Contacts of the helix formed by residues 107 - 115 (chain D) in PDB entry 5IYB
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 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D PRO* 4.1 0.5 - - - +
106D GLU* 1.3 89.6 - - + +
108D ALA* 1.3 55.6 + - - +
109D GLU* 4.1 8.8 - - - +
110D GLU* 3.3 29.2 + - - +
111D SER* 2.6 32.6 + - - -
128D GLN* 3.2 10.5 - - - +
131D LEU* 3.3 5.6 - - - +
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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
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107D THR* 1.3 70.8 - - - +
109D GLU* 1.3 59.0 + - - +
111D SER* 3.4 8.9 - - - -
112D LYS* 3.0 35.9 + - - +
124D ASP* 3.6 38.6 - - + +
127D LEU* 4.0 18.7 - - + +
128D GLN* 2.6 19.1 + - + +
131D LEU* 3.8 0.8 - - - +
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Residues in contact with GLU 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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107D THR* 3.3 9.3 - - - +
108D ALA* 1.3 77.0 - - - +
110D GLU* 1.3 66.0 + - - +
112D LYS* 3.4 15.1 + - - +
113D ALA* 3.1 21.6 + - + +
124D ASP* 4.8 1.7 + - - +
167G TYR* 3.6 19.1 + - + +
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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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105D PRO* 5.3 9.2 - - + -
106D GLU* 4.8 9.6 + - - +
107D THR* 3.3 20.9 + - - +
109D GLU* 1.3 78.0 - - - +
111D SER* 1.3 64.1 + - - +
113D ALA* 3.1 4.0 + - - +
114D LEU* 2.9 37.0 + - + +
144G ARG* 2.5 35.2 + - - -
167G TYR* 3.8 44.3 + - + +
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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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100D LEU* 5.3 3.1 - - - -
105D PRO* 3.3 27.8 - - - +
107D THR 2.6 20.5 + - - -
108D ALA 3.4 9.0 - - - -
109D GLU 3.3 0.4 - - - -
110D GLU* 1.3 76.6 - - - +
112D LYS* 1.3 62.1 + - - +
114D LEU* 3.3 6.3 + - - +
115D ILE* 3.0 21.2 + - - +
118D LEU* 3.8 16.5 - - - +
127D LEU* 3.9 18.6 - - - +
131D LEU* 3.6 6.4 - - - +
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Residues in contact with LYS 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 ALA 3.0 21.3 + - - +
109D GLU* 3.8 12.9 - - - +
111D SER* 1.3 75.8 - - - +
113D ALA* 1.3 62.4 + - - +
115D ILE 3.0 25.2 - - - +
116D PRO* 3.5 8.5 - - - +
118D LEU* 3.4 26.5 - - + +
119D GLU* 3.7 34.9 - - + +
124D ASP* 2.3 43.4 + - - +
127D LEU* 5.0 4.9 - - + -
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Residues in contact with ALA 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 GLU* 3.1 13.1 + - + +
110D GLU 3.1 10.0 + - - +
112D LYS* 1.3 78.6 - - - +
114D LEU* 1.3 62.6 + - - +
116D PRO* 4.4 8.7 - - - +
119D GLU* 5.3 4.0 - - - -
146G LYS* 5.1 5.5 + - - -
165G ASP* 5.6 0.5 - - - +
167G TYR* 3.8 26.2 - - + -
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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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103D LEU* 3.7 31.6 - - + -
105D PRO* 5.7 5.2 - - + -
110D GLU* 2.9 42.4 + - + +
111D SER* 3.9 5.6 - - - +
113D ALA* 1.3 74.9 - - - +
115D ILE* 1.3 68.2 + - + +
116D PRO* 3.6 7.0 - - - +
82G GLY 5.0 5.9 - - - +
84G VAL* 4.2 33.1 - - + +
144G ARG* 5.0 4.3 - - - +
146G LYS* 5.2 8.9 + - - +
165G ASP* 5.5 1.3 - - - +
166G ASP 4.7 4.9 - - - +
167G TYR* 4.0 28.9 - - + +
168G LEU* 4.8 2.0 - - + -
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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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17D ALA 5.4 6.7 - - - +
18D SER* 5.9 2.0 - - - -
95D PHE* 6.1 3.1 - - + -
96D GLU* 4.2 25.4 - - + +
99D CYS* 4.1 33.7 - - + -
100D LEU* 4.5 7.4 - - + +
103D LEU* 5.5 2.7 - - + -
111D SER 3.0 11.8 + - - +
112D LYS 3.0 10.3 - - - +
114D LEU* 1.3 87.0 - - + +
116D PRO* 1.3 66.1 - - + +
117D SER* 3.2 22.9 - - - +
118D LEU* 3.0 36.6 + - + +
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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