12.3 + - - -
132A LEU 3.6 3.1 - - - -
134A ALA* 1.3 75.7 - - - +
136A LYS* 1.3 63.7 + - - +
138A LEU 3.1 1.4 + - - -
139A GLY 2.9 19.4 + - - -
167A ARG* 3.5 21.5 - - - -
170A GLY 3.7 7.0 - - - -
171A ILE* 3.3 15.7 - - - +
243A PHE* 4.2 10.0 - - - -
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Residues in contact with LYS 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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132A LEU* 3.0 43.5 + - - +
133A LEU* 3.5 21.1 - - + +
135A GLY* 1.3 74.4 - - - +
137A LYS* 1.3 57.5 + - - +
139A GLY 3.2 1.2 + - - -
140A GLU* 2.9 37.2 + - - +
169A TYR* 5.0 2.0 - - - -
170A GLY* 3.4 17.6 - - - +
173A THR* 3.0 33.3 + - - +
174A ILE* 3.3 16.2 - - + +
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Residues in contact with LYS 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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133A LEU* 2.9 22.8 + - + +
134A ALA* 3.5 4.7 - - - +
136A LYS* 1.3 74.8 - - - +
138A LEU* 1.3 64.3 + - - +
140A GLU* 3.4 17.7 + - + +
141A LYS* 3.0 44.9 + - - +
260A TYR* 3.7 16.2 + - - -
262A MSE 3.4 27.2 - - + +
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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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134A ALA 2.9 17.1 + - - +
135A GLY 3.1 4.2 + - - +
137A LYS* 1.3 77.4 - - - +
139A GLY* 1.3 63.3 + - - +
141A LYS* 3.2 2.1 + - - +
142A ALA* 3.0 22.5 + - - +
171A ILE* 4.4 2.7 - - + -
212A PHE* 4.0 24.7 - - + -
213A CYS 5.1 0.7 - - - +
241A TYR* 4.1 15.9 - - + +
242A SER* 3.6 20.4 - - - +
243A PHE* 3.3 33.2 - - + -
260A TYR* 3.9 27.6 - - + +
262A MSE 3.7 20.0 - - + -
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Residues in contact with GLY 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 GLY 2.9 13.0 + - - -
136A LYS 3.6 3.8 - - - -
138A LEU* 1.3 78.5 - - - +
140A GLU* 1.3 61.1 + - - +
142A ALA* 3.4 2.4 + - - +
143A LEU* 3.2 26.7 + - - +
171A ILE* 4.4 6.9 - - - +
174A ILE* 3.7 17.7 - - - -
175A LEU* 5.4 1.8 - - - -
212A PHE* 4.0 17.1 - - - -
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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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133A LEU* 6.2 0.2 - - - +
136A LYS* 2.9 20.8 + - - +
137A LYS* 3.8 24.1 + - + +
138A LEU 3.3 0.2 - - - -
139A GLY* 1.3 74.7 - - - +
141A LYS* 1.3 60.9 + - - +
143A LEU* 3.5 6.2 + - - +
144A GLU* 3.2 21.9 + - - +
174A ILE* 3.9 28.1 - - + +
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Residues in contact with LYS 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 LYS* 3.0 31.1 + - - +
138A LEU* 3.7 4.0 - - + +
140A GLU* 1.3 73.8 - - - +
142A ALA* 1.3 61.4 + - - +
144A GLU* 3.1 23.4 + - - +
145A LEU* 2.9 52.3 + - + +
241A TYR* 4.8 0.2 - - + -
260A TYR* 3.2 65.4 + - + -
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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 3.0 10.3 + - - +
139A GLY 3.7 1.8 - - - +
141A LYS* 1.3 78.5 - - - +
143A LEU* 1.3 55.4 + - + +
146A THR* 2.7 39.2 + - - +
210A ILE* 4.4 5.6 - - + +
212A PHE* 3.5 30.3 - - + -
241A TYR* 3.3 37.2 - - + -
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Residues in contact with LEU 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 GLY 3.2 12.7 + - - +
140A GLU* 3.9 5.8 - - - +
141A LYS 3.2 0.8 - - - -
142A ALA* 1.3 78.7 - - + +
144A GLU* 1.3 61.4 + - - +
146A THR 3.7 2.9 - - - +
147A PRO* 3.7 18.0 - - - +
149A ALA* 4.1 22.9 - - + -
174A ILE* 3.6 24.2 - - + +
175A LEU* 4.0 20.9 - - + -
178A LYS* 3.2 38.6 - - + -
180A ILE* 4.2 8.1 - - + -
210A ILE* 4.8 3.6 - - + -
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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 GLU 3.2 12.7 + - - +
141A LYS* 3.1 30.9 + - - +
143A LEU* 1.3 78.0 - - - +
145A LEU* 1.3 74.6 + - + +
147A PRO* 3.4 17.3 - - - +
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Residues in contact with LEU 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 LYS* 2.9 39.5 + - + +
144A GLU* 1.3 93.1 - - + +
146A THR* 1.3 59.7 + - - +
147A PRO* 3.2 8.2 - - - +
239A GLN* 5.6 0.2 - - - +
241A TYR* 3.4 16.6 - - + +
259A ASN* 4.0 22.6 + - + +
260A TYR* 4.0 19.5 - - + -
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Residues in contact with THR 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 2.7 21.4 + - - +
143A LEU* 3.7 5.4 - - - +
145A LEU* 1.3 75.6 + - - +
147A PRO* 1.3 57.0 - - - +
148A SER* 3.2 11.2 - - - +
149A ALA* 3.0 29.1 + - - +
209A ASN* 4.7 2.7 - - - +
210A ILE* 3.5 28.5 - - + -
239A GLN* 3.4 29.5 - - + +
241A TYR* 2.6 22.4 + - - -
259A ASN* 3.7 1.2 + - - -
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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