Contacts of the helix formed by residues 173 - 176 (chain B) in PDB entry 1SX8
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 LYS 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B TYR* 4.0 31.3 + - - +
107B LEU* 3.4 34.0 + - + +
108B GLY* 5.1 1.8 - - - -
109B GLY 5.6 0.6 + - - -
113B PHE* 4.3 17.4 - - - -
114B ILE* 5.6 1.5 - - - +
125B PHE* 6.3 0.2 - - - -
131B HIS* 2.7 28.5 + - + +
133B ILE* 3.7 33.7 - - + -
171B GLN 3.4 2.6 + - - -
172B ASP* 1.3 72.6 - - - +
174B TRP* 1.3 65.9 + - - +
176B ILE* 3.3 5.4 + - - +
177B ALA* 3.2 19.9 + - - +
189B ILE* 4.2 9.1 - - - +
212B PHE* 4.0 28.5 - - + -
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Residues in contact with TRP 174 (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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172B ASP* 3.2 18.4 - - + +
173B LYS* 1.3 80.5 - - - +
175B VAL* 1.3 91.2 + - + +
176B ILE 3.1 1.4 + - - -
177B ALA* 3.3 14.0 + - - +
206B PHE* 3.8 23.2 - - + +
207B ASP 4.6 2.7 - - - -
208B SER* 3.4 39.3 - - - -
209B GLU* 3.2 47.1 + - + +
212B PHE* 3.6 32.9 - - + -
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLN* 4.0 15.3 - - + +
172B ASP* 3.8 24.5 - - + +
173B LYS 3.3 1.2 - - - -
174B TRP* 1.3 111.3 - - + +
176B ILE* 1.3 59.3 + - + +
177B ALA 4.4 0.5 - - - +
202B GLY* 3.3 42.4 - - - +
204B GLY* 3.0 30.5 - - - +
205B ILE 4.4 1.0 + - - -
206B PHE 5.5 0.5 + - - -
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Residues in contact with ILE 176 (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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105B PHE* 5.0 1.1 - - + -
107B LEU* 4.4 14.6 - - + -
133B ILE* 4.1 22.0 - - + -
169B PHE* 3.9 20.4 - - + -
171B GLN* 3.4 27.8 - - + -
172B ASP 3.9 6.1 - - - +
173B LYS* 3.8 9.6 - - - +
174B TRP 3.2 0.2 - - - -
175B VAL* 1.3 79.1 - - + +
177B ALA* 1.3 58.3 + - - +
191B SER* 3.2 7.2 - - - -
192B ILE* 2.8 39.8 + - + +
199B PHE* 3.8 45.3 - - + +
202B GLY* 5.1 1.1 - - - -
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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