Contacts of the helix formed by residues 163 - 174 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158B MET 4.4 3.1 + - - -
159B GLY* 3.1 24.1 + - - -
160B ALA* 4.2 1.2 - - - -
161B PRO 3.2 3.6 - - - +
162B ARG* 1.3 72.5 - - - +
164B GLY* 1.3 63.2 + - - +
165B LEU* 3.5 12.0 + - - +
166B ALA* 2.9 34.8 + - - +
167B GLU* 3.4 16.5 + - - +
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Residues in contact with GLY 164 (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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48B LEU* 5.8 0.2 - - - +
161B PRO 4.2 3.5 + - - -
162B ARG 3.4 7.1 + - - -
163B SER* 1.3 73.3 - - - +
165B LEU* 1.3 58.4 + - - +
167B GLU* 3.4 8.3 + - - +
168B TYR* 3.0 28.4 + - - +
157C LYS* 3.4 35.8 + - - +
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Residues in contact with LEU 165 (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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163B SER* 3.1 9.5 + - - +
164B GLY* 1.3 73.8 - - - +
166B ALA* 1.3 59.7 + - - +
168B TYR* 3.3 3.4 + - - +
169B LEU* 2.9 57.1 + - + +
157C LYS 3.4 5.7 + - - -
158C MET* 3.8 52.3 - - + +
163C SER* 5.7 2.9 - - - +
165C LEU* 5.0 14.1 - - + -
166C ALA* 5.1 3.1 - - - -
169C LEU* 4.2 13.9 - - + -
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Residues in contact with ALA 166 (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 LEU* 4.7 2.0 - - + +
158B MET* 3.3 53.2 - - + +
160B ALA* 3.9 13.2 - - + +
163B SER* 2.9 23.3 + - - +
165B LEU* 1.3 76.3 - - - +
167B GLU* 1.3 63.7 + - - +
169B LEU* 3.4 1.7 + - - -
170B PHE* 3.0 22.3 + - - +
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Residues in contact with GLU 167 (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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48B LEU* 4.1 20.7 - - + +
51B PHE* 3.8 5.1 - - + -
95B SER* 3.6 14.7 - - - -
96B GLY* 2.9 28.4 + - - -
97B LEU* 2.9 22.2 + - - +
155B LEU* 4.2 11.6 - - + +
160B ALA* 3.5 21.6 - - + +
161B PRO* 3.8 7.1 - - - +
163B SER 3.4 13.6 + - - +
164B GLY* 3.4 8.9 + - - +
165B LEU 3.3 0.4 - - - -
166B ALA* 1.3 76.1 - - - +
168B TYR* 1.3 58.7 + - - +
170B PHE* 3.4 1.2 + - - +
171B ASP* 2.9 32.1 + - - +
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Residues in contact with TYR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.0 10.1 - - + +
164B GLY 3.0 14.5 + - - +
165B LEU 3.5 7.0 - - - +
167B GLU* 1.3 77.8 - - - +
169B LEU* 1.3 81.5 + - + +
171B ASP* 3.4 0.2 - - - +
172B LYS* 3.1 59.0 + - + +
154C ASN* 3.4 25.6 - - - +
158C MET* 3.4 48.2 - - + -
169C LEU 4.5 2.2 - - - -
170C PHE* 3.5 13.9 - + - -
173C HIS* 3.4 20.1 - - + +
174C THR* 2.6 32.3 + - - -
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Residues in contact with LEU 169 (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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158B MET* 4.0 13.2 - - + -
165B LEU* 2.9 41.8 + - + +
166B ALA* 4.0 3.4 - - - +
168B TYR* 1.3 96.2 - - + +
170B PHE* 1.3 57.3 + - - +
172B LYS* 3.2 1.4 + - - -
173B HIS* 2.9 60.1 + - + +
169C LEU* 4.4 21.8 - - + -
173C HIS* 4.5 8.7 - - + -
169E LEU* 6.5 0.7 - - + -
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Residues in contact with PHE 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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51B PHE* 3.7 19.7 - + - -
100B MET* 4.4 2.2 - - + -
151B HIS* 3.5 40.2 - + + -
154B ASN* 3.8 23.3 - - + -
155B LEU* 3.7 27.6 - - + -
158B MET* 3.8 20.3 - - - +
166B ALA 3.0 18.1 + - - +
167B GLU 3.8 2.2 - - - +
169B LEU* 1.3 73.7 - - - +
171B ASP* 1.3 64.6 + - - +
173B HIS* 4.5 0.7 - - - +
174B THR* 2.9 48.4 + - + +
175B LEU* 3.1 32.1 + - + -
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Residues in contact with ASP 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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48B LEU* 3.3 19.1 - - + +
49B LYS* 4.2 4.5 + - - +
50B ASN* 2.8 59.9 + - - +
51B PHE* 3.1 26.3 + - + -
167B GLU 2.9 18.8 + - - +
168B TYR 3.4 5.4 - - - +
170B PHE* 1.3 76.5 - - - +
172B LYS* 1.3 84.8 + - - +
175B LEU* 3.6 5.3 - - - +
176B GLY 3.2 11.8 + - - -
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Residues in contact with LYS 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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47B ALA 5.6 0.8 + - - -
48B LEU* 4.5 3.6 - - - +
50B ASN* 4.4 7.9 - - - +
168B TYR* 3.1 60.6 + - + +
169B LEU* 3.7 5.4 - - - +
170B PHE 3.2 0.4 - - - -
171B ASP* 1.3 105.7 + - - +
173B HIS* 1.3 76.3 + - + +
176B GLY* 3.5 20.6 - - - -
154C ASN* 5.0 0.8 + - - -
173C HIS* 4.0 33.4 - - + +
174C THR* 4.0 8.3 - - - -
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Residues in contact with HIS 173 (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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169B LEU* 2.9 50.2 + - + +
170B PHE* 5.3 0.4 - - - -
172B LYS* 1.3 84.0 - - + +
174B THR* 1.3 60.6 + - - +
176B GLY 4.6 1.1 - - - -
173C HIS* 3.2 37.2 + + - -
173E HIS* 4.5 6.8 + + - -
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Residues in contact with THR 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 HIS* 3.8 20.6 - - + +
154B ASN* 5.7 2.1 - - - +
170B PHE* 2.9 49.9 + - + -
173B HIS* 1.3 78.2 + - - +
175B LEU* 1.3 67.1 + - + +
176B GLY 3.4 5.0 + - - +
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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