Contacts of the helix formed by residues 163 - 174 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158L MET 4.3 3.0 + - - -
159L GLY* 3.0 23.3 + - - -
160L ALA* 4.3 1.7 - - - -
161L PRO 3.9 5.4 - - - +
162L GLU* 1.3 73.4 - - - +
164L GLY* 1.3 62.4 + - - +
165L LEU* 3.6 10.0 + - - +
166L ALA* 3.0 38.2 + - - +
167L GLU* 3.4 10.6 + - - +
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Residues in contact with GLY 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L LEU* 5.8 0.2 - - - +
161L PRO 4.2 2.8 + - - -
162L GLU 3.2 8.3 + - - -
163L SER* 1.3 69.4 - - - +
165L LEU* 1.3 60.5 + - - +
167L GLU* 3.4 7.7 + - - +
168L TYR* 3.0 29.0 + - - +
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Residues in contact with LEU 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163L SER* 3.7 8.5 - - - +
164L GLY* 1.3 74.6 - - - +
166L ALA* 1.3 58.9 + - - +
168L TYR* 3.3 12.4 + - + +
169L LEU* 2.9 62.2 + - + +
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Residues in contact with ALA 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L LEU* 4.8 1.3 - - + -
158L MET* 3.4 54.6 - - + +
160L ALA* 3.9 10.8 - - + +
163L SER* 3.0 25.0 + - - +
165L LEU* 1.3 75.9 - - - +
167L GLU* 1.3 57.3 + - - +
169L LEU* 4.8 1.6 - - - -
170L PHE* 2.9 27.9 + - - +
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Residues in contact with GLU 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L LEU* 4.2 21.2 - - + +
51L PHE* 3.8 6.7 - - + -
95L SER* 3.6 14.8 - - - -
96L GLY* 2.9 27.3 + - - -
97L LEU* 2.9 24.0 + - - +
155L LEU* 4.1 11.9 - - + -
160L ALA* 3.6 25.4 - - + +
161L PRO* 4.1 6.6 - - - +
163L SER 3.4 6.9 + - - +
164L GLY* 3.4 10.3 + - - +
165L LEU 3.4 0.2 - - - -
166L ALA* 1.3 72.5 - - - +
168L TYR* 1.3 65.2 + - - +
170L PHE 3.5 0.2 + - - -
171L ASP* 3.0 25.6 + - - +
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Residues in contact with TYR 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L LEU* 4.0 15.6 - - + +
164L GLY 3.0 17.8 + - - +
165L LEU* 3.6 14.4 - - + +
166L ALA 3.3 0.2 - - - -
167L GLU* 1.3 77.4 - - - +
169L LEU* 1.3 82.2 + - + +
172L LYS* 3.1 71.3 + - + +
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Residues in contact with LEU 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158L MET* 4.0 15.3 - - + -
165L LEU* 2.9 47.0 + - + +
166L ALA* 5.2 0.7 - - - +
168L TYR* 1.3 93.5 - - + +
170L PHE* 1.3 57.6 + - - +
172L LYS* 3.2 1.9 + - + -
173L HIS* 2.9 59.4 + - + +
204L CL 4.1 9.9 - - + -
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Residues in contact with PHE 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L PHE* 3.6 23.3 - + - -
100L MET* 4.5 2.2 - - + -
151L HIS* 3.6 40.8 - + + -
154L ASN* 3.9 22.0 - - + -
155L LEU* 3.6 23.6 - - + -
158L MET* 3.7 22.1 - - - +
166L ALA 2.9 16.7 + - - +
167L GLU 3.8 1.1 - - - +
169L LEU* 1.3 75.3 - - - +
171L ASP* 1.3 65.3 + - - +
173L HIS* 5.2 1.1 - - - -
174L THR* 2.9 51.2 + - + +
175L LEU* 3.3 30.9 + - + -
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Residues in contact with ASP 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L LEU* 3.2 21.8 - - + +
49L LYS* 4.3 2.8 + - - +
50L ASN* 2.9 51.0 + - - +
51L PHE* 3.0 25.4 + - + -
167L GLU 3.0 18.7 + - - +
168L TYR 3.4 4.9 - - - +
169L LEU 3.3 0.2 - - - -
170L PHE* 1.3 75.6 - - - +
172L LYS* 1.3 82.8 + - - +
175L LEU* 3.6 5.4 + - - -
176L GLY 3.1 23.0 + - - -
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Residues in contact with LYS 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48L LEU* 4.6 4.0 - - - +
49L LYS* 5.6 5.4 - - - +
50L ASN* 4.3 8.1 - - - +
168L TYR* 3.1 66.0 + - + +
169L LEU* 3.8 5.8 - - + +
170L PHE 3.2 0.2 - - - -
171L ASP* 1.3 109.8 + - - +
173L HIS* 1.3 74.6 + - + +
176L GLY* 3.6 19.2 + - - +
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Residues in contact with HIS 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158L MET* 6.3 0.2 - - + -
169L LEU* 2.9 41.5 + - + +
170L PHE* 5.2 0.7 - - - -
172L LYS* 1.3 84.8 - - + +
174L THR* 1.3 64.5 + - - +
176L GLY 4.6 4.0 - - - +
202L FE 2.4 31.8 - - - -
204L CL 3.0 13.7 - - + +
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Residues in contact with THR 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151L HIS* 3.7 22.2 - - + +
154L ASN* 5.7 2.6 - - - +
170L PHE* 2.9 49.5 + - + -
173L HIS* 1.3 81.8 + - - +
175L LEU* 1.3 69.0 + - + +
176L GLY 3.3 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