Contacts of the helix formed by residues 163 - 174 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158F MET 4.4 3.2 + - - -
159F GLY* 3.1 20.5 + - - -
160F ALA* 4.2 1.6 - - - -
161F PRO 4.0 2.4 - - - +
162F ARG* 1.3 77.5 - - - +
164F GLY* 1.3 61.7 + - - +
165F LEU* 3.5 11.1 + - - +
166F ALA* 2.9 33.5 + - - +
167F GLU* 3.4 16.1 + - - +
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Residues in contact with GLY 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 5.8 0.3 - - - +
161F PRO 4.2 2.8 + - - -
162F ARG 3.3 8.1 + - - -
163F SER* 1.3 72.7 - - - +
165F LEU* 1.3 57.8 + - - +
167F GLU* 3.4 7.7 + - - +
168F TYR* 3.0 28.1 + - - +
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Residues in contact with LEU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F SER* 3.2 8.9 + - - +
164F GLY* 1.3 72.9 - - - +
166F ALA* 1.3 65.6 + - - +
168F TYR* 3.3 14.0 + - + +
169F LEU* 2.9 57.5 + - + +
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Residues in contact with ALA 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F LEU* 4.8 1.6 - - + -
158F MET* 3.3 48.0 - - + +
160F ALA* 3.9 12.3 - - + +
163F SER* 2.9 27.9 + - - +
165F LEU* 1.3 77.1 - - - +
167F GLU* 1.3 64.1 + - - +
169F LEU* 4.8 1.8 - - - -
170F PHE* 3.0 21.7 + - - +
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Residues in contact with GLU 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 4.2 21.7 - - + +
51F PHE* 3.7 7.0 - - + -
95F SER* 3.7 14.0 - - - -
96F GLY* 2.8 27.0 + - - -
97F LEU* 2.8 24.9 + - - +
155F LEU* 4.2 11.4 - - + +
160F ALA* 3.5 26.0 - - + +
161F PRO* 4.0 6.6 - - - +
163F SER 3.4 8.5 + - - +
164F GLY* 3.4 7.6 + - - +
165F LEU 3.4 0.6 - - - -
166F ALA* 1.3 76.2 - - - +
168F TYR* 1.3 64.4 + - - +
170F PHE 3.4 0.2 + - - -
171F ASP* 2.9 25.5 + - - +
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Residues in contact with TYR 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 4.0 15.8 - - + +
164F GLY 3.0 18.1 + - - +
165F LEU* 3.3 14.1 + - + +
167F GLU* 1.3 78.4 - - - +
169F LEU* 1.3 82.9 + - + +
172F LYS* 3.0 74.6 + - + +
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Residues in contact with LEU 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F MET* 4.0 14.8 - - + -
165F LEU* 2.9 50.6 + - + +
166F ALA* 4.0 3.4 - - - +
168F TYR* 1.3 89.4 - - + +
170F PHE* 1.3 60.2 + - - +
172F LYS* 3.3 1.2 + - - +
173F HIS* 2.9 59.7 + - + +
204F CL 3.9 10.3 - - + -
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Residues in contact with PHE 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F PHE* 3.6 20.4 - + - -
100F MET* 4.4 2.0 - - + -
151F HIS* 3.6 33.4 - + + -
154F ASN* 3.9 22.7 - - + -
155F LEU* 3.6 26.0 - - + -
158F MET* 3.7 22.3 - - - +
166F ALA 3.0 18.1 + - - +
167F GLU 3.8 1.6 - - - +
169F LEU* 1.3 71.5 - - - +
171F ASP* 1.3 66.1 + - - +
173F HIS* 4.5 0.9 - - - +
174F THR* 3.0 55.0 + - + +
175F LEU* 3.2 30.9 + - + -
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Residues in contact with ASP 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 3.3 17.2 - - + -
49F LYS* 4.3 2.3 + - - +
50F ASN* 2.9 50.4 + - - +
51F PHE* 3.0 27.8 + - + -
167F GLU 2.9 19.0 + - - +
168F TYR 3.5 5.4 - - - +
169F LEU 3.3 0.2 - - - -
170F PHE* 1.3 77.2 - - - +
172F LYS* 1.3 83.5 + - - +
175F LEU* 3.6 5.0 - - - -
176F GLY 3.1 19.9 + - - -
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Residues in contact with LYS 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 4.5 4.2 - - - +
50F ASN* 4.3 8.3 - - - +
168F TYR* 3.0 77.3 + - + +
169F LEU* 3.3 4.9 + - - +
170F PHE 3.2 0.2 - - - -
171F ASP* 1.3 107.9 + - - +
173F HIS* 1.3 75.5 + - + +
176F GLY* 3.6 18.0 + - - -
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Residues in contact with HIS 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F LEU* 2.9 42.2 + - + +
170F PHE* 5.2 0.4 - - - -
172F LYS* 1.3 89.1 - - + +
174F THR* 1.3 65.8 + - - +
176F GLY 4.7 3.4 - - - +
202F FE 2.2 31.5 - - - -
204F CL 3.2 16.4 - - + -
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Residues in contact with THR 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F HIS* 3.7 22.0 - - + +
154F ASN* 5.7 1.7 - - - +
170F PHE* 3.0 49.4 + - + -
173F HIS* 1.3 82.2 + - - +
175F LEU* 1.3 65.7 + - + +
176F GLY 3.4 5.8 + - - +
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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