Contacts of the strand formed by residues 162 - 166 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126E SER* 3.5 38.1 - - - +
127E MET* 3.7 22.9 - - + +
130E ALA* 3.9 13.0 - - + -
137E VAL* 3.3 22.9 - - + +
139E GLY 5.1 0.2 - - - +
153E ILE* 3.6 30.5 - - + +
158E LEU* 2.9 21.2 + - + +
159E ASP* 3.2 21.7 - - - +
161E ILE* 1.3 77.9 - - - +
163E THR* 1.3 67.8 + - - +
164E ILE* 4.0 12.8 - - + -
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Residues in contact with THR 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E LYS* 3.5 22.0 + - - -
137E VAL 2.9 6.3 + - - -
138E PHE* 3.3 20.2 - - - -
139E GLY 3.0 22.3 + - - +
159E ASP 4.9 1.4 + - - -
162E ILE* 1.3 77.3 + - - +
164E ILE* 1.3 69.4 + - - +
165E PHE* 4.0 22.0 - - + -
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Residues in contact with ILE 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E SER* 3.9 22.4 - - - +
123E GLY* 5.4 0.9 - - - -
126E SER* 5.0 2.5 - - - +
139E GLY* 3.4 16.8 - - - +
141E GLU* 5.0 1.1 - - + -
146E SER* 4.2 17.0 - - - -
149E SER* 3.6 22.4 - - - +
150E GLU* 3.8 34.2 + - + +
153E ILE* 3.7 29.2 - - + -
162E ILE* 4.0 11.0 - - + -
163E THR* 1.3 81.3 - - - +
165E PHE* 1.3 75.4 + - - +
166E LYS* 3.8 3.4 + - + +
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Residues in contact with PHE 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E PHE* 3.9 23.1 - + + -
139E GLY 2.7 18.1 + - - +
140E ILE* 3.5 5.3 - - + +
141E GLU 3.2 20.1 + - - -
163E THR* 4.0 24.0 - - + -
164E ILE* 1.3 75.9 - - - +
166E LYS* 1.3 60.9 + - - +
167E GLY* 3.1 8.1 + - - -
172E VAL* 4.2 23.1 - - + -
173E GLU 4.1 17.9 - - - -
174E LEU* 3.8 24.5 - - + -
175E PRO* 3.6 26.7 - - + -
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Residues in contact with LYS 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E GLU 3.5 4.5 - - - +
142E CYS 4.6 6.7 + - - +
143E SER 4.2 4.9 - - - +
144E SER* 3.8 23.1 - - - +
146E SER* 2.9 35.7 - - - +
147E ASP* 3.4 26.9 + - - +
150E GLU* 6.0 4.9 - - - +
164E ILE* 3.8 5.7 + - + +
165E PHE* 1.3 67.7 - - - +
167E GLY* 1.3 59.3 + - - +
172E VAL* 4.4 4.8 - - - +
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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