Contacts of the strand formed by residues 381 - 388 (chain A) in PDB entry 3LX9
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 ALA 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A CYS* 3.1 7.6 + - - -
380A PRO* 1.3 84.1 - - + +
382A CYS* 1.3 62.9 + - - +
396A PHE* 5.3 5.4 - - + -
397A TYR 3.2 16.8 - - - +
398A GLU* 4.0 11.7 - - + -
419A ASN* 3.1 23.0 + - - -
420A THR* 3.2 26.2 + - + +
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Residues in contact with CYS 382 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A ALA 3.5 9.2 - - - +
378A CYS* 2.0 47.6 - - - -
381A ALA* 1.3 74.7 - - - +
383A PHE* 1.3 58.9 + - - +
384A ILE* 3.8 24.0 - - - -
395A GLY 3.9 0.2 - - - +
396A PHE* 3.4 3.4 - - - -
397A TYR* 2.7 40.6 + - - +
417A LEU* 4.3 2.5 - - + -
418A GLU 3.1 20.4 - - - +
420A THR* 4.2 5.6 - - - -
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Residues in contact with PHE 383 (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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382A CYS* 1.3 71.9 - - - +
384A ILE* 1.3 66.7 + - - +
385A THR* 3.6 22.7 + - - -
393A LYS* 3.9 41.7 - - + -
395A GLY* 3.5 28.3 - - - -
396A PHE* 3.6 42.8 - + + -
416A GLN 3.5 3.8 - - - +
418A GLU* 2.7 46.4 + - + +
420A THR* 4.6 1.2 - - + +
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Residues in contact with ILE 384 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369A VAL* 4.3 7.0 - - + -
372A LEU* 5.4 0.2 - - + -
382A CYS* 3.8 21.3 - - - -
383A PHE* 1.3 77.0 - - - +
385A THR* 1.3 64.3 + - - +
394A LEU* 2.8 47.7 + - + +
395A GLY 3.0 8.9 + - - -
397A TYR* 3.5 40.6 - - + -
403A LEU* 4.1 19.3 - - + -
415A LEU* 4.0 24.0 - - + -
416A GLN 3.6 2.5 - - - -
417A LEU* 4.1 16.4 - - + -
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Residues in contact with THR 385 (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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383A PHE* 3.6 20.3 + - - -
384A ILE* 1.3 75.3 - - - +
386A GLN* 1.3 74.4 + - - +
387A LEU* 3.6 14.1 + - + +
391A LYS* 4.3 15.0 - - - -
392A ARG 3.7 13.9 - - - +
393A LYS* 4.3 10.4 - - + +
415A LEU* 3.4 3.5 - - - -
416A GLN* 2.8 44.9 + - - +
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Residues in contact with GLN 386 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A THR* 1.3 74.3 - - - +
387A LEU* 1.3 61.0 + - - +
388A LEU 3.5 17.5 - - - +
389A PRO* 4.0 6.7 - - - +
390A VAL* 2.9 41.3 + - - +
391A LYS* 3.2 7.8 - - - +
392A ARG* 2.8 64.0 + - - +
394A LEU* 4.1 13.0 - - + +
405A SER* 5.1 2.9 + - - -
413A VAL* 3.8 16.7 - - + +
414A LEU 3.8 2.7 - - - +
415A LEU* 3.5 20.3 - - + +
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Residues in contact with LEU 387 (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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313A ASP* 4.5 5.1 - - - +
315A ASP* 3.7 39.7 - - + +
316A VAL* 4.5 7.6 - - + +
319A ILE* 3.5 32.1 - - + -
385A THR* 4.1 15.9 - - + +
386A GLN* 1.3 80.1 - - - +
388A LEU* 1.3 69.4 + - - +
390A VAL* 3.4 17.4 + - - -
391A LYS* 3.6 19.1 + - + +
414A LEU* 2.7 26.9 + - + +
416A GLN* 3.7 20.6 - - + +
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Residues in contact with LEU 388 (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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277A TRP* 6.4 0.2 - - + -
281A VAL* 3.9 22.9 - - + +
285A ALA* 4.0 28.3 - - + +
310A LEU* 3.9 24.2 - - + -
313A ASP* 3.9 16.8 - - - +
316A VAL* 3.8 22.0 - - + -
386A GLN* 3.5 10.4 - - - +
387A LEU* 1.3 86.5 - - - +
389A PRO* 1.3 77.8 - - + +
390A VAL 3.3 2.0 - - - -
412A THR 4.0 1.6 - - - +
413A VAL* 3.3 3.5 - - - -
414A LEU* 2.9 34.9 + - + +
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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