Contacts of the strand formed by residues 179 - 183 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114N VAL* 3.4 25.4 - - + +
116N LEU* 3.8 19.3 - - + +
138N PHE* 4.8 3.4 - - + -
174N LEU* 4.4 18.8 - - + -
176N VAL* 4.1 10.1 - - + -
178N LYS* 1.3 81.7 - - - +
180N ASP* 1.3 66.7 + - - +
181N ILE 3.3 27.8 - - - +
182N ILE* 4.6 4.5 - - + -
207N TRP* 2.7 21.3 + - + +
208N LEU* 3.6 4.4 - - + +
209N LYS* 3.0 25.3 + - - +
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Residues in contact with ASP 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112N ASP 4.9 0.3 - - - +
113N LYS* 3.6 34.3 - - + +
114N VAL* 3.0 38.7 + - - +
179N VAL* 1.3 73.8 - - - +
181N ILE* 1.3 63.5 + - + +
208N LEU* 4.1 1.1 - - - -
209N LYS* 2.9 34.8 + - - +
212N GLY* 3.4 8.1 - - - -
213N LEU* 3.3 21.5 + - - +
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Residues in contact with ILE 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109N VAL* 3.4 34.8 - - + +
110N PHE* 3.7 39.0 - - + -
113N LYS* 4.3 12.1 - - + -
114N VAL 3.4 1.8 + - - -
115N VAL* 3.4 10.5 - - + +
116N LEU 2.9 24.9 + - - -
179N VAL* 3.3 5.2 - - - +
180N ASP* 1.3 88.9 - - + +
182N ILE* 1.3 70.0 + - - +
183N ILE* 4.1 4.0 - - + -
208N LEU* 4.5 0.4 - - - -
213N LEU* 3.4 21.5 - - + +
215N PHE* 3.9 17.7 - - + -
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Residues in contact with ILE 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N LEU* 3.5 24.7 - - + -
118N VAL* 4.0 19.5 - - + -
179N VAL* 4.6 3.1 - - + -
181N ILE* 1.3 77.1 - - - +
183N ILE* 1.3 69.7 + - - +
184N SER* 4.8 4.5 - - - -
200N VAL* 4.8 2.2 - - + -
203N ALA* 3.9 9.4 - - + +
204N ARG* 3.6 35.4 - - - +
207N TRP 5.3 0.2 - - - -
208N LEU* 4.1 19.5 - - + +
213N LEU 3.0 7.5 + - - +
214N MET* 3.3 30.5 - - + -
215N PHE* 2.9 24.9 + - - +
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Residues in contact with ILE 183 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99N TYR* 5.6 0.9 - - + -
103N MET* 3.9 21.3 - - + -
110N PHE* 4.3 6.5 - - + -
115N VAL* 3.8 24.2 - - + -
116N LEU 2.9 15.1 + - - +
117N ASP* 3.5 16.8 - - + +
118N VAL 3.0 24.9 + - - -
125N LEU* 3.6 37.0 - - + +
126N SER* 4.2 1.1 - - - +
129N ALA* 4.0 6.1 - - + -
181N ILE* 4.1 8.5 - - + -
182N ILE* 1.3 77.5 - - - +
184N SER* 1.3 62.9 + - - +
215N PHE* 3.4 22.9 - - + +
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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