Contacts of the strand formed by residues 364 - 369 (chain A) in PDB entry 4LG8
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 364 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A PHE* 3.8 6.6 - - - -
359A HIS* 2.9 58.3 + - + +
363A LEU* 1.3 89.0 - - + +
365A PHE* 1.3 65.9 + - - +
376A ILE* 4.2 20.4 - - + -
377A TRP 3.1 14.6 - - - +
378A ASP* 4.5 9.9 - - + -
385A VAL* 5.4 4.3 - - + -
400A PHE* 4.8 7.2 - - + -
421A LEU* 5.0 10.5 - - + -
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Residues in contact with PHE 365 (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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322A LEU* 3.6 34.1 - - + -
330A TRP* 3.6 38.1 - + - -
357A GLN 3.2 15.3 - - - +
358A PHE* 3.8 19.1 - + + -
359A HIS 4.1 2.2 - - - +
364A ILE* 1.3 78.3 - - - +
366A GLY* 1.3 63.4 + - - +
367A THR* 4.3 4.0 - - + -
376A ILE* 3.3 6.4 - - - +
377A TRP* 2.8 67.9 + + + -
379A LEU* 3.9 34.1 - - + -
400A PHE* 4.2 7.0 - - - -
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Residues in contact with GLY 366 (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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356A ALA* 3.3 4.5 - - - +
357A GLN 2.9 33.0 + - - +
365A PHE* 1.3 75.9 - - - +
367A THR* 1.3 65.4 + - - +
374A ILE* 5.1 1.1 - - - -
375A LYS 3.2 8.5 - - - -
376A ILE* 4.2 11.0 - - - -
398A ILE* 3.5 18.4 - - - -
400A PHE* 3.8 4.5 - - - -
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Residues in contact with THR 367 (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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324A SER* 4.8 0.9 - - - -
330A TRP* 4.4 7.0 - - + -
353A LEU* 4.0 32.9 - - + +
355A CYS 3.2 13.2 - - - +
356A ALA* 4.3 8.7 - - + -
365A PHE* 4.3 13.0 - - + -
366A GLY* 1.3 78.0 - - - +
368A GLY* 1.3 62.9 + - - +
374A ILE* 4.6 3.6 - - - +
375A LYS* 2.8 39.2 + - - +
377A TRP* 3.1 29.5 + - + +
398A ILE* 4.2 0.2 - - - +
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Residues in contact with GLY 368 (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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353A LEU* 3.2 9.0 - - - +
354A THR* 2.8 31.2 + - - -
355A CYS* 3.2 20.7 + - - -
367A THR* 1.3 75.9 - - - +
369A THR* 1.3 56.2 + - - +
373A GLN 3.5 7.2 - - - -
374A ILE* 4.5 4.0 - - - -
395A ILE* 3.7 18.6 - - - -
398A ILE* 4.8 2.2 - - - +
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Residues in contact with THR 369 (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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349A SER* 5.7 2.7 - - - -
351A CYS* 3.8 8.7 - - - -
352A SER 3.4 5.2 - - - -
353A LEU* 3.8 10.5 - - + -
354A THR* 3.7 5.6 + - - -
368A GLY* 1.3 78.8 - - - +
370A MET* 1.3 62.9 + - - +
371A ASP* 2.5 28.2 + - - +
372A SER 3.3 4.2 + - - -
373A GLN* 3.0 32.3 + - + +
375A LYS* 3.6 33.2 - - + -
395A ILE* 3.1 23.1 + - - +
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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