Contacts of the helix formed by residues 110 - 120 (chain D) in PDB entry 5DO7
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 GLY 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D GLY* 4.5 5.1 - - - -
88D ILE* 4.7 8.7 - - - +
108D GLY 3.0 7.7 + - - -
109D CYS* 1.3 79.2 - - - +
111D ARG* 1.3 54.0 + - - +
113D SER* 3.5 23.1 - - - -
114D LEU* 2.8 35.1 + - - +
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Residues in contact with ARG 111 (chain D).
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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103D ILE* 4.1 19.2 - - + +
105D GLY* 3.3 36.6 - - - +
106D SER 3.6 13.3 + - - +
107D SER* 4.2 4.6 - - - +
108D GLY* 3.6 14.3 - - - +
109D CYS* 3.2 26.6 - - - +
110D GLY* 1.3 74.4 - - - +
112D ALA* 1.3 92.9 + - - +
113D SER* 3.0 1.1 + - - +
114D LEU* 3.2 19.8 + - - +
115D LEU* 3.9 10.6 + - - +
238D GLU* 3.4 37.3 + - - +
268D SER* 4.0 15.9 + - - -
269D LEU 4.6 3.1 - - - -
270D HIS* 4.3 11.7 - - - +
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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
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108D GLY* 5.3 3.4 - - - -
111D ARG* 1.3 101.2 - - - +
113D SER* 1.3 58.9 + - - +
115D LEU 4.4 0.6 + - - -
116D ASP* 3.2 22.3 + - - +
152D ARG* 5.2 0.5 + - - -
153D GLN* 5.9 4.3 - - - +
237D ASP* 3.4 24.8 - - - +
238D GLU* 5.8 0.2 - - + -
268D SER* 4.9 0.2 - - - -
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Residues in contact with SER 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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88D ILE* 6.5 0.4 - - - -
108D GLY* 6.2 0.2 - - - -
110D GLY* 3.5 22.6 - - - -
111D ARG 3.0 0.6 + - - +
112D ALA* 1.3 77.9 - - - +
114D LEU* 1.3 65.8 + - - +
115D LEU 3.2 0.7 - - - -
116D ASP* 2.8 21.1 + - - +
117D VAL* 2.8 24.1 + - - +
122D GLY 4.9 6.7 - - - -
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Residues in contact with LEU 114 (chain D).
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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38D PHE* 6.0 0.7 - - + -
88D ILE* 4.4 10.8 - - + -
91D LEU* 4.2 24.0 - - + -
93D PHE* 5.2 1.8 - - + -
103D ILE* 3.9 36.1 - - + -
109D CYS* 5.9 0.9 - - - -
110D GLY 2.8 22.1 + - - +
111D ARG* 3.2 14.0 + - + +
113D SER* 1.3 72.6 - - - +
115D LEU* 1.3 59.2 + - + +
117D VAL* 2.9 20.1 - - + +
118D ILE* 2.8 52.7 + - + +
284D LEU* 5.0 2.9 - - + -
286D MET* 4.2 19.3 - - + -
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Residues in contact with LEU 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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103D ILE* 3.6 30.7 - - + -
111D ARG 4.2 7.9 - - - +
113D SER 3.2 0.8 - - - -
114D LEU* 1.3 76.2 - - + +
116D ASP* 1.3 58.5 + - - +
118D ILE* 3.2 16.2 + - + +
119D THR* 2.8 30.3 + - - -
150D HIS* 4.1 5.8 + - + -
235D ILE* 3.8 29.4 - - + +
236D LEU 3.6 18.8 - - - +
237D ASP* 3.6 23.8 - - + +
266D LEU* 4.8 8.3 - - + -
267D ILE* 4.7 2.2 - - - +
268D SER* 3.4 28.5 - - - +
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Residues in contact with ASP 116 (chain D).
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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112D ALA 3.2 9.9 - - - +
113D SER* 2.8 10.6 + - - +
115D LEU* 1.3 76.8 - - - +
117D VAL* 1.3 56.0 + - - +
119D THR* 3.3 8.3 - - - +
120D GLY 2.8 8.1 + - - -
121D ARG* 2.8 60.6 + - + +
122D GLY 4.9 2.5 - - - +
123D HIS* 4.6 7.4 - - + -
150D HIS* 4.0 6.8 + - - -
152D ARG* 2.8 28.2 + - - -
237D ASP* 3.2 22.5 - - - +
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Residues in contact with VAL 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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43D GLN* 2.9 39.0 - - - +
88D ILE* 4.2 9.2 - - + -
113D SER* 2.8 25.5 + - - +
114D LEU* 2.9 39.0 - - + +
116D ASP* 1.3 69.4 - - - +
118D ILE* 1.3 66.4 + - + +
120D GLY* 3.0 14.8 + - - -
122D GLY* 3.7 23.3 - - - +
127D ILE* 5.4 6.7 - - + +
132D ILE* 4.7 5.8 - - - +
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Residues in contact with ILE 118 (chain D).
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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36D LEU* 4.9 14.4 - - + -
38D PHE* 3.8 36.6 - - + -
91D LEU* 6.2 0.2 - - + -
93D PHE* 5.3 7.2 - - + -
103D ILE* 5.1 4.5 - - + -
114D LEU* 2.8 50.1 + - + +
115D LEU* 3.5 18.6 - - + +
117D VAL* 1.3 75.7 - - + +
119D THR* 1.3 59.0 + - - +
120D GLY* 4.7 0.2 - - - -
132D ILE* 4.2 19.7 - - + +
134D ILE* 5.8 0.5 - - - +
139D SER* 4.8 4.3 + - - -
144D VAL* 4.6 9.2 - - - +
235D ILE* 4.7 16.2 - - + -
266D LEU* 5.2 7.9 - - + -
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Residues in contact with THR 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 LEU 2.8 13.6 + - - -
116D ASP* 3.3 26.5 - - + +
118D ILE* 1.3 72.7 - - - +
120D GLY* 1.3 56.5 + - - +
121D ARG* 3.9 22.6 + - + +
141D PRO* 5.0 7.3 - - - +
144D VAL* 3.3 39.1 - - - +
148D VAL* 5.1 3.6 - - - +
150D HIS* 4.6 24.8 + - + +
235D ILE* 5.4 6.3 - - - +
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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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116D ASP 2.8 6.5 + - - -
117D VAL* 3.0 12.5 + - - -
118D ILE 3.3 0.4 - - - -
119D THR* 1.3 78.5 - - - +
121D ARG* 1.3 57.4 + - - -
122D GLY* 2.9 10.2 + - - -
141D PRO* 5.2 14.5 - - - +
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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