Contacts of the helix formed by residues 135 - 147 (chain A) in PDB entry 3Q2K
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 ASN 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A GLN 4.3 1.4 - - - +
132A ASN* 2.9 38.3 + - - +
134A ARG* 1.3 76.9 - - - +
136A ALA* 1.3 65.2 + - - +
137A THR* 3.6 13.7 - - - +
138A LEU* 3.8 5.7 - - + +
139A GLN* 3.0 19.8 + - - +
267A ALA 3.7 6.5 + - - -
268A VAL* 3.2 37.8 + - - +
293A THR* 3.7 16.8 - - + +
296A VAL* 5.9 4.3 - - - +
303A LEU* 6.1 0.7 - - - -
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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 ARG 3.1 5.1 + - - +
135A ASN* 1.3 72.7 - - - +
137A THR* 1.3 63.9 + - - +
139A GLN* 3.8 9.1 - - + +
140A LEU* 3.2 26.7 + - + +
289A ALA* 4.2 13.0 - - + -
292A GLU* 3.7 35.7 - - + +
293A THR* 3.0 13.6 + - - +
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Residues in contact with THR 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 ASN* 3.6 6.6 - - - +
136A ALA* 1.3 78.0 - - - +
138A LEU* 1.3 68.4 + - - +
140A LEU* 3.1 14.9 + - - +
141A VAL* 3.3 15.7 + - - +
263A VAL* 3.9 9.2 - - - +
268A VAL 2.6 24.1 + - - -
269A ASN 3.7 22.2 - - - +
270A ARG 4.1 0.4 - - - +
271A ILE* 3.8 19.8 - - + +
289A ALA* 3.9 7.2 - - - +
290A ASN* 3.5 25.1 - - - +
293A THR* 3.1 16.3 + - - +
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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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132A ASN* 3.4 26.7 - - + +
133A ARG 4.7 0.4 - - - +
135A ASN* 3.2 13.3 + - + +
137A THR* 1.3 78.7 + - - +
139A GLN* 1.3 61.3 + - - +
141A VAL* 3.0 5.6 + - + +
142A LYS* 2.7 32.6 + - - +
195A LEU* 3.7 27.8 - - + -
198A TRP* 4.2 15.7 - - + -
199A LEU* 4.4 12.2 - - + +
252A ILE* 4.5 7.6 - - + -
263A VAL* 4.4 17.7 - - + -
268A VAL* 3.9 39.5 - - + -
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Residues in contact with GLN 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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133A ARG 3.0 22.3 + - - +
134A ARG* 3.1 34.8 + - - +
135A ASN 3.0 18.9 + - - +
136A ALA* 3.8 9.2 - - - +
137A THR 3.3 0.2 - - - -
138A LEU* 1.3 77.6 - - - +
140A LEU* 1.3 60.7 + - + +
142A LYS* 3.7 6.9 - - - +
143A LYS* 2.8 55.7 + - + +
198A TRP* 3.9 11.9 - - - -
319A GLU* 3.8 8.3 + - - -
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Residues in contact with LEU 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* 3.2 14.3 + - + +
137A THR 3.1 7.8 + - - +
139A GLN* 1.3 74.8 - - + +
141A VAL* 1.3 68.1 + - - +
143A LYS* 3.5 5.6 + - + +
144A ALA* 3.0 23.2 + - - +
271A ILE* 3.9 14.4 - - + -
274A TRP* 3.6 17.5 - - + -
282A ASP* 3.7 35.8 - - + +
285A LYS* 4.4 12.1 - - + +
286A ILE* 4.0 19.3 - - + -
289A ALA* 3.9 23.1 - - + -
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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 THR 3.3 9.6 + - - +
138A LEU* 3.0 9.9 + - - +
140A LEU* 1.3 76.8 - - - +
142A LYS* 1.3 65.3 + - - +
144A ALA* 3.0 7.6 + - - +
145A ILE* 2.9 31.4 + - + +
150A PHE* 4.8 7.2 - - + -
199A LEU* 4.2 12.6 - - + -
252A ILE* 6.2 0.4 - - + -
254A ILE* 4.0 27.4 - - + -
261A VAL* 3.9 15.5 - - + -
263A VAL* 3.7 30.5 - - + -
271A ILE* 5.2 0.9 - - + -
274A TRP* 4.1 12.1 - - + -
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Residues in contact with LYS 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 2.7 16.8 + - - +
139A GLN* 3.7 13.7 - - - +
141A VAL* 1.3 78.3 - - - +
143A LYS* 1.3 59.8 + - + +
145A ILE* 3.3 5.9 + - + +
146A GLU* 3.1 55.3 + - + +
198A TRP* 3.3 54.3 + - + +
199A LEU* 3.7 29.2 + - + +
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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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139A GLN* 2.8 42.4 + - + +
140A LEU* 3.8 6.1 - - + +
142A LYS* 1.3 74.1 - - + +
144A ALA* 1.3 66.6 + - - +
145A ILE 3.1 1.3 - - - -
146A GLU* 3.3 26.2 + - - +
147A GLN* 3.0 45.6 + - - +
280A HIS* 6.4 0.2 - - + -
282A ASP* 4.8 11.9 - - - +
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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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140A LEU 3.0 13.2 + - - +
141A VAL* 3.0 11.3 + - - +
143A LYS* 1.3 74.7 - - - +
145A ILE* 1.3 64.2 + - - +
147A GLN* 3.6 2.9 + - - -
149A ARG* 3.0 45.2 + - - +
150A PHE* 4.0 8.4 - - + -
274A TRP* 4.2 8.5 - - + -
276A PHE* 3.9 29.6 - - + -
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Residues in contact with ILE 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* 2.9 20.5 + - + +
142A LYS* 3.6 6.5 - - + +
143A LYS 3.1 0.4 - - - -
144A ALA* 1.3 79.0 - - - +
146A GLU* 1.3 64.4 + - + +
148A GLY* 3.0 15.8 + - - -
149A ARG 4.9 0.2 - - - +
150A PHE* 3.6 25.1 - - + +
153A ILE* 4.6 18.8 - - + -
199A LEU* 3.4 48.7 - - + +
200A VAL* 4.7 3.6 - - - +
254A ILE* 4.1 17.3 - - + -
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Residues in contact with GLU 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 LYS* 3.1 48.1 + - - +
143A LYS* 3.7 32.3 - - - +
145A ILE* 1.3 77.9 - - + +
147A GLN* 1.3 59.5 + - + +
148A GLY 3.1 4.0 + - - -
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Residues in contact with GLN 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 35.2 + - - +
144A ALA* 4.0 4.2 - - - +
145A ILE 3.3 0.4 - - - -
146A GLU* 1.3 75.9 - - + +
148A GLY* 1.3 62.3 + - - +
149A ARG* 3.3 19.5 + - + +
280A HIS* 3.3 37.4 + - - -
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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