Contacts of the strand formed by residues 406 - 414 (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 TYR 406 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A HIS 3.6 0.3 - - - +
395A LEU* 3.6 2.3 - - - -
396A GLN* 2.9 30.3 + - + +
402A ARG 5.4 1.6 - - - -
403A CYS* 3.5 22.0 + - + +
404A ALA 3.3 19.0 - - - -
405A ASN* 1.3 79.2 - - - +
407A ILE* 1.3 62.7 + - - +
474A VAL 3.9 14.1 - - - +
475A THR* 3.6 43.2 - - + -
477A MET* 3.6 5.6 - - - -
478A HIS* 3.5 46.8 + + + +
479A LEU* 4.7 1.6 - - - +
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Residues in contact with ILE 407 (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* 4.9 1.1 - - + -
393A LEU* 3.6 32.8 - - + -
394A HIS 3.4 4.5 - - - +
395A LEU* 3.8 8.7 - - + -
406A TYR* 1.3 73.3 - - - +
408A SER* 1.3 64.4 + - - +
409A LEU* 5.3 1.3 - - + -
434A ILE* 4.2 25.1 - - + -
474A VAL 3.5 1.4 - - - +
475A THR 4.0 0.2 - - - -
476A PHE* 3.0 31.5 + - + +
477A MET* 2.8 27.6 + - + +
479A LEU* 3.7 28.9 - - + -
482A LEU* 4.3 20.2 - - + -
493A LEU* 4.8 8.3 - - + -
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ARG 4.2 0.4 - - - -
393A LEU* 3.3 10.0 - - - +
394A HIS* 2.8 45.5 + - - -
396A GLN* 3.0 26.8 + - - +
407A ILE* 1.3 73.7 - - - +
409A LEU* 1.3 59.8 + - - +
410A PHE* 4.1 12.3 - - - -
473A TYR 3.3 10.1 - - - -
474A VAL* 2.6 24.5 + - - -
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Residues in contact with LEU 409 (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* 4.5 5.8 - - + -
391A MET* 4.2 22.4 - - + -
392A ARG 3.3 15.7 - - - +
393A LEU* 4.7 9.4 - - + -
407A ILE* 5.3 0.7 - - + -
408A SER* 1.3 74.4 - - - +
410A PHE* 1.3 69.1 + - - +
432A LEU* 3.9 34.8 - - + +
434A ILE* 5.2 1.3 - - + -
472A GLY* 3.4 2.1 - - - -
473A TYR* 2.9 33.5 + - - -
476A PHE* 3.9 36.3 - - + +
495A VAL* 3.9 23.3 - - + -
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Residues in contact with PHE 410 (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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391A MET* 3.3 9.4 - - - +
392A ARG* 2.9 50.7 + - + -
394A HIS* 5.9 2.2 - + - -
408A SER* 4.1 10.8 - - - -
409A LEU* 1.3 79.2 - - - +
411A VAL* 1.3 66.5 + - - +
412A HIS* 4.8 1.1 - - - +
432A LEU* 5.3 0.7 - - - -
470A GLY 3.9 5.4 - - - -
471A PHE 3.3 13.9 - - - +
472A GLY 3.0 31.2 - - - -
473A TYR 3.7 16.8 - - - -
474A VAL* 3.7 23.3 - - + -
605B GLN* 3.5 13.2 - - + -
607B ILE* 3.4 34.3 - - + -
609B PHE* 4.0 17.3 - + + -
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Residues in contact with VAL 411 (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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380A PHE* 6.1 0.7 - - + -
389A LEU* 4.3 20.2 - - + -
390A CYS 3.6 6.5 - - - +
391A MET* 4.3 8.3 - - + -
410A PHE* 1.3 78.1 - - - +
412A HIS* 1.3 74.0 + - - +
413A THR* 5.9 1.1 - - + -
430A ILE* 4.2 22.2 - - + -
432A LEU* 4.0 20.4 - - + -
450A MET* 3.8 22.0 - - + -
458A ALA* 5.6 1.6 - - - +
459A PHE* 5.8 4.5 - - + -
469A LYS 4.6 0.2 - - - +
470A GLY* 3.3 4.2 - - - -
471A PHE* 2.9 36.1 + - + +
497A CYS* 4.7 3.8 - - - -
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Residues in contact with HIS 412 (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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376A HIS* 4.7 3.3 - + - -
389A LEU* 3.2 7.6 - - - +
390A CYS* 3.0 51.8 + - - -
392A ARG* 3.3 42.2 + - + -
410A PHE* 4.8 0.6 - - - +
411A VAL* 1.3 80.3 - - - +
413A THR* 1.3 63.4 + - - +
414A MET* 4.1 0.2 - - - +
458A ALA 5.6 0.2 - - - -
466A ARG* 3.9 21.5 + - + -
467A ASN 2.9 24.5 + - - +
468A PRO* 4.0 1.3 - - + -
469A LYS 3.3 9.4 + - - -
470A GLY* 3.5 19.4 - - - -
609B PHE* 3.6 20.8 - + + -
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Residues in contact with THR 413 (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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387A TYR* 5.7 1.1 - - + -
388A LYS 4.7 0.4 - - - -
389A LEU* 3.8 22.0 - - + -
411A VAL* 5.9 1.1 - - + -
412A HIS* 1.3 76.4 - - - +
414A MET* 1.3 62.7 + - - +
424A TRP* 4.7 13.0 - - + -
426A PHE* 5.1 5.2 - - + -
458A ALA 3.3 17.4 + - - +
459A PHE* 4.4 17.0 - - + +
460A GLN 3.1 14.1 + - - +
462A PRO* 3.7 5.4 - - - +
467A ASN* 3.0 53.7 + - - +
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Residues in contact with MET 414 (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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379A GLY* 4.0 17.7 - - - +
388A LYS* 2.9 50.0 + - + +
389A LEU 4.1 2.2 - - - -
390A CYS* 3.6 28.5 - - - -
412A HIS 4.1 7.0 - - - +
413A THR* 1.3 81.3 - - - +
415A GLN* 1.3 64.8 + - - +
416A GLY 3.2 3.5 + - - -
419A ASP* 4.0 5.2 - - - +
424A TRP* 4.8 5.0 - - - -
462A PRO* 3.9 10.2 - - - +
465A PRO* 3.2 26.0 - - + +
466A ARG* 4.2 21.3 - - + -
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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