Contacts of the helix formed by residues 135 - 147 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131D GLN* 3.9 2.5 + - - +
132D ASN* 3.1 37.3 + - - +
134D ARG* 1.3 80.2 - - - +
136D ALA* 1.3 65.4 + - - +
137D THR* 3.0 0.8 + - - +
138D LEU* 3.7 12.0 - - + +
139D GLN* 3.0 18.9 + - - +
267D ALA 4.2 4.4 + - - -
268D VAL* 3.9 26.9 + - - +
292D GLU 6.0 0.2 - - - -
293D THR* 3.8 32.8 + - + +
296D VAL* 5.4 8.3 - - - +
300D GLY* 6.1 0.5 - - - -
303D LEU* 6.3 0.2 - - - -
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Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D ARG 2.7 7.7 + - - -
135D ASN* 1.3 69.4 - - - +
137D THR* 1.3 55.6 + - - +
139D GLN* 3.2 9.0 + - - +
140D LEU* 2.9 31.0 + - - +
289D ALA* 3.7 20.0 - - + +
292D GLU* 4.0 25.2 + - + +
293D THR* 2.8 17.4 + - - +
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Residues in contact with THR 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ASN* 4.0 2.4 - - - +
136D ALA* 1.3 76.5 - - - +
138D LEU* 1.3 70.7 + - - +
140D LEU* 3.3 8.6 + - - +
141D VAL* 3.1 24.1 + - - +
263D VAL* 4.8 8.5 - - - -
268D VAL 3.0 23.1 + - - +
269D ASN 4.6 2.2 - - - -
271D ILE* 4.8 8.9 - - - +
289D ALA* 3.6 13.9 - - + +
290D ASN* 3.3 30.1 - - - +
293D THR* 3.2 31.6 - - + +
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ASN* 3.3 27.1 - - + +
133D ARG 5.0 0.2 - - - +
135D ASN* 3.2 22.8 + - + +
137D THR* 1.3 85.8 + - - +
139D GLN* 1.3 53.7 + - - +
141D VAL* 2.9 8.0 + - + +
142D LYS* 2.8 35.0 + - - +
195D LEU* 3.8 24.9 - - + -
198D TRP* 4.2 15.7 - - + -
199D LEU* 4.0 19.3 - - + +
252D ILE* 4.7 7.9 - - + -
263D VAL* 5.0 8.1 - - + -
268D VAL* 4.2 29.6 - - + +
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Residues in contact with GLN 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ARG* 2.8 24.3 + - - +
134D ARG* 3.7 24.5 + - - +
135D ASN 3.0 14.9 + - - +
136D ALA* 3.2 13.2 - - - +
138D LEU* 1.3 77.7 - - - +
140D LEU* 1.3 61.7 + - - +
142D LYS* 3.3 9.3 + - - +
143D LYS* 3.0 53.0 + - - +
198D TRP* 3.7 20.0 - - - -
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ALA 2.9 11.7 + - - +
137D THR 3.5 8.5 - - - +
139D GLN* 1.3 75.3 - - - +
141D VAL* 1.3 62.1 + - - +
143D LYS* 3.7 7.7 + - + +
144D ALA* 3.3 14.9 + - - +
271D ILE* 4.6 6.1 - - + -
274D TRP* 3.5 23.5 - - + -
282D ASP* 3.8 40.3 - - + +
285D LYS* 3.2 30.7 - - + +
286D ILE* 4.1 8.3 - - + -
289D ALA* 3.1 34.3 - - + -
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D THR 3.1 12.2 + - - +
138D LEU* 2.9 12.4 + - + +
140D LEU* 1.3 73.2 - - - +
142D LYS* 1.3 67.3 + - - +
144D ALA* 3.2 4.6 + - - +
145D ILE* 3.1 38.4 + - + +
150D PHE* 4.9 8.5 - - + -
199D LEU* 4.1 16.2 - - + -
252D ILE* 6.1 0.9 - - + -
254D ILE* 4.1 11.9 - - + -
261D VAL* 4.0 9.6 - - + -
263D VAL* 4.0 25.4 - - + -
271D ILE* 5.3 1.6 - - + -
274D TRP* 3.8 22.2 - - + -
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Residues in contact with LYS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU 2.8 11.9 + - - +
139D GLN* 3.5 15.5 - - - +
141D VAL* 1.3 76.0 - - - +
143D LYS* 1.3 64.8 + - + +
145D ILE* 3.1 8.2 + - + +
146D GLU* 2.2 72.9 + - + +
198D TRP* 3.1 57.8 + - + +
199D LEU* 3.6 28.7 + - + +
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Residues in contact with LYS 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D GLN* 3.0 42.2 + - - +
140D LEU* 3.7 7.2 + - + +
141D VAL 3.3 0.2 - - - -
142D LYS* 1.3 77.1 - - + +
144D ALA* 1.3 56.6 + - - +
146D GLU* 3.0 14.8 + - - +
147D GLN* 2.7 55.5 + - - +
282D ASP* 4.5 12.8 - - - +
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D LEU 3.3 12.1 + - - +
141D VAL* 3.2 9.5 + - - +
143D LYS* 1.3 77.4 - - - +
145D ILE* 1.3 63.2 + - - +
147D GLN* 3.7 2.1 + - - +
148D GLY 3.4 2.6 + - - -
149D ARG* 3.0 47.7 + - - +
150D PHE* 4.1 6.5 - - + -
274D TRP* 4.3 8.7 - - + -
276D PHE* 3.9 28.3 - - + -
282D ASP* 5.7 0.2 + - - -
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Residues in contact with ILE 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D VAL* 3.1 27.6 + - + +
142D LYS* 3.5 6.7 - - + +
144D ALA* 1.3 78.4 - - - +
146D GLU* 1.3 61.5 + - + +
148D GLY* 3.0 19.4 + - - -
150D PHE* 3.5 26.2 - - + -
153D ILE* 4.3 18.6 - - + -
199D LEU* 3.2 49.8 - - + +
200D VAL* 4.8 4.9 - - - +
254D ILE* 4.2 9.4 - - + -
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Residues in contact with GLU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ARG* 5.5 11.2 + - - +
142D LYS* 2.2 64.1 + - + +
143D LYS* 3.6 14.8 - - - +
145D ILE* 1.3 81.4 - - + +
147D GLN* 1.3 58.7 + - + +
148D GLY* 3.1 4.9 + - - -
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Residues in contact with GLN 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D LYS* 2.7 48.0 + - - +
144D ALA* 3.9 5.6 - - - +
146D GLU* 1.3 71.3 - - + +
148D GLY* 1.3 60.6 + - - +
149D ARG* 3.4 22.3 + - + +
280D HIS* 3.0 38.3 + - + +
282D ASP* 4.1 8.0 + - - +
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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