Contacts of the strand formed by residues 331 - 336 (chain A) in PDB entry 5TOL
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 331 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A VAL* 4.9 3.4 - - + -
255A GLU 3.5 3.8 - - - +
256A ILE* 3.7 23.1 - - + -
282A LEU* 4.9 10.3 - - + -
284A LEU* 6.5 0.9 - - + -
292A ALA* 6.2 0.7 - - + -
296A ILE* 4.0 16.2 - - + -
329A PRO 4.6 1.3 - - - +
330A VAL* 1.3 78.2 - - - +
332A SER* 1.3 67.8 + - - +
333A LEU* 4.6 14.0 - - + +
346A ILE 3.7 0.9 - - - +
347A THR* 3.3 1.1 - - - -
348A ILE* 2.8 50.8 + - + +
353A TYR* 3.9 21.3 - - + -
372A ILE* 3.4 33.9 - - + -
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Residues in contact with SER 332 (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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254A VAL* 3.5 6.9 - - - +
255A GLU* 2.9 49.3 + - - +
258A GLY 5.9 1.2 + - - -
330A VAL* 4.3 3.1 - - - +
331A ILE* 1.3 71.1 - - - +
333A LEU* 1.3 67.7 + - - +
334A TYR* 4.4 3.1 - - - -
345A ARG* 3.7 19.6 + - - -
346A ILE 3.0 6.3 - - - -
347A THR* 2.6 30.4 + - - +
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ILE* 4.1 25.1 - - + -
253A ARG 3.8 2.0 - - - -
254A VAL* 4.0 25.1 - - + -
282A LEU* 4.7 11.4 - - + -
284A LEU* 5.4 7.6 - - + -
331A ILE* 4.6 11.9 - - + +
332A SER* 1.3 82.6 - - - +
334A TYR* 1.3 63.4 + - - +
335A LEU* 3.9 8.9 + - + +
344A PHE 3.9 0.2 - - - +
345A ARG* 3.2 0.9 - - - -
346A ILE* 2.8 46.1 + - + +
379A THR* 5.3 0.2 - - + -
381A MET* 4.2 25.4 - - + -
385A ILE* 4.2 23.3 - - + -
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Residues in contact with TYR 334 (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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251A ILE* 3.4 8.1 - - - +
252A VAL* 2.8 40.7 + - + -
253A ARG* 2.8 45.7 + - + +
255A GLU* 2.9 41.4 + - + -
332A SER* 4.4 5.2 - - - -
333A LEU* 1.3 76.3 - - - +
335A LEU* 1.3 60.2 + - - +
343A SER* 3.8 17.0 - - - +
344A PHE 3.1 7.4 - - - +
345A ARG* 2.7 50.8 + - + -
422A PHE* 4.0 24.7 - + + -
424A THR* 4.9 1.3 - - - -
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Residues in contact with LEU 335 (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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239A THR* 3.5 15.5 - - + +
249A VAL* 4.6 14.1 - - + -
250A ILE 3.6 7.4 - - - +
251A ILE* 3.8 27.8 - - + -
252A VAL* 4.2 1.1 - - - -
333A LEU* 4.4 10.8 - - + +
334A TYR* 1.3 77.4 - - - +
336A MET* 1.3 66.5 + - - +
343A SER* 3.2 7.8 - - - -
344A PHE* 2.8 57.8 + - + -
346A ILE* 4.3 13.9 - - + -
381A MET* 4.6 8.1 - - - -
402A PHE* 3.8 28.3 - - + -
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Residues in contact with MET 336 (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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239A THR* 2.7 33.5 + - - +
240A PRO* 3.4 21.5 - - + +
250A ILE* 3.2 46.3 + - + +
252A VAL* 3.8 7.4 - - + +
335A LEU* 1.3 71.3 - - - +
337A GLY* 1.3 70.2 + - - +
344A PHE* 3.8 1.2 - - - -
427A MET* 3.5 59.5 - - + +
428A GLU* 3.6 9.6 - - + +
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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