Contacts of the helix formed by residues 145 - 156 (chain B) in PDB entry 4KYI
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 GLU 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B TYR* 5.9 0.2 - - - -
142B ARG* 3.5 18.2 + - - +
143B ALA 4.0 5.2 + - - +
144B VAL* 1.3 80.5 - - - +
146B PHE* 1.3 62.7 + - - +
147B GLN* 4.4 13.7 - - + +
148B GLU* 2.9 38.5 + - + +
149B ALA* 3.1 13.7 + - - +
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TYR* 5.8 0.4 - - - -
142B ARG* 3.0 15.2 - - - +
145B GLU* 1.3 74.7 + - - +
147B GLN* 1.3 60.7 + - + +
149B ALA* 4.0 4.5 - - - +
150B GLN* 3.0 61.0 + - + +
160B PHE* 3.4 16.5 - + - -
161B MET* 5.6 1.3 - - - -
162B GLU* 3.2 37.5 - - + +
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLU* 3.2 12.0 - - + +
146B PHE* 1.3 85.0 - - + +
148B GLU* 1.3 68.0 + - - +
150B GLN* 4.1 4.3 - - - +
151B ALA* 3.2 26.1 + - - +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PHE* 4.2 22.5 - - + -
113B LYS* 4.6 8.0 + - - -
144B VAL* 4.4 4.5 - - - +
145B GLU* 2.9 31.3 + - + +
147B GLN* 1.3 84.7 + - - +
149B ALA* 1.3 61.3 + - - +
151B ALA* 3.1 7.6 + - - +
152B TYR* 2.9 28.3 + - + +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TYR* 3.2 27.4 - - + +
109B PHE* 4.1 23.8 - - + -
131B LEU* 4.3 2.9 - - + +
144B VAL* 4.9 1.6 - - + -
145B GLU 3.1 10.4 + - - +
146B PHE* 4.3 0.4 - - - +
148B GLU* 1.3 76.1 - - - +
150B GLN* 1.3 59.5 + - - +
152B TYR* 3.8 1.3 - - - +
153B ALA* 2.8 32.7 + - - +
160B PHE* 3.5 20.2 - - + -
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Residues in contact with GLN 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B PHE* 3.0 46.7 + - + +
147B GLN* 4.1 6.5 - - - +
149B ALA* 1.3 76.0 - - - +
151B ALA* 1.3 56.7 + - - +
153B ALA* 3.9 1.1 - - - +
154B ASP* 2.8 62.1 + - - +
160B PHE* 3.2 37.3 + - - +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLN* 3.2 21.9 + - - +
148B GLU* 3.1 12.4 + - + +
150B GLN* 1.3 77.8 - - - +
152B TYR* 1.3 59.8 + - - +
154B ASP* 3.2 4.6 + - - +
155B ASP* 2.9 42.9 + - - +
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Residues in contact with TYR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PHE* 4.4 26.2 - + + -
112B ALA* 5.6 0.7 - - + -
113B LYS* 3.4 59.5 + - + +
116B VAL* 4.3 10.5 - - + +
117B LYS* 5.1 1.7 + - - +
131B LEU* 4.5 9.6 - - + -
148B GLU* 2.9 19.9 + - + +
149B ALA 3.9 2.7 - - - +
151B ALA* 1.3 73.4 - - - +
153B ALA* 1.3 63.6 + - - +
155B ASP* 3.5 5.8 + - + -
156B ASN* 2.3 66.4 + - + +
158B LEU* 4.6 12.3 - - + -
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 4.1 6.3 - - + -
149B ALA 2.8 18.4 + - - +
150B GLN 3.9 2.5 - - - +
152B TYR* 1.3 74.8 - - - +
154B ASP* 1.3 60.4 + - - +
155B ASP 3.1 1.6 - - - -
156B ASN 2.8 20.3 + - - -
157B SER 2.9 12.0 + - - -
158B LEU* 3.1 31.9 + - + +
160B PHE* 3.5 29.2 - - + +
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLN* 2.8 47.9 + - - +
151B ALA* 3.2 4.9 + - - +
153B ALA* 1.3 77.8 - - - +
155B ASP* 1.3 63.8 + - - +
157B SER* 4.0 7.8 + - - +
158B LEU 5.2 5.0 - - - +
160B PHE* 5.4 0.2 - - - +
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Residues in contact with ASP 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ALA* 2.9 27.8 + - - +
152B TYR* 3.7 3.4 - - + +
153B ALA 3.1 0.2 - - - -
154B ASP* 1.3 81.3 - - - +
156B ASN* 1.3 72.8 + - - +
157B SER* 3.5 3.4 + - - -
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Residues in contact with ASN 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B VAL* 4.9 3.2 - - + +
120B GLN* 3.9 29.1 + - - +
152B TYR* 2.3 65.5 + - + +
153B ALA 2.8 3.7 + - - +
155B ASP* 1.3 87.5 - - - +
157B SER* 1.3 70.8 + - - +
158B LEU* 3.2 28.1 - - + +
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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