Contacts of the strand formed by residues 162 - 166 (chain J) in PDB entry 5DST
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 ILE 162 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126J SER* 3.5 37.2 - - - +
127J MET* 3.8 22.9 - - + -
130J ALA* 3.9 17.5 - - + -
137J VAL* 3.3 17.3 - - + +
139J GLY 5.1 0.7 - - - +
153J ILE* 3.6 29.6 - - + +
158J LEU* 2.9 25.3 + - + +
159J ASP* 2.9 22.0 - - - +
161J ILE* 1.3 73.3 - - - +
163J THR* 1.3 68.4 + - - +
164J ILE* 3.9 13.2 - - + -
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Residues in contact with THR 163 (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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136J LYS* 3.5 21.8 + - - -
137J VAL 2.9 5.7 + - - -
138J PHE* 3.4 19.5 - - - -
139J GLY 3.0 22.5 + - - +
159J ASP 4.8 1.0 + - - -
162J ILE* 1.3 78.3 + - - +
164J ILE* 1.3 70.3 + - - +
165J PHE* 4.0 22.9 - - + -
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Residues in contact with ILE 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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120J SER* 3.8 22.4 - - - +
123J GLY* 5.4 0.7 - - - -
126J SER* 4.9 3.1 - - - +
139J GLY* 3.3 16.8 - - - +
141J GLU* 5.0 1.1 - - + -
146J SER* 4.2 17.5 - - - -
149J SER* 3.6 23.3 - - - +
150J GLU* 4.0 31.0 + - + +
153J ILE* 3.8 29.2 - - + -
162J ILE* 3.9 11.7 - - + -
163J THR* 1.3 78.9 - - - +
165J PHE* 1.3 75.1 + - - +
166J LYS* 3.9 2.9 + - + +
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Residues in contact with PHE 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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138J PHE* 3.8 24.0 - + + -
139J GLY 2.6 17.4 + - - +
140J ILE* 3.5 5.9 - - + +
141J GLU 3.3 19.2 + - - -
163J THR* 4.0 25.4 - - + -
164J ILE* 1.3 76.6 - - - +
166J LYS* 1.3 61.0 + - - +
167J GLY 3.1 7.6 + - - -
172J VAL* 4.3 22.2 - - + -
173J GLU 4.3 13.2 - - - -
174J LEU* 3.7 25.4 - - + -
175J PRO* 3.5 29.8 - - + -
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Residues in contact with LYS 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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141J GLU 3.5 4.0 - - - +
142J CYS 4.6 6.9 + - - +
143J SER 4.2 5.3 - - - +
144J SER* 3.8 23.1 - - - +
146J SER* 2.9 30.3 - - - +
147J ASP* 3.2 29.6 + - - +
150J GLU* 6.1 2.9 - - - +
164J ILE* 3.9 4.2 + - + +
165J PHE* 1.3 68.4 - - - +
167J GLY* 1.3 59.2 + - - +
172J VAL* 4.4 4.4 - - - +
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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