Contacts of the helix formed by residues 461 - 475 (chain A) in PDB entry 5E8W
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 CYS 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A VAL* 4.2 9.2 - - - -
417A ILE* 3.7 33.2 - - + -
457A ARG 4.9 0.2 - - - +
458A TRP 3.2 4.9 + - - +
460A SER* 1.3 81.6 + - - +
462A GLU* 1.3 62.6 + - - +
463A ALA* 3.6 13.0 - - - -
464A LEU* 3.6 28.9 - - + -
465A ARG* 2.9 30.3 + - - +
499A GLU* 6.0 0.2 - - - -
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Residues in contact with GLU 462 (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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460A SER 4.2 0.8 + - - -
461A CYS* 1.3 73.0 - - - +
463A ALA* 1.4 58.1 - - - +
465A ARG* 2.8 47.9 + - - +
466A VAL* 3.0 46.6 + - + +
495A LEU* 4.7 9.8 - - + +
499A GLU* 4.9 7.0 - - - +
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Residues in contact with ALA 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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299A VAL* 3.6 30.1 - - + -
302A MET* 3.9 13.2 - - + -
303A ILE* 3.9 13.9 - - + -
461A CYS* 3.4 6.9 - - - -
462A GLU* 1.4 77.1 - - - +
464A LEU* 1.4 57.3 + - - +
466A VAL* 3.4 3.1 + - - +
467A MET* 3.0 31.5 + - - +
495A LEU* 3.9 15.9 - - + +
499A GLU* 4.0 8.7 + - - +
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Residues in contact with LEU 464 (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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302A MET* 3.6 31.0 - - + -
412A ALA* 4.0 25.6 - - + +
415A CYS* 4.2 3.4 - - + -
417A ILE* 3.6 27.6 - - + -
457A ARG* 3.7 20.6 - - - +
458A TRP* 3.3 44.5 - - + +
461A CYS* 3.3 17.1 + - + +
463A ALA* 1.4 75.2 - - - +
465A ARG* 1.4 57.7 + - - +
467A MET* 3.5 3.4 + - + +
468A ALA* 2.9 30.5 + - - +
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Residues in contact with ARG 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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458A TRP 3.6 6.7 - - - +
459A GLN* 2.7 52.8 + - + +
460A SER* 3.7 18.0 + - - +
461A CYS 2.9 16.8 + - - +
462A GLU* 2.8 46.3 + - - +
464A LEU* 1.4 72.4 - - - +
466A VAL* 1.3 65.1 + - + +
468A ALA* 3.6 6.0 + - - +
469A LYS* 3.1 23.6 + - - +
472A ARG* 5.2 1.0 + - - -
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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
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462A GLU* 3.0 40.5 + - - +
463A ALA 3.8 4.7 - - - +
464A LEU 3.4 0.2 - - - -
465A ARG* 1.3 77.3 - - + +
467A MET* 1.3 57.3 + - - +
469A LYS* 3.4 8.1 + - - +
470A ILE* 3.0 34.2 + - + +
491A THR* 3.7 30.3 - - + -
492A LEU* 4.9 0.9 - - + -
495A LEU* 4.2 29.8 - - + -
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Residues in contact with MET 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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302A MET* 3.9 35.7 - - + -
303A ILE* 5.7 1.3 - - + -
306A ALA* 3.8 33.2 - - + -
408A PHE* 3.6 44.3 - - + +
411A ILE* 4.8 2.2 - - + -
412A ALA* 4.6 2.5 - - + +
463A ALA 3.0 20.7 + - - +
464A LEU* 3.7 7.0 - - - +
465A ARG 3.4 0.2 - - - -
466A VAL* 1.3 75.1 - - - +
468A ALA* 1.4 56.1 + - - +
470A ILE* 3.2 7.2 + - - +
471A MET* 2.9 40.5 + - + +
492A LEU* 3.9 19.7 - - + -
495A LEU* 5.3 2.5 - - + -
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Residues in contact with ALA 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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454A ILE* 3.8 29.0 - - + +
458A TRP* 4.3 6.7 - - + -
464A LEU 2.9 18.3 + - - +
465A ARG* 3.9 7.2 - - - +
466A VAL 3.4 0.2 - - - -
467A MET* 1.4 74.9 - - - +
469A LYS* 1.3 60.6 + - - +
471A MET* 3.4 15.8 + - - +
472A ARG* 3.1 41.1 + - - +
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Residues in contact with LYS 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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465A ARG 3.1 17.5 + - - +
466A VAL* 3.6 8.5 - - - +
467A MET 3.3 0.2 - - - -
468A ALA* 1.3 71.8 - - - +
470A ILE* 1.4 67.0 + - + +
472A ARG* 3.4 20.2 + - - +
473A GLU* 3.0 58.2 + - + +
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Residues in contact with ILE 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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408A PHE* 3.8 26.7 - - + -
466A VAL* 3.0 30.5 + - + +
467A MET* 3.5 8.5 - - - +
469A LYS* 1.4 73.8 - - + +
471A MET* 1.4 63.3 + - - +
473A GLU* 3.1 5.8 + - - +
474A CYS* 3.0 29.9 + - - -
483A LEU* 4.2 15.4 - - + +
488A ILE* 4.0 25.4 - - + -
491A THR* 4.0 16.6 - - + -
492A LEU* 3.8 36.3 - - + -
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Residues in contact with MET 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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405A GLY* 3.7 19.3 - - - +
408A PHE* 3.7 21.1 - - + +
409A TRP* 3.7 18.4 - - - -
412A ALA* 3.6 19.7 - - + -
454A ILE* 4.6 3.4 - - + -
458A TRP* 3.6 30.3 - - + -
467A MET* 2.9 33.9 + - + +
468A ALA* 3.5 10.8 - - - +
469A LYS 3.3 0.2 - - - -
470A ILE* 1.4 75.4 - - - +
472A ARG* 1.4 62.3 + - - +
474A CYS* 3.0 15.5 + - - +
475A TRP* 3.1 42.5 - - + -
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Residues in contact with ARG 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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454A ILE* 3.7 32.2 - - + +
459A GLN* 5.5 9.7 - - - +
465A ARG 5.2 0.8 + - - -
468A ALA* 3.1 27.8 + - - +
469A LYS* 3.7 33.7 - - - +
471A MET* 1.4 77.3 - - - +
473A GLU* 1.3 61.1 + - + +
475A TRP* 3.1 28.7 + - + +
476A TYR* 3.7 18.1 + - + +
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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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469A LYS* 3.0 52.3 + - + +
470A ILE* 3.1 4.2 + - - +
472A ARG* 1.3 77.2 - - + +
474A CYS* 1.4 57.4 + - - +
475A TRP 3.4 0.4 - - - -
476A TYR* 3.5 31.1 + - + +
481A ALA 5.7 0.2 - - - +
482A ARG* 3.3 9.9 - - - -
483A LEU* 3.2 59.6 + - + +
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Residues in contact with CYS 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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401A ILE* 3.5 40.6 - - - +
402A TYR* 3.3 10.6 - - - -
404A MET* 5.1 2.0 - - - -
405A GLY* 3.8 20.4 - - - -
408A PHE* 5.8 0.2 - - - -
470A ILE* 3.0 23.1 + - - -
471A MET 3.0 8.0 + - - +
473A GLU* 1.4 77.1 - - - +
475A TRP* 1.3 60.0 + - + +
476A TYR 3.6 1.3 - - - -
482A ARG* 3.1 24.5 + - - -
483A LEU* 5.1 1.1 - - - -
488A ILE* 3.7 20.6 - - - -
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Residues in contact with TRP 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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402A TYR* 3.8 24.0 - + - -
405A GLY* 3.4 22.2 - - - -
406A LEU* 3.4 37.7 - - + +
409A TRP* 3.9 10.8 - + + -
451A ARG* 2.9 53.5 + - + +
452A PRO* 3.6 36.1 - - + -
454A ILE* 4.0 14.4 - - + -
471A MET* 3.1 42.6 - - + +
472A ARG* 3.1 14.2 + - + +
474A CYS* 1.3 85.0 - - + +
476A TYR* 1.3 67.1 + - - +
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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