Contacts of the strand formed by residues 188 - 193 (chain L) in PDB entry 5FHX
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 GLY 188 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140L THR* 6.5 0.2 - - - -
141L CYS 3.9 2.0 - - - -
142L HIS* 4.8 7.0 - - - -
184L GLY* 3.3 20.1 - - - -
185L SER 3.7 6.8 + - - +
187L THR* 1.3 78.8 + - - +
189L PHE* 1.4 62.9 + - - -
190L THR* 5.7 0.7 - - - -
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Residues in contact with PHE 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L THR* 3.5 2.8 - - - +
141L CYS* 2.8 44.9 + - + +
143L ALA* 4.8 1.1 - - + -
147L ILE* 3.6 23.1 - - + -
148L ASP 3.4 22.9 - - - -
149L VAL* 4.4 1.3 - - - -
151L LEU* 3.7 42.4 - - + -
153L TRP* 4.6 1.6 - - - -
169L ALA* 3.7 16.6 - - + -
183L SER 3.2 6.3 - - - +
184L GLY* 3.4 29.6 - - - -
185L SER* 3.8 1.8 - - - -
186L GLY 3.6 29.8 - - - -
187L THR 3.6 11.0 - - - -
188L GLY* 1.4 74.5 - - - -
190L THR* 1.4 69.4 + - - +
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Residues in contact with THR 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L THR* 4.1 18.4 - - + +
139L LEU 3.2 7.2 - - - +
140L THR* 4.0 17.0 - - + +
153L TRP* 3.9 9.6 + - - -
181L SER 4.5 0.2 - - - -
182L GLY* 3.2 6.1 - - - -
183L SER* 2.7 52.6 + - - +
188L GLY 5.7 0.4 - - - -
189L PHE* 1.4 82.1 - - - +
191L LEU* 1.3 60.2 + - - +
192L THR* 4.7 4.0 + - - -
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Residues in contact with LEU 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L ILE 3.8 0.2 - - - +
138L THR* 3.2 4.5 - - - -
139L LEU* 2.8 49.5 + - + +
153L TRP* 3.7 44.8 - - + -
165L LEU* 4.4 9.2 - - + -
166L ILE* 3.8 28.7 - - + -
180L PHE* 4.4 7.4 - - + -
181L SER 3.3 7.6 - - - +
190L THR* 1.3 73.4 - - - +
192L THR* 1.3 65.2 + - - +
193L ILE* 4.4 10.7 - - + +
204L TYR* 3.7 32.5 - - + -
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Residues in contact with THR 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136L THR* 4.1 13.5 - - + -
137L ILE 3.1 10.8 - - - +
138L THR* 2.8 25.6 + - - +
179L ARG 3.1 6.1 - - - +
180L PHE* 3.2 3.6 - - - -
181L SER* 2.7 49.2 + - - +
190L THR* 4.7 4.2 + - - -
191L LEU* 1.3 73.3 - - - +
193L ILE* 1.3 64.6 + - - +
194L SER* 3.9 17.7 - - - +
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Residues in contact with ILE 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L ASP 3.6 3.2 - - - +
136L THR* 3.3 2.6 - - - -
137L ILE* 2.8 47.3 + - + +
139L LEU* 5.0 2.7 - - + -
179L ARG* 3.4 10.3 - - + -
180L PHE* 3.7 33.9 - - + -
191L LEU* 4.4 13.9 - - + +
192L THR* 1.3 77.1 - - - +
194L SER* 1.3 60.0 + - - +
196L LEU* 4.2 16.3 - - + +
200L ASP* 3.4 25.8 - - - +
204L TYR* 4.0 13.5 - - + +
222L LEU* 4.0 26.9 - - + -
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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