Contacts of the strand formed by residues 162 - 166 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D SER* 3.6 36.1 - - - +
127D MET* 3.8 22.7 - - + -
130D ALA* 4.0 10.8 - - + -
137D VAL* 3.4 22.4 - - + +
139D GLY 5.0 0.4 - - - +
153D ILE* 3.5 31.4 - - + +
158D LEU* 2.9 31.9 + - + +
159D ASP* 3.2 20.6 - - - +
161D ILE* 1.3 72.5 - - - +
163D THR* 1.3 66.6 + - - +
164D ILE* 3.9 14.0 + - + +
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Residues in contact with THR 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D LYS* 3.5 21.8 + - - -
137D VAL 2.9 6.7 + - - -
138D PHE* 3.3 20.1 - - - -
139D GLY 3.0 22.9 + - - +
159D ASP 4.9 1.7 + - - -
162D ILE* 1.3 76.4 + - - +
164D ILE* 1.3 69.1 - - - +
165D PHE* 4.0 22.6 - - + -
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Residues in contact with ILE 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D SER* 3.9 18.4 - - - +
123D GLY* 5.4 0.4 - - - -
126D SER* 5.0 2.9 - - - +
139D GLY* 3.4 18.2 - - - +
141D GLU* 5.0 1.1 - - + -
146D SER* 4.2 17.3 - - - +
149D SER* 3.6 26.9 - - - +
150D GLU* 3.8 32.0 + - + +
153D ILE* 3.7 29.4 - - + -
162D ILE* 3.9 11.4 - - + +
163D THR* 1.3 80.5 - - - +
165D PHE* 1.3 74.6 + - - +
166D LYS* 3.9 3.3 + - + +
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Residues in contact with PHE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D PHE* 3.9 22.4 - + + -
139D GLY 2.8 14.7 + - - +
140D ILE* 3.6 5.9 - - + +
141D GLU 3.2 24.9 + - - +
163D THR* 4.0 26.2 - - + -
164D ILE* 1.3 76.8 - - - +
166D LYS* 1.3 62.9 + - - +
167D GLY 3.3 1.4 + - - -
172D VAL* 4.4 22.7 - - + -
173D GLU 4.1 18.4 - - - -
174D LEU* 3.8 24.0 - - + -
175D PRO* 3.5 26.0 - - + -
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Residues in contact with LYS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D GLU 3.5 3.8 - - - +
142D CYS 4.4 8.0 + - - +
143D SER 4.2 6.0 - - - +
144D SER* 3.9 21.1 - - - +
146D SER* 2.8 28.9 - - - +
147D ASP* 3.2 30.6 + - - +
150D GLU* 5.9 6.1 - - - +
164D ILE* 3.9 4.2 + - + +
165D PHE* 1.3 68.0 - - - +
167D GLY* 1.3 59.0 + - - +
172D VAL* 4.4 3.9 - - - +
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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