Contacts of the helix formed by residues 105 - 120 (chain D) in PDB entry 1GZ0
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 105 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D VAL* 3.5 3.1 - - - +
104D THR* 1.3 78.5 + - - +
106D PRO* 1.3 72.7 - - - +
107D HIS* 2.8 39.0 + - - +
108D ASN* 2.9 36.9 + - - +
109D LEU* 3.0 10.4 + - - +
132D ALA* 3.9 1.6 - - - -
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Residues in contact with PRO 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 THR 3.2 9.6 - - - +
105D ASP* 1.3 89.1 - - - +
107D HIS* 1.3 55.1 - - - +
109D LEU* 3.2 4.7 + - + +
110D GLY 2.9 25.6 + - - -
132D ALA* 4.0 15.9 - - + -
133D GLN 4.5 5.8 - - - +
135D ASN* 3.1 37.7 - - - +
137D THR* 4.7 5.8 - - + -
138D ALA* 3.6 13.9 - - + +
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Residues in contact with HIS 107 (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 ASP* 2.8 21.9 + - - +
106D PRO* 1.3 73.3 - - - +
108D ASN* 1.3 62.9 + - - +
110D GLY* 3.4 1.6 + - - -
111D ALA* 3.0 27.2 + - + +
137D THR* 4.7 14.0 - - + +
141D VAL* 3.7 39.2 - - + +
107E HIS* 6.4 2.5 - + - -
226E ASN* 6.1 2.5 - - - -
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Residues in contact with ASN 108 (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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103D VAL* 3.8 16.2 - - + +
105D ASP* 2.9 25.7 + - - +
107D HIS* 1.3 81.9 + - - +
109D LEU* 1.3 57.5 + - - +
111D ALA* 2.9 1.3 + - - +
112D CYS* 2.7 39.2 + - - -
226D ASN* 3.7 18.7 + - - +
227D VAL* 3.8 27.4 - - + +
228D SER* 3.7 14.8 + - - +
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Residues in contact with LEU 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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100D LEU* 5.1 7.7 - - + +
103D VAL* 3.8 13.3 - - + +
105D ASP 3.0 10.6 + - - +
106D PRO* 3.4 9.0 - - + +
108D ASN* 1.3 78.7 - - - +
110D GLY* 1.3 65.8 + - - +
112D CYS* 3.3 5.3 + - - +
113D LEU* 3.0 31.5 + - + +
126D VAL* 5.3 8.5 - - + -
131D SER* 5.5 0.4 - - - +
132D ALA* 3.5 40.2 - - + +
133D GLN 4.2 1.6 - - - +
134D LEU* 3.4 39.0 - - + +
138D ALA* 3.5 8.3 - - + -
151D LEU* 4.5 15.7 - - + -
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Residues in contact with GLY 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 PRO 2.9 14.8 + - - -
107D HIS 3.8 2.0 - - - -
109D LEU* 1.3 83.3 - - - +
111D ALA* 1.3 57.9 + - - +
113D LEU* 3.4 4.6 + - - +
114D ARG* 3.0 22.9 + - - +
138D ALA* 3.5 25.4 - - - -
141D VAL* 3.9 7.9 - - - -
142D ALA* 3.3 14.4 - - - -
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Residues in contact with ALA 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 HIS* 3.0 19.4 + - + +
108D ASN* 2.9 5.7 + - - +
110D GLY* 1.3 74.6 - - - +
112D CYS* 1.3 63.9 + - - +
114D ARG* 3.2 9.7 + - - +
115D SER* 3.1 24.0 + - - -
141D VAL* 3.8 12.3 - - + +
228D SER* 2.9 32.0 - - - +
226E ASN* 5.0 11.7 - - - +
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Residues in contact with CYS 112 (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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98D LEU* 4.2 5.5 - - + +
100D LEU* 3.8 35.2 - - + -
103D VAL* 5.1 2.2 - - - -
108D ASN* 2.7 25.5 + - - +
109D LEU 3.8 1.1 - - - +
111D ALA* 1.3 71.5 - - - +
113D LEU* 1.3 60.6 - - - +
115D SER* 3.1 8.4 + - - +
116D ALA* 2.7 30.5 + - - +
227D VAL* 4.5 8.3 - - - -
228D SER* 4.1 15.0 - - - -
231D THR* 3.6 30.7 - - + -
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Residues in contact with LEU 113 (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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109D LEU* 3.0 24.2 + - + +
110D GLY* 3.5 7.9 - - - +
112D CYS* 1.3 75.5 - - - +
114D ARG* 1.3 64.1 + - - +
116D ALA* 3.0 6.5 + - - +
117D ASP* 3.0 21.0 + - - +
124D VAL* 4.1 28.3 - - + -
134D LEU* 3.7 34.3 - - + -
142D ALA* 4.3 11.9 - - + -
145D ALA* 3.2 18.0 - - + +
146D ALA* 4.5 8.1 - - - -
149D VAL* 4.1 26.8 - - + +
151D LEU* 4.8 12.3 - - + -
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Residues in contact with ARG 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 GLY 3.0 13.6 + - - +
111D ALA* 3.3 12.3 - - - +
113D LEU* 1.3 78.0 - - - +
115D SER* 1.3 60.8 + - - +
117D ASP* 3.5 3.6 + - - +
118D ALA* 3.2 20.8 + - - +
141D VAL* 3.6 20.9 + - - +
142D ALA 3.7 11.9 - - - +
143D CYS* 4.0 24.2 - - - +
145D ALA* 3.6 10.7 - - - +
198E GLU* 2.7 30.3 + - - -
222E VAL* 4.0 13.4 - - + +
224E SER* 2.9 37.5 + - - +
225E LEU* 3.4 9.5 - - + +
226E ASN* 3.3 33.9 - - - +
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Residues in contact with SER 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 ALA 3.1 9.9 + - - -
112D CYS* 3.1 10.7 + - - -
114D ARG* 1.3 76.6 - - - +
116D ALA* 1.3 61.6 + - - +
118D ALA* 3.3 8.0 + - - +
119D ALA* 2.9 30.5 + - - +
228D SER 4.5 3.0 + - - -
231D THR* 4.9 0.4 - - - -
232D GLY* 4.2 20.7 - - - -
235D LEU* 4.1 8.4 - - - +
236D PHE* 4.1 4.8 - - - -
225E LEU* 4.2 7.4 - - - +
229E VAL* 3.6 27.0 - - - +
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Residues in contact with ALA 116 (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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98D LEU* 4.1 6.5 - - + -
112D CYS 2.7 14.1 + - - +
113D LEU* 3.2 11.0 - - - +
115D SER* 1.3 76.7 - - - +
117D ASP* 1.3 58.3 + - - +
119D ALA* 3.1 3.3 + - - +
120D GLY 3.0 23.9 + - - -
121D VAL* 3.0 28.2 + - + +
124D VAL* 3.9 25.6 - - + -
149D VAL* 4.4 5.8 - - + -
235D LEU* 4.2 5.6 - - - +
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Residues in contact with ASP 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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17D ARG* 4.2 2.4 + - - -
113D LEU 3.0 12.7 + - - +
114D ARG 3.8 4.3 - - - +
116D ALA* 1.3 76.2 - - - +
118D ALA* 1.3 62.7 + - - +
120D GLY* 3.3 8.6 + - - +
121D VAL 5.0 1.1 - - - +
145D ALA* 3.9 9.4 - - + -
148D SER* 2.8 24.9 + - - -
149D VAL* 3.5 21.8 - - + +
220E GLY* 3.3 18.5 + - - -
221E SER* 2.8 18.9 + - - -
222E VAL* 2.7 36.2 + - + +
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Residues in contact with ALA 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 ARG 3.2 6.3 + - - +
115D SER 3.5 6.3 - - - +
116D ALA 3.2 0.2 - - - -
117D ASP* 1.3 82.4 + - - +
119D ALA* 1.3 59.7 + - - +
236D PHE* 3.7 14.2 - - + -
239D VAL* 5.1 0.7 - - - +
217E PRO 4.0 5.9 - - - +
218E MSE 3.8 16.0 - - - -
219E ALA* 2.9 29.0 + - - +
220E GLY 4.7 0.4 - - - +
222E VAL* 4.9 2.9 - - + +
225E LEU* 3.4 33.4 - - + -
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Residues in contact with ALA 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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96D PHE* 3.4 20.5 - - + -
115D SER 2.9 17.2 + - - +
116D ALA 3.1 5.3 + - - +
118D ALA* 1.3 78.2 - - - +
120D GLY* 1.3 57.3 + - - +
121D VAL* 4.3 0.9 - - + -
235D LEU* 3.6 28.3 - - + -
236D PHE* 3.9 4.7 - - + -
239D VAL* 3.4 31.2 - - + +
219E ALA* 4.2 4.6 - - - +
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Residues in contact with GLY 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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96D PHE* 3.7 10.4 - - - +
116D ALA 3.0 3.6 + - - -
117D ASP* 3.3 7.7 + - - -
118D ALA 3.3 4.2 + - - -
119D ALA* 1.3 79.8 - - - +
121D VAL* 1.3 65.1 + - - +
122D HIS* 3.5 16.6 + - - -
219E ALA* 4.1 14.1 - - - -
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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