Contacts of the strand formed by residues 179 - 183 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H VAL* 3.5 24.2 - - + +
116H LEU* 3.9 20.0 - - + +
138H PHE* 4.7 3.6 - - + -
174H LEU* 4.5 18.8 - - + -
176H VAL* 4.0 9.6 - - + -
178H LYS* 1.3 80.2 - - - +
180H ASP* 1.3 66.6 + - - +
181H ILE 3.3 28.7 - - - +
182H ILE* 4.6 5.2 - - + -
207H TRP* 2.7 21.7 + - + +
208H LEU* 3.7 3.1 - - + +
209H LYS* 3.0 26.9 + - - +
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Residues in contact with ASP 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H ASP 4.9 0.5 - - - +
113H LYS* 3.6 35.1 + - + +
114H VAL* 3.1 36.2 + - - +
179H VAL* 1.3 75.0 - - - +
181H ILE* 1.3 63.1 + - + +
208H LEU* 3.8 1.3 - - - +
209H LYS* 2.8 35.8 + - - +
212H GLY* 3.4 9.2 - - - -
213H LEU* 3.2 21.5 + - - +
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Residues in contact with ILE 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H VAL* 3.4 36.3 - - + +
110H PHE* 3.8 32.8 - - + -
113H LYS* 4.3 12.3 - - + -
114H VAL 3.3 1.8 + - - -
115H VAL* 3.3 11.6 - - + +
116H LEU 2.9 24.6 + - - -
179H VAL* 3.3 7.2 - - - +
180H ASP* 1.3 88.5 - - + +
182H ILE* 1.3 73.2 + - - +
183H ILE* 4.1 3.8 - - + -
208H LEU* 4.4 0.9 - - - -
213H LEU* 3.3 22.4 - - + +
215H PHE* 4.0 18.8 - - + -
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Residues in contact with ILE 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H LEU* 3.5 26.9 - - + -
118H VAL* 4.0 18.8 - - + -
179H VAL* 4.6 2.9 - - + -
181H ILE* 1.3 74.9 - - - +
183H ILE* 1.3 71.4 + - - +
184H SER* 4.8 1.6 - - - -
200H VAL* 4.8 5.6 - - + +
203H ALA* 3.9 10.3 - - + +
204H ARG* 3.6 35.2 - - - +
207H TRP 5.4 0.2 - - - -
208H LEU* 4.2 18.5 - - + +
213H LEU 3.0 7.1 + - - +
214H MET* 3.4 31.8 - - + -
215H PHE 3.0 24.1 + - - +
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Residues in contact with ILE 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H TYR* 5.5 0.9 - - + -
103H MET* 3.9 20.2 - - + -
110H PHE* 4.3 6.3 - - + -
115H VAL* 3.9 23.8 - - + -
116H LEU 2.8 14.7 + - - +
117H ASP* 3.4 16.4 - - + -
118H VAL 3.0 21.1 + - - -
125H LEU* 3.5 37.9 - - + +
126H SER* 4.2 1.1 - - - +
129H ALA* 4.1 5.8 - - + -
137H VAL* 5.3 0.2 - - + -
181H ILE* 4.1 8.1 - - + -
182H ILE* 1.3 80.1 - - - +
184H SER* 1.3 62.7 - - - +
215H 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
------------------------------------------------------------
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