Contacts of the helix formed by residues 132 - 139 (chain D) in PDB entry 2Q41
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 GLY 132 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D GLY 4.6 1.9 + - - -
130D GLY* 3.4 3.6 - - - -
131D ASP* 1.3 77.7 - - - +
133D GLY* 1.3 58.6 + - - +
134D VAL 3.5 2.5 - - - -
135D LEU* 3.1 28.4 + - - +
136D ARG* 2.8 24.3 + - - +
149D MSE 5.7 0.4 - - - -
167D VAL 3.5 17.3 - - - +
171D TYR* 4.1 12.0 + - - -
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Residues in contact with GLY 133 (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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107D GLN* 2.9 35.6 - - - +
130D GLY* 5.5 0.6 - - - -
131D ASP* 2.8 12.1 + - - +
132D GLY* 1.3 74.4 - - - +
134D VAL* 1.3 67.9 + - - +
135D LEU 3.0 1.6 - - - -
136D ARG* 2.9 9.6 + - - +
137D GLU* 2.9 23.0 + - - +
167D VAL* 3.9 4.2 - - - +
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Residues in contact with VAL 134 (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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106D TYR* 5.3 1.1 - - + -
107D GLN* 3.9 9.4 - - + +
110D ILE* 4.1 11.7 - - + -
111D THR* 3.4 27.1 - - + -
126D VAL* 3.9 27.4 - - + -
132D GLY 3.5 0.4 - - - -
133D GLY* 1.3 74.2 - - - +
135D LEU* 1.3 54.6 + - + +
137D GLU* 3.2 2.3 + - - +
138D VAL* 2.5 52.0 + - + +
199D ILE* 4.5 5.6 - - + -
201D ASP* 3.6 34.3 - - + +
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Residues in contact with LEU 135 (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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126D VAL* 4.9 9.9 - - + -
132D GLY* 3.2 16.8 - - - +
133D GLY 3.0 0.4 - - - -
134D VAL* 1.3 76.5 - - + +
136D ARG* 1.3 68.3 + - - +
137D GLU 2.9 1.1 - - - -
138D VAL* 4.1 4.5 - - + +
139D ALA* 2.9 28.1 + - - +
147D ILE* 4.5 11.4 - - + -
149D MSE 3.4 46.7 - - + -
170D GLY* 3.3 34.3 - - - +
171D TYR* 3.6 17.9 - - + +
176D VAL* 4.5 17.9 - - + -
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Residues in contact with ARG 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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103D GLU* 5.4 8.5 + - - +
104D CYS* 5.7 6.7 - - - +
107D GLN* 5.1 4.4 + - - -
132D GLY 2.8 17.0 + - - +
133D GLY* 2.9 11.2 + - - +
135D LEU* 1.3 73.2 - - - +
137D GLU* 1.3 80.0 + - - +
139D ALA* 4.2 4.7 - - - +
140D ARG* 3.8 19.8 + - - +
167D VAL* 4.1 31.8 - - + +
169D ILE* 5.1 9.9 - - + -
170D GLY* 3.9 6.9 - - - -
305D GLY* 3.5 31.9 + - - +
306D PRO 5.1 2.0 + - - -
308D LYS* 5.6 9.5 - - - +
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Residues in contact with GLU 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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104D CYS* 6.0 0.7 - - - -
107D GLN* 3.8 27.7 - - + +
108D GLU* 3.8 15.2 - - - +
111D THR* 3.1 20.2 - - + +
112D HIS* 2.6 37.6 + - - +
133D GLY 2.9 13.8 + - - +
134D VAL 3.6 4.5 - - - +
135D LEU 2.9 0.2 + - - -
136D ARG* 1.3 97.8 + - + +
138D VAL* 1.3 65.2 + - - +
139D ALA 3.2 1.3 - - - -
140D ARG* 2.8 53.3 + - - +
141D HIS 3.9 0.5 + - - -
307D LEU* 3.7 1.6 - - - +
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Residues in contact with VAL 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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111D THR* 3.9 11.2 - - + -
115D LEU* 3.9 20.6 - - + -
124D VAL* 4.3 10.3 - - + -
126D VAL* 4.3 6.3 - - + -
134D VAL* 2.5 50.4 + - + +
135D LEU* 4.0 6.1 - - + +
137D GLU* 1.3 72.2 - - - +
139D ALA* 1.3 58.0 + - - +
141D HIS* 2.8 29.6 + - - +
144D ILE* 4.2 8.3 - - + +
147D ILE* 4.0 30.5 - - + -
199D ILE* 4.2 10.8 - - + -
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Residues in contact with ALA 139 (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 LEU 2.9 18.5 + - - +
136D ARG* 4.2 5.2 - - - +
138D VAL* 1.3 74.6 - - - +
140D ARG* 1.3 63.8 + - - +
142D ALA* 3.9 2.4 + - - +
147D ILE* 4.4 10.0 - - + +
170D GLY* 5.6 0.7 - - - +
173D ASP* 4.0 14.6 - - + +
175D ARG* 2.4 53.3 + - - +
176D VAL* 5.5 1.3 - - + -
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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