Contacts of the strand formed by residues 179 - 183 (chain L) 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 VAL 179 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L VAL* 3.3 25.4 - - + +
116L LEU* 3.8 23.8 - - + +
138L PHE* 4.8 3.6 - - + -
174L LEU* 4.5 9.0 - - + -
176L VAL* 4.2 10.3 - - + -
178L LYS* 1.3 78.0 - - - +
180L ASP* 1.3 66.2 + - - +
181L ILE 3.1 29.2 - - - +
182L ILE* 4.7 4.7 - - + -
207L TRP* 2.7 24.7 + - + +
208L LEU* 3.8 2.8 - - + +
209L LYS* 3.0 25.0 + - - +
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Residues in contact with ASP 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L ASP 4.8 0.7 - - - +
113L LYS* 3.4 35.6 - - + +
114L VAL* 2.9 39.5 + - - +
179L VAL* 1.3 72.8 - - - +
181L ILE* 1.3 63.2 + - + +
208L LEU* 3.8 1.7 - - - +
209L LYS* 3.0 33.2 + - - +
212L GLY* 3.3 8.8 - - - -
213L LEU* 3.2 21.0 + - - +
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Residues in contact with ILE 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109L VAL* 3.4 36.3 - - + +
110L PHE* 3.7 40.2 - - + -
113L LYS* 4.3 8.1 - - + -
114L VAL 3.3 1.8 + - - -
115L VAL* 3.4 13.0 - - + +
116L LEU 2.9 24.4 + - - -
179L VAL* 3.1 6.2 - - - +
180L ASP* 1.3 87.8 - - + +
182L ILE* 1.3 75.6 + - - +
183L ILE* 4.1 3.8 - - + -
208L LEU* 4.3 0.9 - - - -
213L LEU* 3.4 20.4 - - + +
215L PHE* 4.1 13.0 - - + -
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Residues in contact with ILE 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L LEU* 3.5 24.5 - - + -
118L VAL* 4.1 13.2 - - + -
179L VAL* 4.7 2.9 - - + -
181L ILE* 1.3 78.1 - - - +
183L ILE* 1.3 76.1 + - - +
184L SER* 4.8 1.3 - - - +
200L VAL* 4.8 5.6 - - + -
203L ALA* 3.9 9.6 - - + +
204L ARG* 3.6 35.4 - - - +
207L TRP 5.4 0.2 - - - -
208L LEU* 4.0 18.4 - - + +
213L LEU 3.0 7.9 + - - -
214L MET* 3.3 29.8 - - + -
215L PHE 2.8 26.0 + - - +
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Residues in contact with ILE 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L TYR* 5.5 1.3 - - + -
103L MET* 3.9 22.2 - - + -
110L PHE* 4.4 4.5 - - + -
115L VAL* 4.0 23.1 - - + -
116L LEU 2.9 9.5 + - - +
117L ASP* 3.4 23.5 - - + +
118L VAL* 2.9 26.7 + - - +
125L LEU* 3.6 39.0 - - + +
126L SER* 4.1 0.9 - - - +
129L ALA* 4.1 5.4 - - + -
137L VAL* 5.4 0.2 - - + -
181L ILE* 4.1 7.9 - - + -
182L ILE* 1.3 79.3 - - - +
184L SER* 1.3 62.2 + - - +
215L PHE* 3.5 23.1 - - + +
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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