Contacts of the helix formed by residues 141 - 150 (chain D) in PDB entry 2ZUQ
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 GLU 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92D THR* 5.6 0.7 - - + -
95D GLN* 3.4 28.5 + - + +
96D LEU* 5.7 9.0 - - + -
134D GLN* 4.7 8.2 - - - +
136D ASP* 3.4 22.6 - - - +
139D GLY 4.2 2.4 + - - +
140D LEU* 1.3 73.7 - - - +
142D MET* 1.3 60.7 + - - +
143D PRO* 3.8 12.8 - - + +
144D GLN* 2.8 41.7 + - + +
145D TRP* 2.9 12.0 + - - +
177D UQ1 6.2 0.2 - - - +
53E ARG* 3.2 35.8 + - - +
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Residues in contact with MET 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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135D TRP 5.5 0.9 - - - +
136D ASP* 3.4 19.9 + - + +
137D PHE* 3.5 28.5 - - + +
140D LEU 3.2 26.9 + - - +
141D GLU* 1.3 67.1 - - - +
143D PRO* 1.3 61.9 - - - +
144D GLN 2.9 4.7 + - - -
145D TRP* 3.2 33.8 + - + +
146D LEU* 3.0 34.5 + - + +
177D UQ1 3.5 56.3 - - + +
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Residues in contact with PRO 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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47D GLU* 4.9 3.8 - - - +
88D THR* 3.5 5.7 - - - +
91D HIS* 3.5 40.6 - - + +
92D THR* 3.1 17.3 + - - +
95D GLN* 4.7 6.7 - - + -
136D ASP* 5.1 0.4 - - - +
141D GLU* 3.4 20.0 - - + +
142D MET* 1.3 89.6 - - + +
144D GLN* 1.3 55.7 + - + +
146D LEU* 4.0 10.8 - - + -
147D LEU* 3.4 15.9 + - - +
177D UQ1 3.1 31.8 - - + +
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Residues in contact with GLN 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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92D THR* 3.4 22.7 - - + +
96D LEU* 3.4 29.4 - - - +
140D LEU* 3.3 29.1 - - + +
141D GLU* 2.8 40.5 + - + +
143D PRO* 1.3 80.0 - - - +
145D TRP* 1.3 65.1 + - - +
147D LEU* 4.1 9.7 - - + +
148D GLY* 3.6 10.7 + - - -
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Residues in contact with TRP 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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137D PHE* 3.6 11.3 + - - +
138D LEU* 3.5 43.1 - - + -
140D LEU* 4.2 21.2 + - + +
141D GLU 2.9 10.5 + - - -
142D MET* 3.3 45.1 - - + +
144D GLN* 1.3 75.0 - - - +
146D LEU* 1.3 59.7 + - + +
148D GLY* 2.7 29.5 + - - -
149D ILE* 3.2 16.8 + - + +
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Residues in contact with LEU 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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25D LEU* 5.8 1.8 - - + -
47D GLU* 5.5 2.2 - - + +
51D LEU* 5.0 4.3 - - + -
88D THR* 4.1 13.2 - - + -
142D MET* 3.0 21.2 + - + +
143D PRO* 4.2 5.2 - - + -
145D TRP* 1.3 83.1 - - + +
147D LEU* 1.3 61.6 + - - +
148D GLY 2.9 1.4 + - - -
149D ILE* 3.0 30.5 + - + +
150D PHE* 3.0 44.5 + - + -
177D UQ1 3.7 59.7 - - + -
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Residues in contact with LEU 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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85D VAL* 3.4 33.4 - - + +
88D THR* 3.4 17.2 - - - +
89D TYR* 3.5 34.5 - - + -
92D THR* 3.8 9.9 - - + +
143D PRO 3.4 18.3 + - - +
144D GLN* 4.2 11.2 - - + +
145D TRP 3.3 0.6 - - - -
146D LEU* 1.3 77.2 - - - +
148D GLY* 1.3 62.1 + - - +
150D PHE* 4.3 1.7 - - - +
151D ILE* 3.2 25.8 + - + +
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Residues in contact with GLY 148 (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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144D GLN 3.6 6.4 + - - -
145D TRP 2.7 18.7 + - - -
147D LEU* 1.3 74.8 - - - +
149D ILE* 1.3 58.2 + - - -
151D ILE* 2.8 39.4 + - - +
152D ALA* 3.5 4.0 + - - +
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Residues in contact with ILE 149 (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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25D LEU* 4.0 37.2 - - + -
51D LEU* 5.7 2.9 - - + -
145D TRP* 3.2 11.8 + - + +
146D LEU* 3.0 35.9 + - + +
148D GLY* 1.3 73.5 - - - +
150D PHE* 1.3 66.9 + - + +
151D ILE 3.2 0.2 - - - -
152D ALA* 3.3 16.6 + - + +
153D TYR* 3.3 34.1 + - + +
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Residues in contact with PHE 150 (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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47D GLU* 4.0 11.4 - - + -
50D ALA 3.3 25.8 - - - -
51D LEU* 3.7 28.5 - - + -
54D VAL* 5.0 0.9 - - + -
80D SER 3.9 2.2 - - - -
81D ALA* 3.6 17.9 - - - +
84D GLY* 3.4 20.6 - - - -
85D VAL* 3.5 25.7 - - + +
88D THR* 3.6 31.2 - - + -
146D LEU* 3.0 42.0 + - + +
147D LEU 4.4 1.6 - - - +
148D GLY 3.2 0.2 + - - -
149D ILE* 1.3 80.0 - - + +
151D ILE* 1.3 58.4 + - - +
153D TYR* 3.5 9.8 + + - +
154D LEU* 2.9 28.1 + - - +
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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