Contacts of the helix formed by residues 104 - 121 (chain D) in PDB entry 3C6Q
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 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D THR* 1.3 74.2 - - - +
105D ASN* 1.3 58.2 + - - +
106D TYR* 3.8 5.7 + - - +
107D GLN* 3.2 41.9 + - + +
108D ALA* 2.9 29.6 + - - +
278D ASP* 3.9 27.9 + - - +
281D VAL* 5.7 4.2 - - + +
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Residues in contact with ASN 105 (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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89D ASP 3.8 1.0 + - - -
90D THR* 4.9 1.0 - - - +
91D ASP 5.8 0.2 - - - +
100D TYR* 3.3 23.6 + - - -
103D THR* 3.1 16.2 + - - +
104D ASP* 1.3 68.4 + - - +
106D TYR* 1.3 59.0 + - - +
108D ALA* 3.3 3.2 + - - +
109D GLY* 2.8 26.0 + - - -
137D ASN* 3.1 30.3 - - - +
140D GLN* 2.9 39.9 + - + +
141D ARG* 2.9 40.2 + - + +
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Residues in contact with TYR 106 (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 ASP* 3.8 5.1 + - - +
105D ASN* 1.3 78.1 - - - +
107D GLN* 1.3 72.0 + - - +
109D GLY* 2.9 1.9 + - - -
110D TYR* 2.7 56.8 + + + +
140D GLN* 3.7 23.7 - - + +
143D GLN* 3.7 11.7 - - + -
144D GLY* 3.4 30.5 - - - -
147D ASP* 2.6 37.5 + - - +
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Residues in contact with GLN 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D ASP* 3.2 37.8 + - + +
106D TYR* 1.3 93.2 - - - +
108D ALA* 1.3 54.2 + - - +
110D TYR* 3.5 6.4 + - - +
111D THR* 2.8 40.8 + - - +
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D THR* 4.3 10.1 - - + -
104D ASP 2.9 18.9 + - - +
105D ASN 3.6 4.7 - - - +
107D GLN* 1.3 74.6 - - - +
109D GLY* 1.3 65.7 + - - +
111D THR* 3.3 3.3 + - - -
112D ALA* 2.9 24.6 + - - +
215D PHE* 3.8 25.4 - - + -
234D MET* 3.6 19.4 - - + +
281D VAL* 4.4 10.8 - - + -
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Residues in contact with GLY 109 (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 ASN 2.8 14.1 + - - -
106D TYR 3.5 2.7 - - - -
108D ALA* 1.3 74.6 - - - +
110D TYR* 1.3 62.1 - - - +
112D ALA* 3.3 5.8 + - - +
113D GLY 2.9 18.0 + - - -
141D ARG* 3.4 27.1 - - - -
145D PHE* 3.4 16.3 - - - +
187D PHE* 5.0 0.7 - - - -
215D PHE* 4.2 5.8 - - - -
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Residues in contact with TYR 110 (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 TYR* 2.7 46.7 + + + +
107D GLN* 3.5 11.0 - - - +
109D GLY* 1.3 70.8 - - - +
111D THR* 1.3 65.8 + - - +
113D GLY* 2.8 13.9 + - - -
114D LEU* 2.9 44.7 + - + +
144D GLY 3.3 22.1 - - - +
147D ASP* 4.0 8.3 + - + -
148D ALA* 3.5 24.8 + - + +
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Residues in contact with THR 111 (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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107D GLN* 2.8 28.8 + - - +
108D ALA* 3.6 5.0 - - - -
110D TYR* 1.3 73.9 - - - +
112D ALA* 1.3 60.7 + - - +
114D LEU* 3.2 17.3 + - + +
115D ILE* 2.9 31.6 + - + +
234D MET* 3.7 8.0 - - + +
283D VAL* 3.8 29.4 - - + -
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Residues in contact with ALA 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ALA 2.9 17.4 + - - +
109D GLY* 3.6 5.4 - - - +
111D THR* 1.3 73.1 - - - +
113D GLY* 1.3 61.1 + - - +
115D ILE* 3.0 13.8 + - - +
116D MET* 2.9 27.5 + - - +
145D PHE* 4.5 2.2 - - - -
187D PHE* 4.0 23.1 - - + -
213D VAL* 4.0 12.0 - - + +
215D PHE* 4.6 0.7 - - + -
234D MET* 3.7 22.2 - - + -
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Residues in contact with GLY 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D GLY 2.9 8.1 + - - -
110D TYR 2.8 13.3 + - - -
112D ALA* 1.3 69.2 - - - +
114D LEU* 1.3 57.9 + - - -
116D MET* 3.2 2.8 + - - +
117D LYS* 2.8 31.4 + - - +
145D PHE* 3.5 25.7 - - - -
148D ALA* 4.0 14.1 - - - -
149D ILE* 3.8 7.0 - - - +
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Residues in contact with LEU 114 (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* 2.9 48.0 + - + +
111D THR* 3.3 15.9 - - + +
113D GLY* 1.3 74.8 - - - +
115D ILE* 1.3 63.2 + - + +
117D LYS* 3.5 16.1 + - + +
118D GLU* 3.0 23.6 + - - +
148D ALA* 3.7 15.5 - - + +
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Residues in contact with ILE 115 (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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111D THR* 2.9 23.1 + - + +
112D ALA* 3.0 14.6 + - - +
114D LEU* 1.3 74.3 - - + +
116D MET* 1.3 66.9 + - - +
118D GLU* 3.3 5.6 + - - +
119D LEU* 3.1 40.1 + - + +
213D VAL* 4.3 4.7 - - + -
232D ALA* 3.7 27.8 - - + -
234D MET* 5.1 2.5 - - - -
283D VAL* 4.3 28.9 - - + -
285D THR* 6.2 1.1 - - + -
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Residues in contact with MET 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ALA 2.9 11.6 + - - +
113D GLY 3.4 7.0 - - - +
115D ILE* 1.3 72.5 - - - +
117D LYS* 1.3 67.9 + - - +
119D LEU* 2.9 7.2 + - - +
120D LEU* 2.8 43.5 + - + +
126D VAL* 4.2 6.5 - - + -
145D PHE* 3.9 21.5 - - + -
149D ILE* 5.1 1.1 - - + -
154D ILE* 4.8 3.4 - - + -
185D ALA* 3.3 27.1 - - + -
186D PHE 3.3 28.3 - - - +
187D PHE* 3.9 15.7 - - + -
211D LYS* 5.0 3.4 - - - -
213D VAL* 3.5 32.0 - - + +
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Residues in contact with LYS 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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113D GLY 2.8 20.8 + - - +
114D LEU* 3.6 17.1 - - + +
116D MET* 1.3 73.0 - - - +
118D GLU* 1.3 64.5 + - - +
121D GLY* 2.9 3.8 + - - -
122D GLY* 2.8 40.3 + - - +
148D ALA 4.4 11.5 + - - +
149D ILE* 4.6 6.3 - - + +
151D ASP* 2.8 40.4 + - - +
152D SER* 4.6 8.1 - - - +
154D ILE* 3.8 16.3 - - + +
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Residues in contact with GLU 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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114D LEU 3.0 14.4 + - - +
115D ILE* 3.4 11.0 - - - +
116D MET 3.1 0.2 - - - -
117D LYS* 1.3 78.1 - - - +
119D LEU* 1.3 80.7 + - + +
121D GLY* 2.9 15.3 + - - -
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Residues in contact with LEU 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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115D ILE* 3.1 25.3 + - + +
116D MET* 2.9 8.2 + - - +
118D GLU* 1.3 95.0 - - + +
120D LEU* 1.3 63.8 + - + +
211D LYS* 3.8 40.1 + - + +
213D VAL* 3.9 26.0 - - + -
231D GLN* 3.8 31.2 - - + +
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Residues in contact with LEU 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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116D MET* 2.8 23.6 + - + +
119D LEU* 1.3 77.3 - - + +
121D GLY* 1.3 61.1 - - - +
123D LYS* 3.6 25.9 - - - +
124D GLY* 4.7 2.9 - - - -
126D VAL* 3.8 26.2 - - + -
154D ILE* 3.6 28.0 - - + -
184D ASP* 3.9 36.3 - - + +
185D ALA* 4.0 7.6 - - + -
211D LYS* 4.1 14.8 - - + -
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Residues in contact with GLY 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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117D LYS 2.9 5.2 + - - -
118D GLU* 2.9 10.0 + - - -
120D LEU* 1.3 77.0 - - - +
122D GLY* 1.3 58.4 + - - +
123D LYS* 3.0 19.1 + - - +
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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