Contacts of the helix formed by residues 163 - 174 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158J MET 4.5 3.3 + - - -
159J GLY* 3.0 23.2 + - - -
160J ALA* 4.2 1.6 - - - -
161J PRO 3.9 5.9 - - - +
162J GLU* 1.3 75.3 - - - +
164J GLY* 1.3 61.1 + - - +
165J LEU* 3.6 10.0 + - - +
166J ALA* 2.8 38.1 + - - +
167J GLU* 3.5 9.5 + - - +
165K LEU* 5.9 2.1 - - - +
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Residues in contact with GLY 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H LYS* 3.4 38.4 + - - +
158H MET* 4.6 0.2 - - - -
161J PRO 4.4 2.6 + - - -
162J GLU 3.4 6.9 + - - -
163J SER* 1.3 68.9 - - - +
165J LEU* 1.3 59.2 + - - +
167J GLU* 3.3 8.4 + - - +
168J TYR* 3.0 29.9 + - - +
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Residues in contact with LEU 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H LYS 3.6 7.1 + - - -
158H MET* 3.8 50.7 - - + +
165H LEU* 4.9 14.8 - - + -
166H ALA* 5.2 4.7 - - - +
169H LEU* 4.3 14.6 - - + -
163J SER* 3.6 8.7 - - - +
164J GLY* 1.3 75.3 - - - +
166J ALA* 1.4 56.4 + - - +
168J TYR* 3.3 4.0 + - - +
169J LEU* 2.9 58.2 + - + +
165K LEU* 5.0 12.6 - - + -
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Residues in contact with ALA 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J LEU* 4.8 1.3 - - + -
158J MET* 3.2 55.4 - - + +
160J ALA* 4.0 11.0 - - + +
163J SER* 2.8 28.0 + - - +
165J LEU* 1.4 72.6 - - - +
167J GLU* 1.3 64.1 + - - +
169J LEU* 3.3 0.8 + - - -
170J PHE* 3.0 21.9 + - - +
165K LEU* 5.2 4.7 - - - +
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Residues in contact with GLU 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J LEU* 4.2 20.9 - - + +
51J PHE* 3.7 7.4 - - + -
95J SER* 3.6 13.8 - - - -
96J GLY* 2.8 28.8 + - - -
97J LEU* 2.9 24.5 + - - +
155J LEU* 4.2 10.1 - - + -
160J ALA* 3.6 26.7 - - + +
161J PRO* 3.9 7.0 - - - +
163J SER 3.5 7.8 + - - +
164J GLY* 3.3 9.9 + - - +
166J ALA* 1.3 75.9 - - - +
168J TYR* 1.3 63.4 - - - +
171J ASP* 2.9 25.8 + - - +
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Residues in contact with TYR 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H ASN* 3.4 24.9 - - - +
158H MET* 3.4 46.7 - - + -
169H LEU 4.5 2.7 - - - -
170H PHE* 3.5 15.7 - + - -
173H HIS* 3.4 20.9 - - + +
174H THR* 2.7 29.9 + - - -
48J LEU* 4.1 10.6 - - + +
164J GLY 3.0 17.0 + - - +
165J LEU 3.5 3.8 - - - +
166J ALA 3.3 0.2 - - - -
167J GLU* 1.3 77.0 - - - +
169J LEU* 1.3 81.7 + - + +
171J ASP 3.3 1.0 + - - -
172J LYS* 3.1 63.4 + - + +
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Residues in contact with LEU 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H LEU* 4.4 18.2 - - + -
173H HIS* 4.5 4.5 - - + +
204H CL 4.0 8.7 - - + -
158J MET* 4.0 10.1 - - + -
165J LEU* 2.9 41.3 + - + +
166J ALA 4.0 2.9 - - - +
168J TYR* 1.3 94.3 - - + +
170J PHE* 1.3 57.1 + - - +
172J LYS* 3.3 1.7 + - + +
173J HIS* 2.8 60.5 + - + +
165K LEU* 4.2 21.8 - - + -
168K TYR* 4.3 0.7 - - - -
169K LEU* 4.3 16.4 - - + -
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Residues in contact with PHE 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J PHE* 3.6 23.1 - + - -
100J MET* 4.4 4.0 - - + -
151J HIS* 3.6 31.6 - + + -
154J ASN* 3.8 22.0 - - + -
155J LEU* 3.5 23.3 - - + -
158J MET* 3.7 17.0 - - - +
166J ALA 3.0 18.1 + - - +
167J GLU 3.8 1.8 - - - +
169J LEU* 1.3 72.3 - - - +
171J ASP* 1.3 64.8 + - - +
174J THR* 2.9 55.4 + - + -
175J LEU* 3.3 29.2 + - + -
168K TYR* 3.5 10.5 - + - -
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Residues in contact with ASP 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J LEU* 3.3 18.8 - - + -
49J LYS* 4.3 3.2 + - - +
50J ASN* 2.9 57.4 + - - +
51J PHE* 3.0 27.0 + - + -
167J GLU 2.9 17.5 + - - +
168J TYR 3.4 5.2 - - - +
169J LEU 3.3 0.2 - - - -
170J PHE* 1.3 75.9 - - - +
172J LYS* 1.3 81.5 + - - +
175J LEU* 3.6 5.1 + - - -
176J GLY 3.1 23.2 + - - -
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Residues in contact with LYS 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H ASN* 5.0 1.0 + - - -
173H HIS* 4.0 33.7 - - + +
174H THR* 3.8 10.1 - - - +
47J ALA 5.8 0.6 + - - -
48J LEU* 4.8 3.0 - - - +
50J ASN* 4.3 8.5 - - - +
168J TYR* 3.1 56.9 + - + +
169J LEU* 3.3 6.0 + - - +
170J PHE 3.2 0.2 - - - -
171J ASP* 1.3 107.9 + - - +
173J HIS* 1.3 74.5 + - + +
176J GLY* 3.6 18.0 - - - +
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Residues in contact with HIS 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H HIS* 3.1 18.1 + + - -
202H FE 2.3 31.7 - - - -
204H CL 3.2 15.0 - - + -
169J LEU* 2.8 41.6 + - + +
172J LYS* 1.3 77.7 - - + +
174J THR* 1.3 62.0 + - - +
176J GLY 4.7 2.1 - - - -
168K TYR* 3.3 15.7 - + + +
169K LEU* 4.5 4.6 - - + +
172K LYS* 4.0 28.7 - - + +
173K HIS* 3.1 17.5 + + - -
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Residues in contact with THR 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151J HIS* 3.7 21.3 - - + +
154J ASN* 5.7 0.8 + - - +
170J PHE* 2.9 41.1 + - + -
173J HIS* 1.3 78.5 - - - +
175J LEU* 1.3 66.4 + - + +
176J GLY 3.3 4.4 + - - -
168K TYR* 2.7 30.8 + - - -
172K LYS* 3.8 7.9 - - - +
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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