Contacts of the strand formed by residues 233 - 237 (chain A) in PDB entry 5FHK
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 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 4.3 4.7 - - + -
165A VAL 3.5 6.7 - - - +
166A ALA* 4.2 7.9 - - + -
170A TYR* 4.0 11.0 - - + -
176A MET* 5.1 1.8 - - - -
177A PRO* 4.3 8.3 - - + -
183A LEU* 4.4 6.5 - - + -
186A HIS* 3.6 42.0 - - + +
187A PHE 2.8 10.9 + - - +
188A LEU* 3.2 7.9 - - + -
189A LEU* 2.7 31.5 + - - -
197A TRP* 3.5 22.2 - - + -
232A GLY* 1.3 73.6 - - - -
234A THR* 1.3 66.2 + - - +
253A ILE* 3.5 36.3 - - + -
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Residues in contact with THR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE 3.8 0.2 - - - +
164A LEU* 3.3 7.0 - - - +
165A VAL* 3.1 38.8 + - + -
189A LEU* 2.9 25.0 + - - -
190A LYS* 4.9 0.3 - - - -
197A TRP* 3.7 6.7 - - - -
220A LEU* 5.1 0.2 - - - +
223A VAL* 3.4 18.2 - - + +
227A CYS* 3.5 29.8 - - + -
232A GLY 4.1 0.4 + - - -
233A ILE* 1.3 73.7 - - - +
235A LEU* 1.3 76.9 + - - +
236A MET* 3.7 20.5 - - + +
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASP* 3.7 21.3 - - + +
163A ILE* 3.5 32.8 - - - +
164A LEU* 3.6 15.5 - - + -
191A GLY 5.5 0.9 + - - -
194A LEU* 3.6 29.1 - - + +
196A LYS 4.8 1.1 - - - +
197A TRP* 3.4 52.3 + - + +
198A THR 5.2 0.4 - - - +
199A LEU* 4.2 11.4 - - + -
220A LEU* 4.1 9.5 - - - +
234A THR* 1.3 82.7 + - - +
236A MET* 1.3 63.2 + - - +
258A SER* 6.0 0.2 - - - -
259A ALA* 4.6 9.4 - - + -
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Residues in contact with MET 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASP* 4.0 4.5 - - - -
163A ILE* 3.0 30.9 + - - +
165A VAL* 4.7 0.7 - - + -
194A LEU* 4.3 0.2 - - - -
220A LEU* 3.9 16.2 - - + +
223A VAL* 4.1 4.5 - - + -
224A ARG* 3.8 33.7 - - + +
234A THR* 3.7 33.2 - - + +
235A LEU* 1.3 76.0 - - - +
237A PRO* 1.3 83.7 - - + +
238A ASP* 3.3 1.0 + - - -
240A MET* 3.7 24.7 - - + -
241A ILE* 3.7 37.2 - - + +
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Residues in contact with PRO 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASN* 5.5 0.7 - - + -
101A LEU* 4.0 14.4 - - + -
160A VAL* 3.5 18.8 - - + -
161A LYS 3.9 1.1 - - - +
162A ASP* 3.2 15.4 - - - +
194A LEU* 4.2 1.3 - - + -
220A LEU* 3.5 26.2 - - + -
236A MET* 1.3 93.0 - - + +
238A ASP* 1.3 60.0 + - - +
239A VAL* 3.2 2.2 - - + -
240A MET* 2.8 38.2 + - + +
241A ILE* 3.8 4.0 - - - +
262A ARG* 3.4 22.7 - - - +
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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