Contacts of the helix formed by residues 111 - 124 (chain A) in PDB entry 1COJ
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 LEU 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PRO* 4.4 11.4 - - + -
101A LYS* 3.8 54.5 - - + +
104A ILE* 4.2 20.6 - - + -
105A GLU* 6.2 0.2 - - + -
110A GLY* 1.3 70.4 - - - -
112A ASP* 1.3 58.7 + - - +
114A CYS* 3.3 3.0 + - - +
115A THR* 2.9 34.5 + - - +
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A GLY 4.4 2.6 - - - +
110A GLY* 3.6 14.0 - - - -
111A LEU* 1.3 73.6 - - - +
113A ALA* 1.3 77.2 + - - +
115A THR* 4.0 4.5 - - - +
116A ASN* 3.2 24.1 + - - +
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Residues in contact with ALA 113 (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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108A ILE* 3.9 23.7 - - + +
109A GLY* 4.2 4.0 - - - +
110A GLY 3.2 10.9 + - - +
112A ASP* 1.3 86.1 + - - +
114A CYS* 1.3 58.9 + - - +
116A ASN* 3.4 8.2 + - - +
117A GLU* 2.9 31.2 + - - +
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Residues in contact with CYS 114 (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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104A ILE* 3.6 27.4 - - + -
108A ILE* 3.7 17.4 - - + +
110A GLY 2.9 17.0 + - - +
111A LEU* 3.7 5.2 - - - +
113A ALA* 1.3 74.0 - - - +
115A THR* 1.3 60.9 + - - +
117A GLU* 3.1 4.7 + - - +
118A LEU* 2.8 36.0 + - - +
131A LEU* 4.0 36.1 - - - -
142A VAL* 5.7 1.1 - - - -
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Residues in contact with THR 115 (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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111A LEU* 2.9 19.3 + - - +
112A ASP* 4.0 5.4 - - - +
114A CYS* 1.3 75.9 - - - +
116A ASN* 1.3 59.8 + - - +
118A LEU* 3.3 6.5 + - - +
119A LYS* 3.0 63.5 + - + +
185A PHE* 4.2 20.2 - - + -
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Residues in contact with ASN 116 (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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112A ASP 3.2 15.4 + - - +
113A ALA* 3.6 7.2 + - - +
114A CYS 3.2 0.2 - - - -
115A THR* 1.3 81.4 - - - +
117A GLU* 1.3 63.5 + - - +
119A LYS* 3.9 7.6 - - - +
120A ALA* 3.0 31.4 + - - +
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Residues in contact with GLU 117 (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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108A ILE* 4.7 10.3 - - + +
113A ALA 2.9 18.1 + - - +
114A CYS* 3.1 8.9 + - - +
116A ASN* 1.3 83.4 + - - +
118A LEU* 1.3 56.9 + - - +
120A ALA* 3.4 8.1 + - - +
121A ALA* 3.0 28.2 + - - +
142A VAL* 3.6 29.8 - - + +
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Residues in contact with LEU 118 (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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114A CYS* 2.8 22.6 + - - +
115A THR* 3.8 4.5 - - - +
117A GLU* 1.3 74.9 - - - +
119A LYS* 1.3 59.6 + - - +
121A ALA* 3.3 4.1 + - - +
122A ALA* 2.9 30.2 + - - +
129A ALA* 4.3 8.3 - - + +
130A ILE 4.4 6.1 - - - -
131A LEU* 4.1 35.2 - - + +
142A VAL* 4.4 14.8 - - + -
160A ILE* 4.1 32.8 - - + -
162A ILE* 4.4 13.9 - - + +
185A PHE* 4.0 26.0 - - + -
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Residues in contact with LYS 119 (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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115A THR* 3.0 41.0 + - + +
116A ASN* 3.9 7.6 - - - +
118A LEU* 1.3 75.2 - - - +
120A ALA* 1.3 57.1 + - - +
122A ALA* 3.3 7.7 + - - +
123A MET* 3.0 35.4 + - + +
181A ILE* 4.0 19.2 - - + +
182A ASP* 3.1 28.0 + - - +
185A PHE* 3.5 29.2 - - + +
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Residues in contact with ALA 120 (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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116A ASN* 3.0 21.7 + - - +
117A GLU* 3.5 11.7 - - - +
119A LYS* 1.3 77.1 - - - +
121A ALA* 1.3 57.0 + - - +
123A MET* 3.1 8.0 + - - +
124A ALA* 2.8 32.0 + - - +
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Residues in contact with ALA 121 (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 GLU 3.0 10.3 + - - +
118A LEU 3.8 3.8 - - - +
120A ALA* 1.3 76.2 - - - +
122A ALA* 1.3 57.1 + - - +
124A ALA* 4.4 1.8 - - - -
125A PHE* 2.9 50.9 + - + +
129A ALA* 3.9 12.8 - - + +
142A VAL* 3.5 32.8 - - + -
144A GLY* 5.1 2.7 - - - +
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Residues in contact with ALA 122 (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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118A LEU 2.9 18.1 + - - +
119A LYS* 3.5 7.2 - - - +
120A ALA 3.2 0.2 - - - -
121A ALA* 1.3 77.6 - - - +
123A MET* 1.3 58.3 + - - +
125A PHE 3.7 1.0 - - - +
129A ALA* 3.7 17.2 - - + +
162A ILE* 4.5 11.4 - - + -
164A THR* 3.3 20.9 - - + +
177A ARG* 2.9 25.6 + - - -
181A ILE* 3.6 21.1 - - + -
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Residues in contact with MET 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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119A LYS* 3.0 21.1 + - + +
120A ALA* 3.6 6.5 - - - +
122A ALA* 1.3 78.1 - - - +
124A ALA* 1.3 59.7 + - - +
125A PHE 3.5 0.2 - - - -
177A ARG* 3.8 21.3 + - + +
178A PRO* 3.7 36.3 - - + -
181A ILE* 3.7 21.8 - - + -
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Residues in contact with ALA 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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120A ALA 2.8 17.6 + - - +
121A ALA* 4.4 0.7 - - - -
123A MET* 1.3 78.3 - - - +
125A PHE* 1.3 80.6 + - + +
126A ARG* 4.2 5.4 + - - +
146A ASP* 4.8 1.4 - - - +
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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