Contacts of the strand formed by residues 254 - 257 (chain J) 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 LEU 254 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J MET* 4.6 7.2 - - + -
149J LEU* 3.4 32.5 - - + -
203J LEU* 5.0 1.8 - - + -
232J LEU* 4.9 3.6 - - + -
233J VAL 3.0 4.4 + - - +
234J CYS* 3.2 25.1 - - + -
235J ILE* 2.9 25.3 + - - -
248J LEU* 4.3 2.7 - - - -
252J ALA* 4.1 5.0 - - - +
253J ASP* 1.3 88.7 - - + +
255J VAL* 1.3 62.6 + - - +
256J LEU* 4.2 0.4 - - + -
274J ILE* 4.6 16.4 - - + -
275J SER 3.5 11.2 - - - +
276J GLY* 4.2 7.4 - - - -
280J LEU* 3.9 32.3 - - + -
281J VAL* 4.5 6.7 - - - +
284J ILE* 4.7 3.8 - - + -
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Residues in contact with VAL 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J GLU* 3.7 24.2 - - - +
235J ILE 3.2 11.0 - - - +
237J GLY* 4.4 6.5 - - - +
245J GLN* 6.2 0.2 - - - +
247J ALA* 4.2 24.0 - - + +
248J LEU* 3.7 20.9 - - + -
254J LEU* 1.3 75.4 - - - +
256J LEU* 1.3 64.2 + - - +
257J HIS* 3.6 24.1 - - + +
274J ILE* 4.6 0.2 - - - -
275J SER* 2.8 45.5 + - - +
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Residues in contact with LEU 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J GLY* 4.6 3.4 - - - +
141J ALA* 4.3 9.6 - - + -
142J SER* 4.2 31.0 - - - +
145J MET* 4.4 4.9 - - + -
205J PHE* 3.6 30.3 - - + -
234J CYS* 3.8 14.4 - - - -
235J ILE 3.0 6.1 + - - -
236J ASP* 2.9 36.6 - - - +
237J GLY 3.1 14.4 + - - -
254J LEU 4.2 0.8 - - - -
255J VAL* 1.3 75.0 - - - +
257J HIS* 1.3 77.0 + - - +
258J SER* 6.1 0.4 - - - -
273J CYS 2.9 14.8 - - - +
274J ILE* 4.0 11.9 - - + -
500J PLP 6.0 2.9 - - + -
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Residues in contact with HIS 257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J ILE* 5.7 1.1 - - + -
127J GLU* 2.5 33.1 + - + -
138J GLY* 4.2 2.6 - - - -
237J GLY* 2.8 38.7 + - - -
238J THR* 3.7 12.2 + - - +
241J THR* 3.8 2.9 - - - -
242J PRO* 3.6 26.9 - - + +
255J VAL* 3.6 15.3 - - + +
256J LEU* 1.3 90.8 - - - +
258J SER* 1.3 62.7 + - - +
263J LEU* 4.0 18.0 - - + +
272J GLY* 4.1 2.1 - - - -
273J CYS* 2.9 40.7 + - + -
275J SER* 5.0 1.8 - - - -
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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