Contacts of the helix formed by residues 127 - 138 (chain D) in PDB entry 5Y1Z
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 CYS 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D CYS* 3.2 15.7 - - + -
106D CYS* 3.8 7.0 - - - -
108D ARG* 4.2 1.3 - - - -
110D TYR* 3.6 25.4 - - + -
125D TRP* 3.7 14.3 + - + -
126D PHE* 1.3 75.3 - - - +
128D PRO* 1.3 70.3 - - + +
129D GLU* 3.6 10.1 - - - -
130D CYS* 2.9 13.5 + - - +
131D GLU* 2.8 25.6 + - - +
501D ZN 2.4 32.5 - - - -
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Residues in contact with PRO 128 (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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110D TYR* 3.7 20.2 - - + +
115D LEU* 3.7 29.2 - - + -
125D TRP* 4.0 12.6 - - + -
126D PHE 4.6 0.4 - - - +
127D CYS* 1.3 88.1 - - + +
129D GLU* 1.3 62.0 + - + +
131D GLU* 3.9 7.9 - - + +
132D LYS* 2.9 28.5 + - - +
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Residues in contact with GLU 129 (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 TRP* 3.4 24.2 + - - +
108D ARG* 3.8 28.9 - - - +
110D TYR* 3.4 17.4 + - - +
127D CYS* 3.3 3.8 - - - -
128D PRO* 1.3 77.8 - - - +
130D CYS* 1.3 58.5 + - - +
132D LYS* 3.8 19.6 + - - +
133D ILE* 2.9 37.8 + - + +
211D GLU* 5.0 1.9 - - - +
215D ALA* 3.4 25.1 - - + +
218D LYS* 4.2 17.4 + - - +
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Residues in contact with CYS 130 (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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105D LEU* 3.7 33.9 - - + -
106D CYS* 3.7 12.3 - - - -
108D ARG* 5.0 4.0 - - - -
126D PHE* 4.9 1.3 - - + -
127D CYS* 2.9 11.3 + - - +
129D GLU* 1.3 76.5 - - - +
131D GLU* 1.3 65.9 + - - +
133D ILE* 3.4 9.7 + - - +
134D THR* 2.9 28.1 + - - +
501D ZN 2.4 35.2 - - - -
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Residues in contact with GLU 131 (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 PHE* 3.7 40.6 - - + +
127D CYS 2.8 23.2 + - - +
128D PRO* 4.0 7.2 - - + +
130D CYS* 1.3 71.9 - - - +
132D LYS* 1.3 65.2 + - - +
134D THR* 3.2 14.2 + - - +
135D VAL* 3.1 28.3 + - + +
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Residues in contact with LYS 132 (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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128D PRO* 2.9 18.8 + - - +
129D GLU* 3.8 21.7 + - - +
131D GLU* 1.3 77.5 - - - +
133D ILE* 1.3 63.6 + - - +
135D VAL* 3.2 8.7 + - - +
136D ALA* 2.9 21.4 + - + +
211D GLU* 4.0 30.6 - - + +
214D LEU* 6.4 0.6 - - - +
218D LYS* 5.8 3.8 - - - +
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Residues in contact with ILE 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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108D ARG* 4.9 7.0 - - - +
129D GLU* 2.9 29.4 + - + +
130D CYS* 3.8 9.2 - - - +
132D LYS* 1.3 73.5 - - + +
134D THR* 1.3 64.7 + - - +
136D ALA* 3.1 9.7 + - - +
137D GLU* 2.9 51.2 + - - +
209D CYS* 4.3 1.1 - - - -
211D GLU* 4.3 6.1 - - + -
212D ALA* 3.6 39.3 - - + +
215D ALA* 4.1 14.4 - - + -
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Residues in contact with THR 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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105D LEU* 5.4 7.3 - - - +
130D CYS 2.9 15.8 + - - -
131D GLU* 3.2 18.4 + - - +
133D ILE* 1.3 76.2 - - - +
135D VAL* 1.3 68.9 + - + +
137D GLU* 3.1 15.2 + - - +
138D CYS* 3.2 17.0 + - + +
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Residues in contact with VAL 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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131D GLU* 3.1 14.7 + - + +
132D LYS* 3.2 8.7 + - - +
134D THR* 1.3 79.4 - - + +
136D ALA* 1.3 62.6 + - - +
137D GLU 3.2 1.0 + - - -
138D CYS* 3.3 6.4 + - - -
141D THR* 2.6 55.6 + - + +
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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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132D LYS* 2.9 16.3 + - + +
133D ILE 3.1 5.1 + - - +
135D VAL* 1.3 77.1 - - - +
137D GLU* 1.3 57.7 + - - +
138D CYS 3.5 0.2 - - - -
141D THR 4.9 1.6 - - - -
142D GLN* 3.6 23.7 - - - +
143D SER 4.8 0.8 + - - +
146D MET* 4.3 6.1 - - + +
209D CYS* 3.7 19.2 - - + +
211D GLU* 3.4 38.6 - - + +
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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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133D ILE* 2.9 36.8 + - - +
134D THR* 3.1 6.1 + - - +
136D ALA* 1.3 75.9 - - - +
138D CYS* 1.3 61.4 + - - +
139D ILE* 3.8 5.2 + - - +
142D GLN* 5.0 5.5 - - - +
206D MET 5.5 0.3 - - - +
208D GLY* 3.4 44.4 + - - +
209D CYS* 3.8 10.3 + - - -
212D ALA* 4.1 3.8 - - - +
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Residues in contact with CYS 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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134D THR* 3.2 15.4 + - + +
135D VAL* 3.3 2.8 + - - -
137D GLU* 1.3 78.8 - - - +
139D ILE* 1.3 74.1 + - - +
140D GLU* 3.7 17.9 - - - -
141D THR* 3.0 19.9 + - - +
142D GLN* 3.0 24.4 + - - +
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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