Contacts of the helix formed by residues 187 - 191 (chain B) in PDB entry 5DSG
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 ILE 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 3.8 20.9 - - + -
113B TYR* 3.5 44.9 - - + -
164B TRP* 4.4 1.3 - - + -
168B ILE* 3.8 33.0 - - + -
186B PHE* 1.3 79.4 - - - +
188B GLN* 1.3 64.0 + - - +
189B PHE* 3.5 28.5 - - + +
190B LEU* 3.1 33.9 + - + +
191B SER* 3.8 0.9 + - - -
1205B P6G 3.3 18.2 - - - -
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Residues in contact with GLN 188 (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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168B ILE 5.8 1.4 + - - -
171B TRP* 3.9 25.8 + - + +
172B GLN* 3.8 13.2 - - + +
175B VAL* 4.2 13.1 - - - +
177B LYS 2.9 22.0 + - - +
178B ARG* 3.4 10.2 - - - +
179B THR* 3.1 46.2 + - - +
180B VAL* 4.1 15.2 - - + +
186B PHE* 3.3 8.2 + - - -
187B ILE* 1.3 72.5 - - - +
189B PHE* 1.3 60.9 + - - +
191B SER* 2.6 28.3 + - - +
1206B OLC 4.1 3.3 - - - +
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Residues in contact with PHE 189 (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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164B TRP* 4.8 5.8 - + - -
167B ALA* 3.4 38.8 - - + +
171B TRP* 3.7 30.1 - + + +
187B ILE* 3.1 10.3 - - + +
188B GLN* 1.3 80.3 - - - +
190B LEU* 1.3 83.6 + - + +
191B SER 3.3 0.4 - - - -
195B VAL* 3.9 9.2 - - + +
199B THR* 4.2 4.7 - - - -
1206B OLC 2.8 103.9 + - + +
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Residues in contact with LEU 190 (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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113B TYR* 3.9 19.5 - - + +
164B TRP* 4.2 4.7 - - + -
187B ILE* 3.1 41.1 + - + +
189B PHE* 1.3 106.4 - - + +
191B SER* 1.3 59.5 + - - +
192B ASN 3.4 2.9 - - - -
195B VAL* 4.3 2.5 - - + +
196B THR* 2.7 41.4 + - + +
199B THR* 3.7 22.2 - - + +
1201B 0HK 3.9 16.4 - - + -
1205B P6G 4.3 20.8 - - - +
1206B OLC 4.5 0.2 - - - -
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Residues in contact with SER 191 (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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179B THR* 4.8 2.4 + - - -
186B PHE* 4.5 10.5 - - - -
187B ILE 4.0 2.0 + - - -
188B GLN* 2.6 33.9 + - - +
189B PHE 3.3 2.8 + - - -
190B LEU* 1.3 78.6 - - - +
192B ASN* 1.3 61.7 + - - +
193B PRO* 3.4 9.5 - - - +
1205B P6G 6.0 1.0 - - - +
1206B OLC 3.6 11.9 + - - -
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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