Contacts of the helix formed by residues 462 - 476 (chain A) in PDB entry 5LS6
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 THR 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A GLN* 3.2 46.0 + - - +
455A ALA* 3.5 6.1 - - - -
461A LYS* 1.3 78.7 - - - +
463A CYS* 1.3 58.0 + - - +
464A ARG* 3.9 12.8 - - - +
465A GLN* 2.3 57.6 + - - +
466A VAL* 3.1 10.2 + - - +
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Residues in contact with CYS 463 (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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320A CYS* 3.3 17.9 - - - -
323A GLN 4.2 1.3 - - - +
324A CYS* 4.0 4.3 - - - -
325A TYR* 3.3 31.3 - - - +
451A PHE* 3.9 6.2 - - - +
452A CYS 3.9 11.2 - - - -
455A ALA* 3.3 16.4 - - + +
462A THR* 1.3 73.1 - - - +
464A ARG* 1.3 63.5 + - - +
466A VAL* 3.6 3.5 + - - +
467A TYR* 3.4 19.4 + - - +
802A ZN 1.9 39.0 - - - -
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Residues in contact with ARG 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A GLN* 3.9 7.5 + - + +
324A CYS 3.7 21.8 - - - +
325A TYR* 3.8 11.3 - - - +
326A GLN 5.5 4.7 - - - +
423A ASN* 5.8 2.4 + - - -
425A GLU* 4.0 30.0 + - - +
426A PRO 4.0 3.0 + - - -
427A PRO* 4.5 3.2 - - - +
428A GLU* 3.6 40.8 + - - +
462A THR* 3.9 10.3 - - - +
463A CYS* 1.3 76.7 - - - +
465A GLN* 1.3 63.6 + - - +
467A TYR* 3.2 15.7 + - - +
468A GLU* 2.5 68.6 + - - +
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Residues in contact with GLN 465 (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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428A GLU* 3.9 19.1 + - - +
430A VAL* 3.2 47.1 - - + +
432A TRP* 3.4 13.9 + - + +
460A THR 5.1 1.6 + - - -
461A LYS* 3.7 24.1 - - + +
462A THR* 2.3 53.6 + - - +
464A ARG* 1.3 73.8 - - + +
466A VAL* 1.3 63.1 + - - +
468A GLU* 3.5 13.7 + - - +
469A PHE* 3.1 18.0 + - - +
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Residues in contact with VAL 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TRP* 4.1 18.6 - - + -
440A PHE* 3.9 14.1 - - + -
451A PHE* 3.5 26.9 - - + -
454A ILE* 3.5 26.9 - - + -
455A ALA* 3.8 26.0 - - + -
458A ILE* 4.4 2.2 - - + -
461A LYS* 4.4 7.9 - - + -
462A THR 3.1 11.3 + - - +
463A CYS 3.8 7.6 - - - +
465A GLN* 1.3 75.1 - - - +
467A TYR* 1.3 59.5 + - - +
469A PHE* 3.0 5.2 + - - +
470A ARG* 2.9 26.7 + - - +
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Residues in contact with TYR 467 (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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325A TYR* 3.6 39.5 - + + -
330A GLY* 2.7 33.2 + - - -
331A ALA* 3.7 9.9 - - - -
334A PHE* 4.3 3.8 - - - +
335A ALA* 4.2 10.8 - - + -
423A ASN* 3.2 35.3 + - - +
451A PHE* 4.0 20.8 - + + -
463A CYS 3.4 3.4 + - - +
464A ARG* 3.2 17.6 + - - +
466A VAL* 1.3 80.3 - - - +
468A GLU* 1.3 67.4 + - + +
470A ARG* 3.4 9.1 + - + +
471A VAL* 3.0 50.6 + - + +
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Residues in contact with GLU 468 (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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423A ASN* 6.2 1.3 - - - +
427A PRO* 3.6 18.6 - - + +
428A GLU* 2.8 44.4 + - - +
430A VAL* 5.6 0.3 - - - +
464A ARG* 2.5 58.9 + - - +
465A GLN* 3.8 12.2 - - - +
466A VAL 3.3 0.4 - - - -
467A TYR* 1.3 86.4 - - + +
469A PHE* 1.3 53.2 + - - +
471A VAL* 3.3 7.8 + - - +
472A LYS* 2.8 35.0 + - - +
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Residues in contact with PHE 469 (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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432A TRP* 3.3 60.6 - + + +
437A ALA* 4.0 28.3 - - + -
440A PHE* 3.6 38.1 - + - -
441A ARG* 4.5 5.8 - - - -
465A GLN 3.1 5.2 + - - +
466A VAL 3.0 5.2 + - - +
468A GLU* 1.3 73.2 - - - +
470A ARG* 1.3 56.5 + - - +
472A LYS* 3.4 20.8 + - + +
473A GLU* 2.7 58.2 + - + +
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Residues in contact with ARG 470 (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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335A ALA* 5.0 2.3 + - - +
338A LEU* 3.4 22.3 + - + +
339A THR* 2.9 46.5 + - - +
342A ARG* 4.8 14.3 - - - +
440A PHE* 3.7 25.4 - - + -
444A ILE* 6.1 4.9 - - - +
449A ASP* 4.2 9.5 + - - -
451A PHE* 3.8 27.1 - - + -
466A VAL 2.9 12.2 + - - +
467A TYR* 3.4 10.3 - - + +
469A PHE* 1.3 74.6 - - - +
471A VAL* 1.3 59.2 + - + +
473A GLU* 2.9 5.3 + - - +
474A SER* 2.7 55.6 + - - +
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Residues in contact with VAL 471 (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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334A PHE* 4.5 13.7 - - + -
338A LEU* 4.2 14.4 - - + -
423A ASN* 4.0 18.6 - - - +
427A PRO* 6.3 2.0 - - + -
467A TYR* 3.0 50.9 + - + +
468A GLU* 3.3 10.5 + - - +
470A ARG* 1.3 78.2 - - + +
472A LYS* 1.3 62.6 + - - +
474A SER* 2.7 22.4 + - - +
475A SER* 3.1 13.6 + - - +
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Residues in contact with LYS 472 (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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427A PRO* 6.5 0.7 - - - -
430A VAL 4.9 9.7 + - - -
432A TRP* 5.6 3.8 - - - -
468A GLU 2.8 20.1 + - - +
469A PHE* 3.7 23.7 - - + +
471A VAL* 1.3 74.3 - - - +
473A GLU* 1.3 57.4 + - + +
475A SER* 2.6 22.8 + - - +
476A ILE* 2.9 35.2 + - + +
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Residues in contact with GLU 473 (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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273A GLN* 4.8 5.0 + - - -
440A PHE* 4.6 8.2 - - + -
441A ARG* 3.4 38.9 + - - +
469A PHE* 2.7 49.7 + - + +
470A ARG* 3.5 7.2 - - - +
472A LYS* 1.3 70.5 - - + +
474A SER* 1.3 63.5 + - - +
475A SER 3.2 1.3 - - - -
476A ILE* 3.4 34.0 - - - +
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Residues in contact with SER 474 (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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338A LEU* 3.2 35.7 - - - +
342A ARG* 6.2 2.7 - - - +
470A ARG* 2.7 41.3 + - - +
471A VAL* 2.7 21.3 + - - +
473A GLU* 1.3 72.8 - - - +
475A SER* 1.3 58.3 + - - +
476A ILE 4.1 3.1 - - - +
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Residues in contact with SER 475 (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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471A VAL* 3.1 14.6 + - - +
472A LYS* 2.6 27.0 + - - +
474A SER* 1.3 76.7 + - - +
476A ILE* 1.3 66.0 + - - +
477A ILE* 3.9 5.9 + - - +
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Residues in contact with ILE 476 (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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472A LYS* 2.9 36.6 + - + +
473A GLU* 3.4 32.5 + - - +
474A SER 4.1 3.5 - - - +
475A SER* 1.3 82.4 - - - +
477A ILE* 1.3 76.2 + - - +
478A ALA 4.0 0.3 + - - -
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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