Contacts of the strand formed by residues 114 - 118 (chain B) 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 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B LYS* 1.3 74.7 - - - +
115B VAL* 1.3 62.4 + - - +
135B LYS* 4.1 22.7 - - - -
136B LYS* 3.4 15.3 - - + +
138B PHE* 4.0 30.7 - - + -
176B VAL* 4.6 11.0 - - + -
178B LYS 4.9 1.8 - - - +
179B VAL* 3.3 20.2 - - + +
180B ASP* 2.9 41.5 + - - +
181B ILE 3.3 7.3 + - - -
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 3.9 19.7 - - + -
113B LYS* 4.0 4.5 - - + +
114B VAL* 1.3 79.4 - - - +
116B LEU* 1.3 57.5 + - - +
117B ASP 4.1 0.2 - - - -
129B ALA* 4.2 6.3 - - + -
134B ALA* 3.8 25.4 - - + -
136B LYS 3.0 9.3 + - - +
137B VAL* 3.3 10.5 - - + +
138B PHE* 2.7 35.4 + - - +
179B VAL* 4.3 2.0 - - - -
181B ILE* 3.3 19.1 - - + +
183B ILE* 3.9 40.2 - - + -
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B VAL* 1.3 73.8 - - - +
117B ASP* 1.3 61.1 + - - +
118B VAL* 3.6 24.1 + - + -
138B PHE* 3.3 24.2 - - + +
140B ILE* 3.7 27.6 - - + -
174B LEU* 4.2 8.1 - - + -
179B VAL* 3.9 17.4 - - + +
181B ILE 2.9 8.7 + - - -
182B ILE* 3.4 19.0 - - + +
183B ILE* 2.9 29.9 + - - +
203B ALA* 4.2 2.9 - - + -
207B TRP* 3.7 34.8 - - + -
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Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B VAL* 4.1 1.4 + - - +
116B LEU* 1.3 70.9 - - - +
118B VAL* 1.3 70.2 + - - +
119B GLY 3.5 2.8 + - - +
120B SER* 3.5 24.6 + - - +
125B LEU* 3.4 21.5 - - - +
126B SER* 2.6 42.7 + - - +
137B VAL* 4.8 1.1 - - + -
138B PHE 2.9 8.5 + - - +
139B GLY* 3.5 5.5 - - - -
140B ILE 3.0 25.1 + - - +
183B ILE* 3.4 20.6 - - + +
401B SAH 4.1 2.9 + - - -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.8 29.2 - - + -
117B ASP* 1.3 70.1 - - - +
119B GLY* 1.3 67.0 + - - +
140B ILE* 4.5 1.1 - - - -
169B VAL* 4.1 11.2 - - + -
182B ILE* 4.1 15.5 - - + -
183B ILE 3.0 5.9 + - - -
184B SER* 2.8 37.8 + - - +
185B GLU 4.5 1.4 + - - +
196B MET* 3.6 7.9 - - + +
199B THR* 3.9 28.9 - - + +
200B VAL* 4.0 14.8 - - + -
203B ALA* 3.8 14.6 - - + -
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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