Contacts of the helix formed by residues 169 - 176 (chain B) in PDB entry 5FDK
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 LYS 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LYS 4.5 11.5 + - - +
109B THR* 3.1 23.5 + - - +
110B SER* 3.9 0.6 - - - +
141B PHE* 3.5 47.8 + - + +
145B TYR* 5.2 1.3 - - - -
167B ILE 3.4 2.2 + - - -
168B ARG* 1.3 71.0 - - - +
170B ASP* 1.3 57.8 + - - +
172B LEU* 3.0 3.5 + - - +
173B GLU* 2.8 51.4 + - - +
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Residues in contact with ASP 170 (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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168B ARG* 4.3 12.2 - - - +
169B LYS* 1.3 74.8 - - - +
171B GLU* 1.3 69.1 + - - +
173B GLU* 3.7 18.2 - - - +
174B GLU* 3.0 27.9 + - - +
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Residues in contact with GLU 171 (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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155B PHE* 4.3 15.4 - - + -
158B ARG* 5.1 4.5 - - - +
167B ILE* 4.2 8.5 - - + -
168B ARG* 2.8 25.0 + - + +
170B ASP* 1.3 87.7 + - - +
172B LEU* 1.3 63.3 + - - +
174B GLU* 3.6 4.3 - - - +
175B THR* 2.9 28.1 + - - -
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Residues in contact with LEU 172 (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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111B PHE* 4.6 7.4 - - + -
138B ILE* 4.2 33.4 - - + -
141B PHE* 3.4 29.4 - - + -
145B TYR* 3.6 31.6 - - + -
147B LEU* 4.4 13.9 - - + -
155B PHE* 5.9 0.4 - - + -
167B ILE* 4.1 19.3 - - + +
168B ARG 2.8 10.5 + - - +
169B LYS 3.0 9.2 + - - +
171B GLU* 1.3 78.3 - - - +
173B GLU* 1.3 61.3 + - + +
175B THR* 3.8 1.7 - - - -
176B ALA* 2.8 40.7 + - + +
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Residues in contact with GLU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TYR* 4.1 29.6 + - + +
169B LYS* 2.8 37.9 + - - +
170B ASP* 3.7 19.4 - - - +
172B LEU* 1.3 78.6 - - - +
174B GLU* 1.3 61.1 + - - +
176B ALA 3.3 12.8 - - - +
177B TYR* 3.9 9.2 - - - -
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Residues in contact with GLU 174 (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 LYS* 5.7 2.6 - - - +
170B ASP 3.0 19.4 + - - +
171B GLU* 3.6 6.5 - - - +
173B GLU* 1.3 77.5 - - - +
175B THR* 1.3 78.8 + - - +
176B ALA 3.4 0.9 + - - -
177B TYR* 3.4 33.1 + - - -
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Residues in contact with THR 175 (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 LEU* 4.3 11.1 - - - +
148B GLU* 5.1 2.1 + - - +
151B LYS* 3.0 41.5 + - - +
155B PHE* 3.8 27.8 - - - -
171B GLU 2.9 18.1 + - - -
172B LEU* 3.8 2.2 - - - -
174B GLU* 1.3 87.5 + - - +
176B ALA* 1.3 57.4 + - - +
177B TYR* 5.2 3.7 - - - -
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Residues in contact with ALA 176 (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 TYR* 4.1 17.6 - - + -
146B PHE 3.4 20.6 - - - +
147B LEU* 3.7 20.4 - - + -
148B GLU 5.3 0.7 - - - +
172B LEU* 2.8 20.1 + - + +
173B GLU* 3.3 14.4 - - - +
175B THR* 1.3 74.4 - - - +
177B TYR* 1.3 78.0 + - - +
178B PRO* 4.8 0.5 - - - +
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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