Contacts of the strand formed by residues 272 - 276 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C LEU 4.5 0.2 - - - -
134C LEU* 3.4 18.0 - - - +
135C MET* 3.0 32.3 + - - -
137C SER 3.3 23.8 - - - -
138C GLY* 3.6 4.7 - - - -
141C ALA* 4.1 5.4 - - - -
259C ALA* 5.1 0.4 - - - -
271C ALA* 1.3 74.0 - - - +
273C CYS* 1.3 62.5 + - - +
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Residues in contact with CYS 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ILE* 3.6 46.4 - - - -
132C THR* 4.3 6.3 - - - -
133C LEU 3.7 2.7 - - - -
134C LEU* 4.9 3.4 - - - -
141C ALA* 3.9 3.6 - - - +
255C VAL 4.6 0.2 - - - -
256C LEU* 2.9 30.4 - - - +
257C HIS* 2.9 37.7 + - + +
259C ALA* 4.9 3.1 - - + +
263C LEU* 4.1 12.6 - - + -
272C GLY* 1.3 77.2 - - - -
274C ILE* 1.3 64.0 + - - +
275C SER* 4.3 2.0 - - - -
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Residues in contact with ILE 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C THR* 3.3 2.2 - - - -
133C LEU* 2.9 41.3 + - + +
135C MET* 4.0 17.5 - - + -
141C ALA* 3.4 42.6 - - + +
145C MET* 4.0 16.2 - - + -
254C LEU* 4.3 18.6 - - + -
255C VAL 3.6 4.9 - - - +
256C LEU* 4.0 8.5 - - + -
273C CYS* 1.3 84.3 - - - +
275C SER* 1.3 64.3 + - - +
281C VAL* 3.8 8.8 - - + +
284C ILE* 4.0 25.4 - - + -
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Residues in contact with SER 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ILE* 3.6 17.2 - - - +
127C GLU* 3.9 9.5 + - - +
129C ALA* 3.7 14.8 - - - -
131C SER 3.4 4.5 - - - -
132C THR* 3.1 20.5 + - - +
248C LEU* 4.4 0.2 - - - +
254C LEU* 3.5 4.9 - - - +
255C VAL* 2.9 49.5 + - - +
257C HIS* 5.4 1.9 - - - -
273C CYS* 4.7 1.6 - - - -
274C ILE* 1.3 79.5 + - - +
276C GLY* 1.3 58.6 + - - +
281C VAL* 5.2 0.2 - - - -
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Residues in contact with GLY 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ALA* 3.7 7.1 - - - +
130C GLU 3.3 6.1 + - - -
131C SER* 3.0 30.4 + - - +
248C LEU* 4.3 6.7 - - - -
253C ASP 3.7 5.6 - - - -
254C LEU* 4.3 5.8 - - - -
274C ILE 4.4 0.2 + - - -
275C SER* 1.3 76.0 - - - +
277C PRO* 1.3 77.1 - - - +
281C VAL* 4.6 2.7 - - - +
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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