Contacts of the helix formed by residues 122 - 133 (chain A) in PDB entry 2C6U
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 THR 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LEU* 1.3 73.2 - - - +
123A TRP* 1.3 60.1 + - - +
124A GLU* 3.6 6.1 + - - +
125A GLU* 3.0 41.9 + - - +
126A SER* 2.8 30.3 + - - -
158A TRP* 3.5 1.1 - - - -
208A CYS 3.7 8.1 - - - -
209A GLU* 3.7 25.6 - - + +
210A ASN 3.3 8.7 - - - +
211A LYS* 4.3 9.8 - - + +
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Residues in contact with TRP 123 (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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122A THR* 1.3 74.7 - - - +
124A GLU* 1.3 81.3 + - + +
126A SER* 3.1 4.0 + - - -
127A LYS* 2.9 42.1 + - + -
137A LEU* 3.6 15.8 - - + +
158A TRP* 3.5 44.7 - + + +
159A VAL 2.9 22.4 + - - -
160A GLY 4.4 6.7 - - - -
161A LEU 4.0 5.1 + - - -
162A SER* 3.7 29.2 - - - -
173A GLU* 3.3 30.5 - - - -
195A CYS* 3.4 32.1 - - + -
196A ALA 4.5 0.7 - - - -
208A CYS* 3.1 14.9 + - + +
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Residues in contact with GLU 124 (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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122A THR* 3.3 6.0 + - - +
123A TRP* 1.3 100.7 - - - +
125A GLU* 1.3 64.0 + - + +
127A LYS* 3.3 22.6 + - - +
128A GLN* 3.0 22.2 + - - +
208A CYS* 4.7 1.4 + - - +
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Residues in contact with GLU 125 (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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120A ASN 4.9 0.2 - - - +
121A LEU* 3.6 31.6 - - + +
122A THR* 3.0 47.0 + - - +
124A GLU* 1.3 76.7 - - + +
126A SER* 1.3 56.9 + - - +
128A GLN* 3.3 8.8 + - - +
129A TYR* 2.9 27.0 + - - +
211A LYS* 5.4 1.2 - - - +
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.5 12.5 - - - +
122A THR 2.8 21.1 + - - -
123A TRP 3.4 4.9 - - - -
125A GLU* 1.3 74.6 - - - +
127A LYS* 1.3 64.8 + - - +
129A TYR* 3.1 9.8 + - - +
130A CYS* 3.0 26.7 + - - -
137A LEU* 4.1 9.9 - - - -
158A TRP* 3.2 24.5 - - - -
212A HIS 4.1 0.3 + - - -
214A LEU* 3.6 24.3 - - - +
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Residues in contact with LYS 127 (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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123A TRP* 2.9 28.2 + - + +
124A GLU* 3.4 28.9 + - - +
126A SER* 1.3 74.5 - - - +
128A GLN* 1.3 59.1 + - - +
130A CYS* 3.3 4.8 + - - +
131A THR* 2.9 37.5 + - - +
137A LEU* 3.8 20.0 - - + +
173A GLU* 2.9 36.8 + - - +
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Residues in contact with GLN 128 (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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124A GLU 3.0 13.2 + - - +
125A GLU* 3.5 11.7 - - - +
126A SER 3.2 0.2 - - - -
127A LYS* 1.3 74.0 - - - +
129A TYR* 1.3 60.6 + - - +
131A THR* 3.2 20.3 + - - +
132A ASP* 2.8 64.7 + - - +
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Residues in contact with TYR 129 (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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117A PHE* 3.9 19.9 - + + -
119A HIS* 2.9 46.5 + + - -
121A LEU* 4.1 17.3 - - + -
125A GLU 2.9 13.5 + - - +
126A SER* 3.1 9.4 + - - +
128A GLN* 1.3 77.0 - - - +
130A CYS* 1.3 63.0 + - - +
132A ASP* 3.2 22.1 + - + +
133A MET* 3.4 42.7 + - + +
214A LEU* 4.0 16.6 - - + -
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Residues in contact with CYS 130 (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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126A SER 3.0 16.7 + - - -
127A LYS 3.7 7.6 - - - +
129A TYR* 1.3 77.2 - - - +
131A THR* 1.3 60.7 + - - +
133A MET* 2.9 11.6 + - - -
135A ALA* 2.9 36.4 + - - +
136A THR* 3.8 10.3 - - - -
137A LEU* 3.7 18.6 - - - +
214A LEU* 3.6 7.6 - - - -
216A CYS* 2.1 54.7 - - - -
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Residues in contact with THR 131 (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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127A LYS* 2.9 24.4 + - - +
128A GLN* 3.4 27.5 - - - +
130A CYS* 1.3 74.8 - - - +
132A ASP* 1.3 58.9 + - - +
134A ASN* 3.0 23.3 + - - +
135A ALA 3.6 10.6 + - - +
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Residues in contact with ASP 132 (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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128A GLN* 2.8 48.4 + - - +
129A TYR* 3.5 15.5 - - + +
130A CYS 3.2 0.6 - - - -
131A THR* 1.3 75.6 - - - +
133A MET* 1.3 62.5 + - + +
134A ASN* 3.4 4.2 + - - +
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Residues in contact with MET 133 (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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106A TRP* 4.2 15.2 - - + -
117A PHE* 3.5 38.6 - - + -
129A TYR* 3.4 47.1 + - + +
130A CYS* 2.9 5.5 + - - +
132A ASP* 1.3 83.4 - - + +
134A ASN* 1.3 70.5 + - - +
135A ALA* 3.2 5.5 + - + +
216A CYS* 3.6 15.3 - - - -
218A ARG* 4.1 11.6 + - - -
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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