Contacts of the strand formed by residues 224 - 229 (chain F) in PDB entry 6S1M
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 THR 224 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F LYS* 4.1 23.9 - - + +
139F MET 3.3 14.8 - - - -
141F SER* 3.7 2.9 - - - +
192F GLU* 3.7 30.3 - - + +
222F SER* 2.8 30.4 + - - +
223F SER* 1.3 89.0 - - - +
225F VAL* 1.3 64.5 + - - +
226F THR* 5.0 3.1 - - - +
239F TYR* 4.2 6.6 - - - -
240F LYS 4.7 0.9 + - - -
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Residues in contact with VAL 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F VAL 3.6 1.6 - - - +
138F LYS* 3.5 0.5 - - - -
139F MET* 2.9 39.2 + - + +
141F SER* 3.8 15.7 - - - -
144F PHE* 3.9 24.7 - - + -
224F THR* 1.3 76.6 - - - +
226F THR* 1.3 70.9 + - - +
227F LEU* 4.6 4.9 - - + -
237F VAL* 3.9 18.6 - - + -
238F GLU 3.3 16.4 - - - +
239F TYR* 3.7 31.4 - - + +
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Residues in contact with THR 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F VAL* 4.5 13.1 - - + +
137F VAL 3.0 8.7 - - - -
138F LYS* 4.2 20.6 - - + -
224F THR* 5.0 3.1 - - - +
225F VAL* 1.3 81.2 - - - +
227F LEU* 1.3 62.0 + - - +
228F SER* 4.5 7.3 + - - -
236F VAL* 3.6 2.8 - - - +
237F VAL* 3.8 1.9 - - - -
238F GLU* 3.2 48.4 + - + +
240F LYS* 6.2 3.8 - - + -
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Residues in contact with LEU 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F CYS 3.5 1.4 - - - +
136F VAL* 3.2 4.0 - - - -
137F VAL* 2.6 48.0 + - + +
139F MET* 3.3 33.7 - - + -
144F PHE* 3.6 41.3 - - + -
160F ILE* 5.4 6.1 - - + -
167F VAL* 6.1 0.2 - - + -
169F PHE* 4.0 14.1 - - + -
225F VAL* 4.6 4.5 - - + +
226F THR* 1.3 78.3 - - - +
228F SER* 1.3 61.9 + - - +
229F MET* 4.1 6.9 + - + +
235F LEU* 4.2 12.3 - - + -
236F VAL 3.3 2.2 - - - -
237F VAL* 3.9 24.2 - - + -
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Residues in contact with SER 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F TYR* 3.7 32.3 - - - -
135F CYS 3.3 4.9 - - - -
136F VAL* 3.4 21.7 - - - +
226F THR* 4.2 6.3 + - - -
227F LEU* 1.3 72.1 - - - +
229F MET* 1.3 62.1 + - - +
235F LEU* 3.7 3.0 - - - +
236F VAL* 2.8 48.6 + - - +
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Residues in contact with MET 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F TYR* 3.4 7.5 - - - +
134F SER 3.2 17.5 + - - -
135F CYS* 2.9 24.1 + - + +
137F VAL* 4.4 13.5 - - + -
160F ILE* 3.3 49.6 - - + +
162F CYS* 3.8 31.6 - - + -
167F VAL* 4.6 0.9 - - + -
203F VAL* 4.3 9.2 - - + -
205F LEU* 4.1 15.9 - - + -
207F PHE* 5.0 3.4 - - + -
227F LEU* 4.9 7.2 - - + +
228F SER* 1.3 78.4 - - - +
230F SER* 1.3 67.4 + - - +
233F VAL 6.0 0.2 - - - -
234F PRO 5.4 0.4 - - - -
235F LEU* 3.7 22.2 - - + +
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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