Contacts of the helix formed by residues 164 - 171 (chain S) in PDB entry 5JBA
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 ASP 164 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162S LEU* 4.3 1.1 + - - -
163S VAL* 1.3 79.8 - - - +
165S ARG* 1.3 59.9 + - - +
166S ALA* 3.3 13.5 + - - +
167S THR* 2.4 42.9 + - - -
168S CYS* 2.9 25.1 + - - +
170S ARG* 5.2 0.3 + - - -
185S HIS* 5.6 1.9 - - - -
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Residues in contact with ARG 165 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163S VAL 3.6 2.3 + - - -
164S ASP* 1.3 74.6 - - - +
166S ALA* 1.3 63.0 + - - +
168S CYS* 3.1 12.3 - - + +
169S LEU* 2.9 41.0 + - + +
176S ILE* 3.1 24.8 + - - +
177S THR 2.4 36.3 + - - -
178S ASN* 3.2 13.2 + - - +
180S MET 2.9 24.7 + - - -
181S PHE* 4.6 4.4 - - - +
230S LYS* 4.3 10.2 - - - +
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Residues in contact with ALA 166 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164S ASP* 3.3 11.5 + - - +
165S ARG* 1.3 77.7 - - - +
167S THR* 1.3 62.7 + - - +
169S LEU* 3.4 11.4 + - - +
170S ARG* 3.1 45.3 + - - +
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Residues in contact with THR 167 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163S VAL* 3.8 11.0 - - + -
164S ASP* 2.4 31.2 + - - -
166S ALA* 1.3 78.8 - - - +
168S CYS* 1.3 64.1 + - - +
170S ARG* 3.3 23.8 + - + +
171S SER* 3.2 21.4 + - - -
185S HIS* 4.4 8.1 - - + -
225S TYR* 3.8 25.4 - - + +
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Residues in contact with CYS 168 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163S VAL* 4.1 2.6 - - - +
164S ASP 2.9 13.2 + - - +
165S ARG* 3.1 21.1 - - + +
167S THR* 1.3 75.3 - - - +
169S LEU* 1.3 58.1 + - + +
171S SER* 2.5 24.9 + - - -
172S THR* 4.0 8.0 - - - +
176S ILE* 3.7 29.2 - - - -
181S PHE* 4.9 0.7 - - - -
182S CYS* 2.1 62.3 - - + -
225S TYR* 4.9 0.4 - - - -
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Residues in contact with LEU 169 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165S ARG* 2.9 33.2 + - + +
166S ALA* 3.7 10.3 - - - +
168S CYS* 1.3 76.9 - - - +
170S ARG* 1.3 58.4 + - + +
171S SER 3.2 0.2 + - - -
172S THR* 3.1 23.7 - - - +
174S PHE 5.3 1.2 - - - +
176S ILE* 3.7 42.8 - - + +
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Residues in contact with ARG 170 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164S ASP* 5.2 0.2 + - - -
166S ALA* 3.1 32.5 + - - +
167S THR* 3.3 33.8 + - - +
169S LEU* 1.3 80.6 - - + +
171S SER* 1.3 60.2 + - - +
172S THR 3.3 2.1 + - - +
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Residues in contact with SER 171 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167S THR 3.2 10.2 + - - -
168S CYS* 2.5 21.7 + - - -
169S LEU 3.1 0.8 - - - -
170S ARG* 1.3 78.5 - - - +
172S THR* 1.3 63.5 + - - +
182S CYS* 4.6 3.6 - - - -
223S GLY 3.4 21.3 - - - +
224S LYS* 2.8 28.8 + - - +
225S TYR* 3.7 24.8 + - - -
227S ILE* 5.5 1.4 - - - +
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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