Contacts of the strand formed by residues 162 - 166 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126G SER* 3.7 29.8 - - - +
127G MET* 3.8 29.8 - - + +
130G ALA* 4.1 8.7 - - + -
137G VAL* 3.3 20.9 - - + +
139G GLY 4.9 0.4 - - - +
153G ILE* 3.6 30.9 - - + +
158G LEU* 3.0 23.0 + - + +
159G ASP* 3.1 20.6 - - - +
161G ILE* 1.3 78.1 - - - +
163G THR* 1.3 67.4 + - - +
164G ILE* 3.9 13.7 - - + -
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Residues in contact with THR 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G LYS* 3.7 19.4 + - - -
137G VAL 3.0 6.1 + - - -
138G PHE* 3.4 20.0 - - + -
139G GLY 3.0 22.0 + - - +
159G ASP 4.8 1.6 + - - -
162G ILE* 1.3 77.1 + - - +
164G ILE* 1.3 70.7 + - - +
165G PHE* 4.0 22.6 - - + -
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Residues in contact with ILE 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G SER* 4.0 15.9 - - - +
123G GLY* 5.4 0.9 - - - -
126G SER* 5.0 2.5 - - - +
139G GLY* 3.4 20.4 - - - +
141G GLU* 5.0 0.9 - - + -
146G SER* 4.3 15.3 - - - -
149G SER* 3.7 25.8 - - - +
150G GLU* 3.7 32.7 + - + +
153G ILE* 3.7 28.3 - - + -
162G ILE* 3.9 11.7 - - + -
163G THR* 1.3 82.2 - - - +
165G PHE* 1.3 76.4 + - - +
166G LYS* 3.9 2.9 + - + +
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Residues in contact with PHE 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G PHE* 3.9 28.9 - + + -
139G GLY 2.7 18.6 + - - +
140G ILE* 3.5 12.2 - - + +
141G GLU 3.3 20.4 + - - -
163G THR* 4.0 23.3 - - + -
164G ILE* 1.3 77.4 - - - +
166G LYS* 1.3 63.4 + - - +
167G GLY 3.2 4.0 + - - -
172G VAL* 4.4 15.9 - - + -
173G GLU 4.3 15.3 - - - -
174G LEU* 4.0 16.8 - - + -
175G PRO* 3.6 26.0 - - + -
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Residues in contact with LYS 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G GLU 3.6 3.4 - - - -
142G CYS 4.7 6.9 + - - +
143G SER 4.3 4.6 + - - +
144G SER* 3.8 23.2 - - - +
146G SER* 3.0 30.7 - - - +
147G ASP* 3.1 29.2 + - - +
150G GLU* 5.9 3.8 - - - +
164G ILE* 3.9 4.7 + - + +
165G PHE* 1.3 68.4 - - - +
167G GLY* 1.3 59.3 + - - +
172G VAL* 4.4 5.1 - - - +
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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