Contacts of the strand formed by residues 388 - 395 (chain A) in PDB entry 1LB6
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 LYS 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A GLY* 4.1 13.2 - - - -
380A PHE 3.3 11.4 - - - +
381A TYR* 3.7 37.8 + - + +
386A GLY 3.9 1.4 + - - -
387A TYR* 1.3 73.6 - - - +
389A LEU* 1.3 67.3 + - - +
413A THR* 3.9 0.5 - - - -
414A MET* 2.9 63.5 + - + +
415A GLN 3.4 21.1 + - - +
416A GLY* 3.8 11.8 - - - -
419A ASP* 4.9 0.6 + - - -
424A TRP* 6.1 0.4 - - - -
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Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLY* 3.3 3.1 - - - -
380A PHE* 2.8 50.8 + - + +
382A THR* 3.8 29.2 - - + -
387A TYR* 4.2 11.9 - - + -
388A LYS* 1.3 83.0 - - - +
390A CYS* 1.3 62.5 + - - +
411A VAL* 4.3 18.8 - - + -
412A HIS 3.2 17.9 - - - +
413A THR* 3.8 23.3 - - + -
414A MET* 4.1 4.7 - - - -
426A PHE* 5.4 6.7 - - + -
430A ILE* 4.8 6.3 - - + -
497A CYS* 5.3 0.7 - - - -
499A VAL* 3.9 20.2 - - + -
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Residues in contact with CYS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A HIS* 4.4 7.9 - - - -
377A SER* 3.5 24.9 - - - +
378A PRO 4.0 2.5 - - - +
379A GLY* 4.1 0.7 - - - +
380A PHE* 3.9 3.6 - - - -
389A LEU* 1.3 78.3 - - - +
391A MET* 1.3 70.4 + - - +
411A VAL* 3.6 4.0 - - - +
412A HIS* 3.0 39.8 + - - +
414A MET* 3.6 18.4 - - - -
466A ARG* 3.5 32.5 - - - -
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Residues in contact with MET 391 (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 TYR* 4.1 14.8 - - + -
355A TRP* 3.8 43.3 - - + -
376A HIS* 3.2 10.6 + - - +
377A SER* 2.8 32.1 + - - +
380A PHE* 4.2 7.8 - - + -
390A CYS* 1.3 76.7 - - - +
392A ARG* 1.3 61.3 - - - +
409A LEU* 4.2 5.2 - - + -
410A PHE 3.3 11.4 - - - +
411A VAL* 4.3 13.2 - - + -
432A LEU* 4.0 10.8 - - + -
495A VAL* 3.7 26.5 - - + +
497A CYS* 3.7 30.3 - - + -
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Residues in contact with ARG 392 (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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374A VAL* 3.2 12.0 - - + +
375A ILE 3.7 3.8 - - - -
376A HIS* 2.7 48.1 + - + +
390A CYS 4.2 0.2 + - - -
391A MET* 1.3 74.8 - - - +
393A LEU* 1.3 61.7 + - - +
394A HIS* 2.8 36.4 + - - +
408A SER 3.6 1.0 - - - +
409A LEU* 3.3 8.0 - - - +
410A PHE* 2.9 39.9 + - + +
412A HIS* 3.3 32.1 - - + -
466A ARG* 4.6 3.8 - - - +
609B PHE* 2.9 53.3 - - - +
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Residues in contact with LEU 393 (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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355A TRP* 3.7 19.7 - - + -
357A ILE* 4.0 18.6 - - + -
360A PHE* 5.1 4.5 - - + -
373A VAL* 5.3 2.2 - - + -
374A VAL* 3.4 4.2 - - - +
375A ILE* 2.9 49.6 + - + +
392A ARG* 1.3 73.9 - - - +
394A HIS* 1.3 66.4 + - - +
395A LEU* 3.9 28.7 - - + +
407A ILE* 3.6 20.6 - - + -
408A SER 3.3 8.1 - - - +
409A LEU* 4.7 7.4 - - + -
434A ILE* 5.4 1.3 - - + -
493A LEU* 4.2 15.3 - - + -
495A VAL* 4.5 9.0 - - + -
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Residues in contact with HIS 394 (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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373A VAL 3.4 4.3 - - - -
374A VAL* 3.4 29.7 - - + +
392A ARG* 2.8 54.9 + - - +
393A LEU* 1.3 73.6 - - - +
395A LEU* 1.3 67.1 + - - +
396A GLN* 3.7 18.6 + - - +
406A TYR 3.6 0.3 - - - +
407A ILE* 3.4 4.5 - - - +
408A SER* 2.8 50.6 + - - +
410A PHE* 5.9 1.6 - + - -
609B PHE* 4.1 9.4 - + - -
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Residues in contact with LEU 395 (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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360A PHE* 4.3 10.5 - - + -
363A HIS* 3.9 24.7 - - + +
364A LEU* 4.1 22.0 - - + -
367A GLN* 3.9 18.5 - - + +
371A LYS 5.3 1.0 - - - +
372A PRO* 5.4 0.5 - - - +
373A VAL* 3.0 49.1 + - + +
393A LEU* 3.9 17.7 - - + -
394A HIS* 1.3 73.8 - - - +
396A GLN* 1.3 66.3 + - - +
397A LEU* 3.6 3.1 + - - +
406A TYR 3.6 2.9 - - - -
407A ILE* 3.8 27.6 - - + -
479A LEU* 4.1 9.9 - - + -
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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