Contacts of the strand formed by residues 162 - 166 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126O SER* 3.6 36.6 - - - +
127O MET* 3.8 22.0 - - + +
130O ALA* 3.9 13.7 - - + -
137O VAL* 3.3 22.4 - - + +
139O GLY 5.1 0.4 - - - +
153O ILE* 3.6 29.8 - - + +
158O LEU* 2.9 22.3 + - + +
159O ASP* 3.0 22.3 - - - +
161O ILE* 1.3 76.9 - - - +
163O THR* 1.3 67.5 + - - +
164O ILE* 3.9 13.6 - - + +
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Residues in contact with THR 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O LYS* 3.7 20.8 + - - -
137O VAL 2.9 6.5 + - - -
138O PHE* 3.5 19.9 - - + -
139O GLY 3.1 22.2 + - - -
159O ASP 4.9 1.0 + - - -
162O ILE* 1.3 75.6 + - - +
164O ILE* 1.3 69.8 + - - +
165O PHE* 3.9 24.3 - - + -
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Residues in contact with ILE 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120O SER* 4.0 19.7 - - - +
123O GLY* 5.4 0.9 - - - -
126O SER* 5.0 2.5 - - - +
139O GLY* 3.3 16.6 - - - +
141O GLU* 4.9 1.3 - - + -
146O SER* 4.2 18.6 - - - +
149O SER* 3.7 24.5 - - - +
150O GLU* 3.9 32.2 + - + +
153O ILE* 3.7 28.5 - - + -
162O ILE* 3.9 11.9 - - + -
163O THR* 1.3 81.5 - - - +
165O PHE* 1.3 74.4 + - - +
166O LYS* 3.8 2.7 + - + +
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Residues in contact with PHE 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138O PHE* 3.9 22.9 - + + -
139O GLY 2.8 15.7 + - - +
140O ILE* 3.6 5.8 - - + +
141O GLU 3.3 19.8 + - - -
163O THR* 3.9 25.6 - - + -
164O ILE* 1.3 78.3 - - - +
166O LYS* 1.3 58.9 + - - +
167O GLY 3.2 7.1 + - - -
172O VAL* 4.5 21.8 - - + -
173O GLU 4.2 16.8 - - - -
174O LEU* 3.8 24.5 - - + -
175O PRO* 3.6 26.2 - - + -
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Residues in contact with LYS 166 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141O GLU 3.5 4.7 - - - +
142O CYS 4.6 7.3 + - - +
143O SER 4.2 5.3 - - - +
144O SER* 3.9 21.2 - - - +
146O SER* 2.8 30.5 - - - +
147O ASP* 3.1 31.2 + - - +
150O GLU* 6.1 2.9 - - - +
164O ILE* 3.8 4.7 + - + +
165O PHE* 1.3 70.3 - - - +
167O GLY* 1.3 56.3 + - - +
172O VAL* 4.5 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