Contacts of the helix formed by residues 108 - 118 (chain D) in PDB entry 3UNE
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 THR 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74D ILE* 4.3 0.4 - - - -
106D THR 3.9 2.4 + - - +
107D MET* 1.3 77.8 - - - +
109D VAL* 1.3 65.2 + - - +
110D GLU* 4.2 6.6 + - - +
111D SER* 2.7 41.2 + - - -
112D VAL* 3.2 13.7 + - - +
147D ASP* 3.4 15.9 - - + +
148D GLU* 3.6 32.3 - - + +
149D LYS* 5.9 3.6 - - + -
152D GLN* 5.2 0.2 - - - -
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Residues in contact with VAL 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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74D ILE* 3.9 21.7 - - + +
108D THR* 1.3 72.4 - - - +
110D GLU* 1.3 56.1 + - - +
112D VAL* 3.5 2.1 + - + +
113D THR* 2.7 33.7 + - - -
143D PHE* 3.8 24.0 - - + +
144D GLY 4.7 0.2 - - - -
145D GLY* 3.5 41.1 - - - +
146D VAL 4.2 0.4 - - - +
147D ASP* 3.0 20.6 + - + +
152D GLN* 3.7 14.8 - - + +
154D PHE* 3.7 19.3 - - + -
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Residues in contact with GLU 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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108D THR* 3.2 7.7 - - - +
109D VAL* 1.3 79.6 - - - +
111D SER* 1.3 57.3 + - - +
113D THR* 3.6 3.5 + - - -
114D GLN* 3.0 34.0 + - - +
149D LYS* 4.6 14.1 + - - -
152D GLN* 4.5 5.0 - - - +
154D PHE* 3.7 36.8 - - + -
162D PHE* 4.2 11.8 - - + -
61E LYS* 3.7 26.3 + - - +
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Residues in contact with SER 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 MET* 3.8 21.9 - - - +
108D THR* 2.7 29.1 + - - -
110D GLU* 1.3 77.1 - - - +
112D VAL* 1.3 60.4 + - - +
114D GLN* 3.4 10.2 + - - +
115D ALA* 3.0 26.9 + - - +
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ILE* 4.3 26.5 - - + -
74D ILE* 3.7 22.7 - - + -
92D ALA* 4.4 11.0 - - + +
95D GLU* 6.2 0.2 - - + -
96D THR* 3.8 23.3 - - + -
107D MET* 3.8 26.2 - - + -
108D THR 3.2 15.0 + - - +
109D VAL* 4.0 5.4 - - + +
111D SER* 1.3 72.8 - - - +
113D THR* 1.3 65.9 + - - +
115D ALA* 3.3 12.8 + - + +
116D VAL* 3.3 16.2 + - - +
143D PHE* 4.5 6.3 - - + -
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Residues in contact with THR 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 VAL 2.7 21.9 + - - -
110D GLU 3.8 4.5 - - - -
111D SER 3.3 0.2 - - - -
112D VAL* 1.3 79.0 - - - +
114D GLN* 1.3 52.8 + - - +
116D VAL* 3.4 3.8 + - - +
117D SER* 2.8 36.2 + - - +
143D PHE* 3.6 46.9 - - + +
154D PHE* 3.7 19.4 - - + +
155D HIS 5.1 0.4 - - - +
156D MET* 4.2 5.6 - - + +
162D PHE* 3.7 29.4 - - + -
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Residues in contact with GLN 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 GLU* 3.0 25.0 + - - +
111D SER* 3.6 9.6 + - - +
112D VAL 3.3 0.2 - - - -
113D THR* 1.3 76.3 - - - +
115D ALA* 1.3 60.5 + - - +
117D SER* 3.3 8.1 + - - -
118D ASN* 3.1 36.3 + - - +
162D PHE* 3.7 29.8 - - + -
61E LYS* 4.3 9.9 - - - +
82E ARG* 4.9 11.9 - - - +
89E ARG* 5.5 5.4 + - - -
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Residues in contact with ALA 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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91D LYS* 5.5 3.8 - - - +
92D ALA* 6.1 1.1 - - - -
95D GLU* 4.3 33.3 - - + +
107D MET* 5.1 3.4 - - + -
111D SER 3.0 13.5 + - - +
112D VAL* 3.5 13.2 - - + +
113D THR 3.3 0.6 - - - -
114D GLN* 1.3 78.3 - - - +
116D VAL* 1.3 61.0 + - + +
118D ASN* 3.6 23.8 + - - +
119D LEU* 4.3 9.4 + - - +
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Residues in contact with VAL 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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88D LEU* 3.9 30.2 - - + +
91D LYS* 6.3 0.9 - - + -
92D ALA* 3.8 26.2 - - + +
112D VAL 3.3 15.4 + - - +
113D THR 3.8 4.9 - - - +
115D ALA* 1.3 72.6 - - + +
117D SER* 1.3 60.6 + - - +
118D ASN 3.1 4.7 - - - -
119D LEU* 3.2 27.2 + - + +
120D ALA* 4.3 0.7 + - - -
141D LEU* 4.2 11.0 - - + -
143D PHE* 3.8 18.2 - - + -
156D MET* 3.9 26.9 - - + +
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Residues in contact with SER 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 THR 2.8 21.8 + - - -
114D GLN* 3.3 7.4 + - - -
116D VAL* 1.3 75.9 - - - +
118D ASN* 1.3 60.1 + - - +
119D LEU 3.3 0.7 - - - -
120D ALA* 3.3 17.2 - - - +
156D MET* 3.2 23.5 - - - +
160D GLY* 3.6 17.7 + - - -
162D PHE* 3.3 21.0 - - - +
79E ALA* 5.0 0.9 - - - +
82E ARG* 3.3 22.8 + - - -
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Residues in contact with ASN 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 GLN* 3.1 22.4 + - - +
115D ALA* 3.6 18.7 + - - +
116D VAL 3.1 1.0 - - - -
117D SER* 1.3 77.6 - - - +
119D LEU* 1.3 59.1 + - + +
120D ALA 3.2 6.0 + - - -
121D LEU 5.0 0.5 + - - -
122D GLN* 3.5 21.8 + - - +
82E ARG* 3.1 21.1 + - - +
83E LEU* 6.0 0.2 - - - +
86E ASN* 4.8 11.5 + - - -
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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