Contacts of the strand formed by residues 272 - 276 (chain F) in PDB entry 1I43
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 272 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133F LEU 4.5 0.7 - - - -
134F LEU* 3.4 15.4 - - - +
135F MET* 3.2 32.3 + - - -
137F SER 3.1 24.4 - - - -
138F GLY* 3.6 5.2 - - - -
141F ALA* 4.2 5.4 - - - -
259F ALA* 5.0 0.7 - - - -
271F ALA* 1.3 75.1 - - - +
273F CYS* 1.3 61.2 + - - +
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Residues in contact with CYS 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F ILE* 3.5 48.0 - - - -
132F THR* 4.2 6.5 - - - -
133F LEU 3.8 2.0 - - - -
134F LEU* 4.8 4.0 - - - -
141F ALA* 4.0 2.6 - - - +
255F VAL 4.6 0.2 - - - -
256F LEU* 2.9 11.5 - - - +
257F HIS* 2.8 57.5 + - + +
259F ALA* 4.9 2.9 - - + +
263F LEU* 4.1 11.2 - - + -
272F GLY* 1.3 75.5 - - - -
274F ILE* 1.3 65.8 + - - +
275F SER* 4.3 2.5 - - - -
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Residues in contact with ILE 274 (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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132F THR* 3.3 1.8 - - - -
133F LEU* 2.8 43.1 + - + +
135F MET* 3.9 16.6 - - + -
141F ALA* 3.3 43.7 - - + +
145F MET* 3.9 16.2 - - + -
254F LEU* 4.5 14.8 - - + -
255F VAL 3.7 4.9 - - - +
256F LEU* 3.9 9.9 - - + +
273F CYS* 1.3 81.2 - - - +
275F SER* 1.3 63.6 + - - +
281F VAL* 3.8 11.7 - - + +
284F ILE* 4.0 25.4 - - + -
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Residues in contact with SER 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F ILE* 3.6 15.1 - - - +
127F GLU* 4.1 9.6 + - - +
129F ALA* 3.8 14.4 - - - -
131F SER 3.4 4.3 - - - -
132F THR* 2.9 22.7 + - - +
254F LEU* 3.4 8.9 - - - +
255F VAL* 2.9 50.6 + - - +
257F HIS* 5.4 1.6 - - - -
273F CYS* 4.6 2.1 - - - -
274F ILE* 1.3 76.0 + - - +
276F GLY* 1.3 59.3 + - - +
281F VAL* 5.2 0.7 - - - -
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Residues in contact with GLY 276 (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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129F ALA* 3.7 2.2 - - - +
130F GLU 3.4 6.0 + - - -
131F SER 3.1 28.2 + - - +
248F LEU* 4.1 12.6 - - - -
253F ASP 3.6 6.3 - - - -
254F LEU* 4.2 4.7 - - - +
275F SER* 1.3 76.7 - - - +
277F PRO* 1.3 78.5 - - - +
281F VAL* 4.8 1.7 - - - +
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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