Contacts of the helix formed by residues 116 - 128 (chain D) in PDB entry 4CQM
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 SER 116 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A PHE* 4.9 1.9 - - - -
136A GLN* 5.8 0.2 - - - -
114D HIS 3.4 4.9 + - - -
115D MET* 1.3 85.4 - - - +
117D GLU* 1.3 63.7 + - - +
118D ASP* 3.6 7.2 + - - +
119D ASP* 3.0 42.7 + - - -
120D TRP* 3.4 4.7 + - - +
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Residues in contact with GLU 117 (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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77A SER 5.2 0.2 - - - +
79A ALA* 3.3 33.4 + - + +
129A LYS* 2.9 30.3 + - - +
132A PHE* 5.5 3.6 - - + -
133A LEU* 5.3 5.2 - - + -
116D SER* 1.3 75.8 - - - +
118D ASP* 1.3 52.1 + - - +
120D TRP* 3.2 7.8 + - + +
121D ASP* 2.7 54.2 + - - +
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Residues in contact with ASP 118 (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 GLN* 4.0 17.5 + - - +
116D SER* 3.3 8.1 + - - +
117D GLU* 1.3 73.6 - - - +
119D ASP* 1.3 67.2 + - - +
120D TRP 3.1 2.0 - - - -
121D ASP* 4.2 8.8 - - - +
122D LYS* 3.1 38.6 + - - +
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Residues in contact with ASP 119 (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 GLN* 2.8 33.9 - - - +
110D GLU* 4.0 17.4 - - - +
114D HIS 4.7 0.2 - - - +
115D MET* 3.6 11.2 - - + -
116D SER* 3.0 37.0 + - - +
117D GLU 3.3 0.4 - - - -
118D ASP* 1.3 80.3 - - - +
120D TRP* 1.3 55.3 + - - +
123D VAL* 3.3 14.7 - - - +
168D ASN* 2.4 31.2 + - - +
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Residues in contact with TRP 120 (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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124A ILE* 6.0 0.8 - - + +
128A LEU* 3.7 21.8 - - + -
129A LYS* 3.4 40.8 - - + +
132A PHE* 3.6 49.6 - + + -
179A LEU* 3.6 24.9 - - + -
115D MET* 4.5 1.1 - - - +
116D SER 3.4 5.6 + - - +
117D GLU* 3.2 9.1 + - + +
118D ASP 3.1 0.4 - - - -
119D ASP* 1.3 78.9 - - - +
121D ASP* 1.3 82.9 + - - +
122D LYS 3.4 0.2 + - - -
123D VAL* 3.5 2.3 + - - +
124D ILE* 3.1 45.0 + - + +
167D THR 4.0 8.3 - - - -
168D ASN* 3.7 37.7 - - + -
171D ALA* 3.8 12.8 - - + -
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Residues in contact with ASP 121 (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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129A LYS* 3.1 33.1 + - - +
117D GLU* 2.7 40.2 + - - +
118D ASP* 4.2 8.4 + - - +
120D TRP* 1.3 82.1 - - - +
122D LYS* 1.3 58.2 + - - +
124D ILE* 3.9 2.9 - - - +
125D ALA* 2.9 31.5 + - - +
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Residues in contact with LYS 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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106D ILE* 4.0 18.9 - - + +
108D GLN* 4.0 23.3 - - - +
118D ASP* 3.1 30.6 + - - +
119D ASP 5.1 0.2 - - - +
121D ASP* 1.3 75.3 - - - +
123D VAL* 1.3 64.7 + - - +
125D ALA* 3.9 4.4 - - + +
126D VAL* 3.1 37.1 + - + +
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Residues in contact with VAL 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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106D ILE* 4.3 15.7 - - + +
107D THR 4.5 0.4 - - - -
108D GLN* 3.7 29.6 - - + +
119D ASP 3.3 9.6 + - - +
120D TRP 3.5 3.0 + - - +
121D ASP 3.4 0.2 - - - -
122D LYS* 1.3 74.2 - - - +
124D ILE* 1.3 60.3 + - - +
127D ASN* 2.9 49.0 + - - +
168D ASN* 3.3 52.3 - - + +
169D TYR* 3.9 5.4 - - + -
172D SER* 3.8 3.5 - - - +
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Residues in contact with ILE 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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120A TRP* 6.1 0.7 - - + +
124A ILE* 4.2 18.8 - - + -
128A LEU* 4.3 9.0 - - + -
120D TRP* 3.1 53.8 + - + +
121D ASP* 3.9 4.3 - - - +
123D VAL* 1.3 76.4 - - - +
125D ALA* 1.3 57.4 + - - +
128D LEU* 3.0 27.0 + - + -
129D LYS* 2.8 29.4 + - + +
168D ASN 3.7 20.2 - - - +
172D SER* 3.8 20.4 - - - +
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Residues in contact with ALA 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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77D SER* 3.5 26.2 - - - +
121D ASP 2.9 20.4 + - - +
122D LYS* 3.9 7.0 - - + +
123D VAL 3.3 0.2 - - - -
124D ILE* 1.3 77.9 - - - +
126D VAL* 1.3 57.3 + - + +
129D LYS* 3.4 20.2 - - + +
130D GLY 2.9 21.3 + - - -
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Residues in contact with VAL 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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75D ASP* 5.2 2.9 - - - +
76D VAL* 4.1 13.2 - - + +
77D SER* 4.0 18.8 - - - +
104D ALA* 4.1 8.6 - - + +
105D GLY* 4.0 17.9 - - - +
106D ILE* 4.0 23.1 - - + +
122D LYS* 3.1 26.0 + - + +
125D ALA* 1.3 77.3 - - + +
127D ASN* 1.3 78.8 + - - +
128D LEU 3.5 0.2 - - - -
130D GLY* 3.3 19.2 - - - -
131D THR 3.8 1.2 + - - -
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Residues in contact with ASN 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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104D ALA 4.5 6.3 - - - -
105D GLY* 3.3 6.3 - - - -
106D ILE* 2.9 47.3 + - - +
123D VAL* 2.9 25.5 + - - +
126D VAL* 1.3 76.6 - - - +
128D LEU* 1.3 58.5 + - - +
131D THR* 2.6 28.8 + - - -
169D TYR* 3.5 24.2 - - - -
172D SER* 3.7 13.9 + - - +
173D LYS* 3.8 16.1 + - + +
176D VAL* 3.4 8.6 - - - +
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Residues in contact with LEU 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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120A TRP* 3.7 18.6 - - + -
124A ILE* 4.2 8.5 - - + -
128A LEU* 3.8 29.6 - - + -
171A ALA* 4.2 5.6 - - + +
124D ILE* 3.0 27.9 + - + +
127D ASN* 1.3 77.1 - - - +
129D LYS* 1.3 66.8 + - - +
130D GLY 3.3 0.9 - - - -
131D THR* 3.2 4.7 + - - -
132D PHE* 3.1 21.3 + - - +
172D SER* 3.6 17.7 - - - +
175D GLY* 3.4 33.0 - - - -
176D VAL* 3.5 6.7 - - - +
179D LEU* 3.6 14.9 - - + +
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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