Contacts of the helix formed by residues 110 - 116 (chain A) in PDB entry 3K3B
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A GLY 3.5 0.4 - - - -
109A THR* 1.3 81.3 - - - +
111A LYS* 1.3 61.5 + - - +
112A THR 3.5 1.6 - - - -
113A PHE* 3.8 2.4 - - - +
114A THR* 2.7 36.9 + - - -
335A THR* 3.9 6.0 - - - +
370A ADP 2.9 37.1 + - - -
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Residues in contact with LYS 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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103A ALA* 3.5 33.4 - - + +
104A TYR* 4.1 0.2 - - - -
105A GLY* 2.8 40.4 + - - +
106A GLN 3.4 9.9 + - - -
107A THR* 3.7 6.9 + - - +
109A THR 4.0 0.2 - - - -
110A GLY* 1.3 75.4 - - - +
112A THR* 1.3 58.0 + - - +
114A THR* 3.7 1.6 - - - -
115A MET* 2.9 33.8 + - - +
233A SER* 5.4 1.6 + - - +
265A ASP* 3.2 16.1 + - - +
266A LEU 3.6 18.3 + - - +
267A ALA 4.8 0.2 - - - +
268A GLY* 3.6 20.8 - - - +
335A THR* 3.7 13.2 - - - +
370A ADP 3.0 34.1 + - - +
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Residues in contact with THR 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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111A LYS* 1.3 70.1 - - - +
113A PHE* 1.3 61.0 + - - +
115A MET* 4.3 2.7 - - - +
116A GLU* 2.8 54.9 + - + +
117A GLY 3.1 8.7 + - - +
232A SER* 5.9 1.0 - - - -
265A ASP* 2.5 18.1 + - - -
369A MG 2.4 27.3 - - - -
370A ADP 2.7 18.2 + - - +
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Residues in contact with PHE 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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24A ARG* 3.6 12.6 - - - -
78A GLN* 2.6 63.3 + - + -
110A GLY 3.8 2.9 - - - +
111A LYS 3.3 0.2 - - - -
112A THR* 1.3 74.1 - - - +
114A THR* 1.3 54.4 + - - +
117A GLY* 3.0 15.6 + - - +
118A GLU* 3.6 26.2 - - + +
132A LEU* 4.3 22.7 - - + -
370A ADP 2.8 101.7 + + + +
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Residues in contact with THR 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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24A ARG* 3.0 35.9 + - - +
78A GLN* 4.2 1.7 - - - +
81A VAL* 4.2 6.7 - - + +
103A ALA* 5.1 1.6 - - + -
110A GLY* 2.7 22.8 + - - -
111A LYS* 3.7 5.2 - - - -
113A PHE* 1.3 78.9 - - - +
115A MET* 1.3 61.7 + - + +
134A GLY* 3.5 2.1 - - - -
135A ILE* 2.9 47.0 + - + +
333A ILE* 3.7 24.0 - - + -
335A THR* 4.2 6.6 - - - +
370A ADP 5.7 0.2 + - - -
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Residues in contact with MET 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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101A ILE* 3.6 24.9 - - + +
102A PHE 3.4 36.6 - - - +
103A ALA* 3.4 13.7 - - + +
111A LYS 2.9 18.9 + - - +
112A THR 4.4 0.2 - - - +
114A THR* 1.3 78.0 - - + +
116A GLU* 1.3 66.3 + - + +
135A ILE* 3.7 18.8 - - + +
136A ILE* 2.8 44.9 + - + +
263A LEU* 4.2 23.6 - - - +
264A VAL 3.7 9.9 - - - +
265A ASP* 4.1 14.4 - - + +
333A ILE* 4.4 3.4 - - + -
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Residues in contact with GLU 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 THR* 2.8 40.9 + - + +
115A MET* 1.3 81.7 - - + +
117A GLY* 1.3 64.7 + - - +
134A GLY* 3.0 16.7 + - - -
136A ILE* 4.2 5.7 - - + +
137A PRO* 3.4 7.3 - - - +
218A ALA* 5.6 1.9 - - - +
221A ARG* 3.0 33.7 + - - -
237A SER* 4.4 2.9 + - - -
265A ASP* 4.6 6.7 - - + +
371A L31 3.0 65.9 + - + +
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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