Contacts of the helix formed by residues 153 - 160 (chain E) in PDB entry 1KXT
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 ASP 153 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142E LYS* 4.2 12.3 + - - -
150E SER* 3.3 18.5 + - - +
151E TYR 3.1 1.5 - - - -
152E ASN* 1.3 80.2 - - - +
154E PRO* 1.3 67.2 - - - +
155E TYR* 3.2 21.1 + - - +
156E GLN* 2.9 37.4 + - - +
157E VAL* 3.3 18.9 + - - +
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Residues in contact with PRO 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E ASN 3.4 9.9 - - - +
153E ASP* 1.3 88.3 - - - +
155E TYR* 1.3 71.2 + - + +
157E VAL* 2.8 26.8 - - + +
158E ARG* 3.3 28.7 + - - +
203E TRP* 4.6 4.3 - - + -
241E ALA* 3.6 21.5 - - + +
242E ILE* 3.6 13.2 - - + -
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Residues in contact with TYR 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LYS* 3.5 32.3 - - + +
153E ASP* 3.2 11.3 + - - +
154E PRO* 1.3 88.5 - - + +
156E GLN* 1.3 57.3 + - - +
159E ASP* 2.9 42.8 + - - +
203E TRP* 3.8 33.1 - + - -
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Residues in contact with GLN 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LYS* 5.0 5.1 - - - +
143E THR* 3.3 20.9 - - + +
148E ILE* 3.3 6.5 - - + +
149E GLU* 2.6 37.7 + - - +
150E SER* 2.9 22.0 + - - +
153E ASP* 2.9 37.4 + - - +
155E TYR* 1.3 77.7 - - - +
157E VAL* 1.3 67.9 + - - +
158E ARG 3.2 0.4 - - - -
160E CYS* 3.0 49.2 + - + +
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Residues in contact with VAL 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E ILE* 3.4 15.0 - - + +
151E TYR* 3.6 33.4 - - + -
153E ASP 3.3 9.4 + - - +
154E PRO* 2.8 39.7 - - + +
156E GLN* 1.3 78.5 - - - +
158E ARG* 1.3 66.0 + - + +
160E CYS 4.4 2.3 - - - +
200E LYS* 4.2 12.8 - - + +
201E HIS* 3.1 47.0 - - + +
242E ILE* 3.5 17.5 - - + -
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Residues in contact with ARG 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ASN* 4.2 2.3 + - - -
154E PRO* 3.3 26.0 + - - +
155E TYR 4.4 0.2 - - - +
157E VAL* 1.3 82.8 - - + +
159E ASP* 1.3 61.9 + - - +
160E CYS 3.7 0.9 - - - -
167E ASP* 3.2 1.9 - - - +
200E LYS 3.2 19.1 + - - +
201E HIS 3.2 12.7 - - - +
202E MET* 3.3 7.4 + - - +
203E TRP* 3.4 57.3 + - + +
204E PRO* 3.9 10.7 - - - +
242E ILE* 3.2 19.4 - - - +
246E GLU* 2.8 28.5 + - - -
247E TYR* 2.8 32.7 + - - -
4005E CA 2.5 24.4 - - - -
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Residues in contact with ASP 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ASN* 3.5 23.3 + - - +
140E LYS* 3.3 40.9 - - + +
141E CYS* 3.4 19.1 - - - +
142E LYS* 5.8 3.0 - - - +
155E TYR* 2.9 31.0 + - - +
156E GLN* 4.7 0.7 - - - -
158E ARG* 1.3 79.8 - - - +
160E CYS* 1.3 61.4 + - - +
167E ASP* 3.6 7.1 - - - +
203E TRP* 3.0 35.1 + - - -
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Residues in contact with CYS 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E CYS* 2.0 49.6 - - - -
142E LYS 4.0 1.3 - - - -
143E THR* 3.6 7.0 - - - -
146E GLY 3.3 6.5 - - - +
147E GLY 3.7 13.0 - - - -
148E ILE* 4.0 5.7 - - - +
156E GLN* 3.0 43.8 + - - +
157E VAL 4.4 3.6 - - - +
158E ARG 4.8 0.2 - - - -
159E ASP* 1.3 79.5 - - - +
161E GLN* 1.3 65.8 + - - +
162E LEU* 3.6 2.3 + - - +
167E ASP* 3.6 17.4 - - - +
201E HIS* 5.9 0.9 - - - +
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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