Contacts of the strand formed by residues 179 - 183 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I VAL* 3.4 20.9 - - + +
116I LEU* 3.8 18.6 - - + +
138I PHE* 4.7 4.0 - - + -
174I LEU* 4.4 18.4 - - + -
176I VAL* 4.0 15.0 - - + -
178I LYS* 1.3 79.8 - - - +
180I ASP* 1.3 67.3 + - - +
181I ILE 3.3 28.5 - - - +
182I ILE* 4.7 4.7 - - + -
207I TRP* 2.6 23.0 + - + +
208I LEU* 3.7 1.8 - - + +
209I LYS* 2.9 27.9 + - - +
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Residues in contact with ASP 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I ASP 5.1 0.3 - - - +
113I LYS* 3.8 24.1 - - + +
114I VAL* 3.0 43.5 + - - +
179I VAL* 1.3 73.8 - - - +
181I ILE* 1.3 64.9 + - + +
208I LEU* 3.6 1.9 - - - +
209I LYS* 2.8 39.1 + - - +
212I GLY* 3.3 10.6 - - - -
213I LEU* 3.3 20.6 + - - +
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Residues in contact with ILE 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I VAL* 3.4 33.7 - - + +
110I PHE* 3.7 33.4 - - + -
113I LYS* 4.2 15.5 - - + -
114I VAL 3.3 1.8 + - - -
115I VAL* 3.3 11.0 - - + +
116I LEU 2.9 24.9 + - - -
179I VAL* 3.3 3.8 - - - +
180I ASP* 1.3 88.7 - - + +
182I ILE* 1.3 71.0 + - - +
183I ILE* 4.1 3.6 - - + -
208I LEU* 4.4 0.2 - - - -
213I LEU* 3.4 21.3 - - + +
215I PHE* 3.9 23.8 - - + -
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Residues in contact with ILE 182 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I LEU* 3.4 23.6 - - + -
118I VAL* 4.0 15.7 - - + -
179I VAL* 4.7 3.1 - - + -
181I ILE* 1.3 76.6 - - - +
183I ILE* 1.3 74.3 + - - +
184I SER* 4.9 1.6 - - - -
200I VAL* 4.8 5.6 - - + -
203I ALA* 3.9 9.2 - - + +
204I ARG* 3.6 35.7 - - - +
207I TRP 5.3 0.2 - - - -
208I LEU* 4.0 19.3 - - + +
213I LEU 3.0 7.3 + - - -
214I MET* 3.3 31.4 - - + -
215I PHE* 2.9 25.3 + - - +
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Residues in contact with ILE 183 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I TYR* 5.6 0.4 - - + -
103I MET* 3.9 19.7 - - + -
110I PHE* 4.3 5.6 - - + -
115I VAL* 3.9 24.2 - - + -
116I LEU 2.9 15.1 + - - +
117I ASP* 3.4 15.9 - - + -
118I VAL 3.0 24.4 + - - -
125I LEU* 3.6 37.0 - - + +
126I SER* 4.2 0.9 - - - +
129I ALA* 4.1 6.1 - - + -
137I VAL* 5.3 0.2 - - + -
181I ILE* 4.1 7.9 - - + -
182I ILE* 1.3 78.7 - - - +
184I SER* 1.3 62.6 + - - +
215I PHE* 3.4 26.2 - - + +
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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