Contacts of the helix formed by residues 121 - 133 (chain D) in PDB entry 2JC2
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 ASP 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D LEU* 5.6 1.9 - - - +
120D VAL* 1.3 78.4 - - - +
122D PRO* 1.3 74.8 - - + +
123D GLN* 3.5 19.0 - - + +
124D GLU* 3.0 62.7 + - - +
125D LEU 3.6 3.3 + - - -
152D GLY 4.8 2.0 - - - -
153D LYS* 5.0 2.5 - - - -
154D ILE* 4.4 1.1 - - - +
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Residues in contact with PRO 122 (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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120D VAL 3.8 1.5 - - - +
121D ASP* 1.3 87.9 - - + +
123D GLN* 1.3 63.6 + - + +
125D LEU* 3.3 13.5 + - - +
126D GLN* 3.4 23.6 + - - +
145D ALA* 4.1 10.5 - - + +
149D SER* 4.0 15.5 - - - +
152D GLY* 3.3 34.5 - - - +
153D LYS* 4.3 1.8 - - - +
154D ILE* 4.2 15.7 - - + -
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Residues in contact with GLN 123 (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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121D ASP* 3.2 15.6 - - + +
122D PRO* 1.3 79.8 - - + +
124D GLU* 1.3 62.2 + - - +
125D LEU 3.3 0.2 - - - -
126D GLN* 3.4 23.8 + - - +
127D LYS* 3.3 26.5 + - + +
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Residues in contact with GLU 124 (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 HIS* 5.6 1.2 + - - -
112D LEU* 3.5 50.2 - - + +
120D VAL* 4.4 9.0 - - + -
121D ASP* 3.0 42.9 + - - +
123D GLN* 1.3 76.7 - - - +
125D LEU* 1.3 61.5 + - - +
127D LYS* 3.6 15.1 + - - +
128D ALA* 3.4 20.3 + - - +
159D TYR* 4.8 4.5 - - + -
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Residues in contact with LEU 125 (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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120D VAL* 5.2 0.2 - - - +
121D ASP 3.6 1.8 + - - -
122D PRO 3.3 9.5 + - - +
123D GLN 3.3 0.2 - - - -
124D GLU* 1.3 78.7 - - - +
126D GLN* 1.3 63.7 + - - +
128D ALA* 3.3 3.4 + - + +
129D LEU* 3.1 44.4 + - + +
145D ALA* 4.1 24.7 - - + -
148D TYR* 4.3 10.1 - - + -
154D ILE* 3.6 36.0 - - + +
159D TYR* 3.8 35.2 - - + +
162D CYS* 4.2 19.7 - - + -
163D CYS* 4.6 1.3 - - - -
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Residues in contact with GLN 126 (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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122D PRO* 3.4 20.9 - - - +
123D GLN* 3.4 26.3 + - - +
124D GLU 3.3 0.2 - - - -
125D LEU* 1.3 78.3 - - - +
127D LYS* 1.3 55.2 + - + +
129D LEU* 3.6 2.4 + - - -
130D THR* 2.7 33.2 + - - -
141D VAL* 3.7 20.6 - - + +
142D ASN* 2.8 36.8 + - - +
145D ALA* 3.8 19.1 - - + +
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Residues in contact with LYS 127 (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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123D GLN 3.3 15.4 + - - +
124D GLU* 3.8 19.1 - - - +
125D LEU 3.3 0.4 - - - -
126D GLN* 1.3 76.7 - - + +
128D ALA* 1.3 58.6 + - - +
130D THR* 3.2 7.4 + - - -
131D THR* 2.9 35.8 + - - +
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Residues in contact with ALA 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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108D HIS* 5.1 8.7 + - + +
124D GLU 3.4 11.0 + - - +
125D LEU 3.3 9.0 + - - +
127D LYS* 1.3 79.1 - - - +
129D LEU* 1.3 66.1 + - + +
131D THR* 3.4 8.6 + - - -
132D MET* 3.3 24.2 + - - +
159D TYR* 3.7 31.4 - - + +
163D CYS* 5.0 4.5 - - - -
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Residues in contact with LEU 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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125D LEU* 3.1 42.8 + - + +
126D GLN* 3.8 4.7 - - - +
127D LYS 3.3 0.2 - - - -
128D ALA* 1.3 74.5 - - - +
130D THR* 1.3 64.8 + - - +
132D MET* 3.1 24.2 + - - +
133D GLY 3.8 1.9 + - - -
134D PHE* 4.8 3.1 + - - +
136D LEU* 5.3 5.3 - - + +
141D VAL* 4.2 28.5 - - + +
144D ILE* 3.8 32.8 - - + -
145D ALA* 5.1 0.9 - - - +
162D CYS* 4.0 13.0 - - - -
163D CYS* 4.2 16.4 - - - -
166D LEU* 3.8 25.8 - - + +
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Residues in contact with THR 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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126D GLN 2.7 19.5 + - - -
127D LYS* 3.2 11.3 + - - -
129D LEU* 1.3 77.0 - - - +
131D THR* 1.3 62.2 + - - +
133D GLY* 3.1 16.6 + - - -
141D VAL* 4.3 14.6 - - - +
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Residues in contact with THR 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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127D LYS* 2.9 18.9 + - - +
128D ALA* 3.7 9.4 - - - -
129D LEU 3.3 0.2 - - - -
130D THR* 1.3 73.9 - - - +
132D MET* 1.3 63.4 + - - +
133D GLY* 3.2 1.3 + - - -
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Residues in contact with MET 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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105D TRP* 3.6 33.2 - - + +
128D ALA 3.3 14.6 + - - +
129D LEU* 3.1 17.9 + - - +
131D THR* 1.3 76.4 - - - +
133D GLY* 1.3 61.4 + - - +
134D PHE* 3.4 42.3 + - + -
163D CYS* 3.7 32.1 - - + +
166D LEU* 3.8 17.5 - - - -
167D ARG* 5.1 7.4 - - + +
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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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129D LEU 3.8 1.0 + - - -
130D THR 3.1 15.6 + - - -
131D THR 3.2 2.4 - - - -
132D MET* 1.3 80.2 - - - +
134D PHE* 1.3 61.1 + - - +
135D ARG* 3.1 17.7 + - - +
174D ARG* 4.8 4.7 + - - -
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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