Contacts of the helix formed by residues 110 - 117 (chain A) in PDB entry 3O71
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 LEU 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A ASP* 1.3 70.4 - - - +
111A TYR* 1.3 60.4 + - - +
113A LEU* 4.1 3.6 - - + -
114A LEU* 2.9 56.8 + - + +
119A LEU* 4.2 12.3 - - + -
127A PHE* 4.4 5.8 - - + -
131A ILE* 5.1 1.1 - - + -
150A PRO* 3.3 19.0 + - + +
153A LEU* 3.0 27.3 + - + +
155A LEU* 3.6 20.7 - - + +
161A LEU* 5.6 2.7 - - + -
215A ILE* 3.7 30.7 - - + -
219A MET* 3.9 26.0 - - + -
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Residues in contact with TYR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASP* 2.9 10.4 + - - +
110A LEU* 1.3 81.0 - - - +
112A LYS* 1.3 74.6 + - + +
114A LEU* 3.4 3.5 + - - +
115A LYS* 3.3 61.7 + - + +
150A PRO* 3.4 19.1 + - + +
151A SER* 3.6 28.7 - - - +
190A TRP* 5.8 8.5 - + - -
191A TYR* 5.7 1.6 - - - -
218A GLU* 5.4 5.2 - - - -
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 2.7 48.9 + - - +
30A GLY* 4.1 5.9 - - - +
107A GLU 5.6 1.0 + - - +
108A THR* 3.5 22.8 - - - +
109A ASP* 2.8 33.8 + - - +
111A TYR* 1.3 84.3 - - + +
113A LEU* 1.3 63.2 + - - +
115A LYS* 3.2 15.6 + - - +
116A THR* 3.3 21.7 + - + +
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A THR* 4.2 6.4 + - + -
109A ASP 3.0 18.4 + - - +
110A LEU* 3.7 10.8 - - + +
111A TYR 3.3 0.2 - - - -
112A LYS* 1.3 77.6 - - - +
114A LEU* 1.3 59.4 + - + +
116A THR* 2.9 20.4 + - - +
117A GLN* 3.0 49.1 + - + +
119A LEU* 3.4 42.2 - - + -
127A PHE* 4.9 1.3 - - + -
155A LEU* 4.2 14.1 - - + -
1152B LEU* 4.4 15.7 - - + -
1154B ILE* 4.9 15.3 - - + -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 2.9 41.7 + - + +
111A TYR* 4.0 3.8 - - - +
112A LYS 3.3 0.2 - - - -
113A LEU* 1.3 74.1 - - + +
115A LYS* 1.3 65.9 + - - +
116A THR 3.2 0.8 + - - -
117A GLN 3.9 1.7 + - - +
119A LEU* 3.8 33.4 - - + -
150A PRO* 4.8 3.6 - - + -
218A GLU* 3.7 41.5 - - + +
219A MET* 4.2 13.7 - - - +
222A ASN* 2.8 50.0 + - - +
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A TYR* 3.3 55.0 + - + +
112A LYS* 3.2 12.0 + - - +
114A LEU* 1.3 79.3 - - - +
116A THR* 1.3 64.6 + - + +
218A GLU* 5.3 6.1 + - - -
222A ASN 5.4 5.9 + - - -
224A PRO* 5.6 6.3 - - - +
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Residues in contact with THR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LYS* 3.3 15.5 + - + +
113A LEU* 2.9 19.6 + - - +
115A LYS* 1.3 84.8 - - + +
117A GLN* 1.3 70.5 + - - +
1155B HIS* 4.6 41.2 + - + -
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU* 3.0 42.5 + - + +
114A LEU* 4.0 4.6 + - - +
115A LYS 3.9 1.0 - - - -
116A THR* 1.3 82.3 + - - +
118A HIS* 1.3 70.8 + - - +
119A LEU* 3.8 3.7 + - + +
222A ASN* 2.9 20.6 + - - -
1152B LEU* 3.6 23.9 - - - +
1153B TRP* 3.0 30.0 + - - +
1154B ILE* 4.9 0.6 - - - +
1155B HIS* 3.9 16.2 + - + +
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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