Contacts of the helix formed by residues 163 - 174 (chain E) in PDB entry 5JKL
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 SER 163 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C LEU* 5.8 2.4 - - - +
158E MET 4.4 3.3 + - - -
159E GLY* 3.0 23.8 + - - -
160E ALA* 4.2 1.4 - - - -
161E PRO 4.0 3.4 - - - +
162E ARG* 1.3 73.4 - - - +
164E GLY* 1.3 62.2 + - - +
165E LEU* 3.6 11.0 + - - +
166E ALA* 3.0 34.4 + - - +
167E GLU* 3.3 17.7 + - - +
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Residues in contact with GLY 164 (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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48E LEU* 5.8 0.2 - - - +
161E PRO 4.4 3.0 + - - -
162E ARG 3.5 6.1 + - - -
163E SER* 1.3 70.3 - - - +
165E LEU* 1.3 65.2 + - - +
167E GLU* 3.4 7.9 + - - +
168E TYR* 3.0 24.0 + - - +
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Residues in contact with LEU 165 (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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165C LEU* 4.9 13.5 - - + -
163E SER* 3.2 8.6 + - - +
164E GLY* 1.3 74.5 - - - +
166E ALA* 1.3 59.7 + - - +
168E TYR* 3.2 13.1 + - + +
169E LEU* 2.8 63.5 + - + +
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Residues in contact with ALA 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 5.1 4.9 - - + +
155E LEU* 4.8 1.8 - - + -
158E MET* 3.3 54.3 - - + +
160E ALA* 3.9 11.9 - - + +
163E SER* 3.0 24.3 + - - +
164E GLY 3.3 0.2 - - - -
165E LEU* 1.3 74.8 - - - +
167E GLU* 1.3 59.5 + - - +
169E LEU* 4.9 0.4 - - - -
170E PHE* 2.9 28.0 + - - +
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Residues in contact with GLU 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LEU* 4.1 21.3 - - + +
51E PHE* 3.7 7.4 - - + -
95E SER* 3.5 14.7 - - - -
96E GLY* 2.9 28.4 + - - -
97E LEU* 2.8 24.8 + - - +
155E LEU* 4.3 10.9 - - + +
160E ALA* 3.7 22.3 - - + +
161E PRO* 3.9 6.3 - - + +
163E SER 3.3 13.2 + - - +
164E GLY* 3.9 8.3 - - - +
165E LEU 3.3 0.4 - - - -
166E ALA* 1.3 75.8 - - - +
168E TYR* 1.3 57.0 + - - +
170E PHE 3.5 0.2 + - - -
171E ASP* 2.9 29.8 + - - +
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Residues in contact with TYR 168 (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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48E LEU* 4.1 15.4 - - + +
164E GLY 3.0 14.7 + - - +
165E LEU* 3.4 17.5 - - + +
167E GLU* 1.3 75.7 - - - +
169E LEU* 1.3 84.4 + - + +
171E ASP 3.3 1.2 + - - -
172E LYS* 3.0 74.2 + - + +
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Residues in contact with LEU 169 (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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165C LEU* 4.3 20.6 - - + -
168C TYR* 4.3 1.8 - - - -
169C LEU* 4.4 17.9 - - + -
158E MET* 4.1 8.3 - - + -
165E LEU* 2.8 49.9 + - + +
166E ALA 4.0 2.2 - - - +
168E TYR* 1.3 93.3 - - + +
170E PHE* 1.3 56.1 + - - +
172E LYS* 3.2 0.8 + - - +
173E HIS* 2.8 61.2 + - + +
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Residues in contact with PHE 170 (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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168C TYR* 3.5 17.3 - + - -
51E PHE* 3.6 21.3 - + - -
100E MET* 4.5 2.2 - - + -
151E HIS* 3.5 41.5 - + + -
154E ASN* 3.9 22.0 - - + -
155E LEU* 3.6 25.1 - - + -
158E MET* 3.8 11.7 - - + +
166E ALA 2.9 17.7 + - - +
167E GLU 3.7 2.2 - - - +
169E LEU* 1.3 72.2 - - - +
171E ASP* 1.3 66.9 + - - +
174E THR* 2.9 47.2 + - + -
175E LEU* 3.2 31.9 + - + -
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Residues in contact with ASP 171 (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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48E LEU* 3.4 19.5 - - + +
49E LYS* 4.3 3.1 + - - +
50E ASN* 2.9 53.7 + - - +
51E PHE* 3.0 25.0 + - + -
167E GLU 2.9 17.7 + - - +
168E TYR 3.3 5.8 - - - +
170E PHE* 1.3 77.3 - - - +
172E LYS* 1.3 81.6 + - - +
175E LEU* 3.6 5.1 - - - -
176E GLY 3.1 22.9 + - - -
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Residues in contact with LYS 172 (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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48E LEU* 4.8 3.4 - - - +
49E LYS* 5.9 1.3 - - - +
50E ASN* 4.3 7.4 - - - +
168E TYR* 3.0 68.8 + - + +
169E LEU 3.7 5.4 - - - +
171E ASP* 1.3 106.3 + - - +
173E HIS* 1.3 74.8 + - + +
176E GLY* 3.4 21.0 - - - -
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Residues in contact with HIS 173 (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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173B HIS* 4.5 6.8 + + - -
168C TYR* 3.4 14.3 - + + +
169C LEU* 4.5 4.8 - - + +
172C LYS* 3.3 33.5 + - + +
173C HIS* 3.2 38.7 + + - -
169E LEU* 2.8 54.0 + - + +
172E LYS* 1.3 84.1 - - + +
174E THR* 1.3 61.5 + - - +
176E GLY 4.6 3.3 - - - -
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Residues in contact with THR 174 (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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168C TYR* 2.7 27.2 + - - -
172C LYS* 3.3 18.2 + - - +
151E HIS* 3.8 20.9 - - + +
170E PHE* 2.9 39.3 + - + -
173E HIS* 1.3 78.2 - - - +
175E LEU* 1.3 64.9 + - + +
176E GLY 3.2 4.8 + - - -
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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