Contacts of the helix formed by residues 445 - 458 (chain E) in PDB entry 4YJL
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 GLN 445 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408E HIS* 5.1 4.9 + - - -
412E GLN* 3.0 28.1 + - - +
442E VAL 3.3 10.2 + - - -
443E GLU 3.7 0.6 - - - -
444E HIS* 1.3 77.6 - - - +
446E ILE* 1.3 62.5 + - - +
447E CYS 3.5 2.0 - - - -
448E PRO* 3.6 27.8 - - + +
449E ALA 3.3 10.7 + - - -
493E TYR* 4.0 7.2 - - - -
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Residues in contact with ILE 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412E GLN* 4.4 6.5 - - + +
413E ILE* 4.2 20.2 - - + -
416E TYR* 3.6 40.8 - - + -
441E PRO* 3.3 27.5 + - + +
444E HIS* 3.6 15.5 - - + +
445E GLN* 1.3 75.7 - - - +
447E CYS* 1.3 65.2 + - - +
449E ALA* 3.2 4.1 + - - +
450E VAL* 3.0 22.2 + - + +
478E LEU* 3.7 29.6 - - + -
493E TYR* 3.3 4.2 + - - -
497E LEU* 4.0 19.7 - - + -
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Residues in contact with CYS 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446E ILE* 1.3 78.7 - - - +
448E PRO* 1.4 60.6 - - + +
450E VAL* 3.4 8.0 - - - +
451E CYS* 3.0 30.5 + - - +
493E TYR* 3.0 38.5 + - + -
496E THR* 3.4 39.7 - - - -
497E LEU* 3.7 15.7 - - + -
500E TYR* 3.9 4.4 - - - -
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Residues in contact with PRO 448 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445E GLN* 3.4 39.9 - - + +
447E CYS* 1.4 93.0 - - + +
449E ALA* 1.3 60.7 + - - +
451E CYS* 3.4 7.0 - - + +
452E VAL* 3.0 32.2 + - + +
493E TYR* 3.6 7.6 - - + +
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Residues in contact with ALA 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409E LEU* 3.9 15.8 - - + +
412E GLN* 3.7 26.2 - - - +
413E ILE* 4.0 18.8 - - + -
445E GLN* 3.3 13.2 + - - +
446E ILE* 3.2 10.4 + - - +
448E PRO* 1.3 79.8 - - - +
450E VAL* 1.3 58.2 + - - +
452E VAL* 3.4 2.9 + - - +
453E LEU* 3.0 32.6 + - - +
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Residues in contact with VAL 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413E ILE* 4.5 10.5 - - + -
446E ILE 3.0 16.6 + - - +
447E CYS 3.4 6.7 - - - +
449E ALA* 1.3 72.6 - - - +
451E CYS* 1.3 58.9 + - - +
453E LEU* 3.8 11.7 - - + +
454E MET* 2.8 35.5 + - - +
475E ILE* 5.3 3.8 - - + -
478E LEU* 3.4 31.4 - - + -
497E LEU* 3.7 31.2 - - + +
500E TYR* 3.7 14.4 - - + +
501E ALA* 4.1 16.4 - - + +
504E ALA* 5.3 0.4 - - + +
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Residues in contact with CYS 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447E CYS 3.0 19.2 + - - +
448E PRO* 3.4 10.3 - - + +
450E VAL* 1.3 78.9 - - - +
452E VAL* 1.3 59.4 + - + +
454E MET* 3.3 4.5 + - - +
455E LYS* 3.0 46.0 + - - +
500E TYR* 3.5 38.6 - - + -
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Residues in contact with VAL 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409E LEU* 3.7 27.6 - - + -
448E PRO* 3.0 19.2 + - + +
449E ALA 3.9 3.1 - - - +
451E CYS* 1.3 74.9 - - + +
453E LEU* 1.3 65.9 + - - +
455E LYS* 3.1 15.8 + - + +
456E LEU* 2.9 34.8 + - + +
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Residues in contact with LEU 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E MET* 4.4 6.7 - - + -
409E LEU* 3.8 34.8 - - + +
410E LEU* 3.9 24.5 - - + -
413E ILE* 3.9 29.4 - - + -
449E ALA 3.0 24.6 + - - +
450E VAL* 3.8 8.7 - - + +
452E VAL* 1.3 77.0 - - - +
454E MET* 1.3 62.4 + - - +
456E LEU* 3.3 3.8 + - + -
457E SER* 2.9 25.4 + - - -
466E MET* 3.7 22.1 - - + +
475E ILE* 4.1 17.0 - - + -
504E ALA* 4.5 3.4 - - + -
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Residues in contact with MET 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450E VAL 2.8 21.4 + - - +
451E CYS* 3.4 8.7 - - - +
452E VAL 3.3 0.2 - - - -
453E LEU* 1.3 72.2 - - - +
455E LYS* 1.3 83.2 + - + +
457E SER* 2.7 24.4 + - - -
458E PHE* 2.9 43.1 - - + -
500E TYR* 3.6 24.5 - - + +
503E MET* 3.5 47.8 - - + +
504E ALA* 4.0 7.5 - - - +
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Residues in contact with LYS 455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E CYS* 3.0 33.7 + - - +
452E VAL* 3.1 17.0 + - + +
454E MET* 1.3 95.8 - - + +
456E LEU* 1.3 63.2 + - + +
458E PHE* 3.3 18.4 + - - +
459E ASP* 4.4 1.9 + - - +
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Residues in contact with LEU 456 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405E HIS* 5.9 0.2 - - + -
406E MET* 4.7 9.2 - - + -
409E LEU* 3.8 26.5 - - + -
452E VAL* 2.9 27.8 + - + +
453E LEU* 3.7 7.6 - - + +
455E LYS* 1.3 75.9 - - + +
457E SER* 1.3 56.9 + - - +
458E PHE 3.1 0.2 - - - -
459E ASP* 3.0 20.3 + - - +
462E HIS* 3.2 49.4 - - + +
466E MET* 3.7 13.0 - - + -
806E EDO 3.9 27.6 - - - +
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Residues in contact with SER 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453E LEU 2.9 14.4 + - - -
454E MET 2.7 19.8 + - - -
456E LEU* 1.3 75.0 - - - +
458E PHE* 1.3 57.3 + - - +
459E ASP 3.2 0.4 - - - -
463E ARG* 2.9 33.3 + - - +
466E MET* 4.0 17.9 - - - -
504E ALA* 3.5 17.8 - - - -
507E ASN* 2.8 33.4 + - - +
508E LEU* 4.7 4.0 - - - -
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Residues in contact with PHE 458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454E MET* 2.9 46.6 + - + -
455E LYS 3.3 8.9 + - - +
456E LEU 3.1 1.2 + - - -
457E SER* 1.3 77.2 + - - +
459E ASP* 1.3 57.5 + - - +
460E GLU 3.9 0.7 + - - -
463E ARG* 3.2 11.4 + - - +
503E MET* 4.6 3.6 - - + -
507E ASN* 3.3 29.6 - - - +
505J LEU* 4.6 18.8 - - + +
506J TYR* 3.3 42.8 - + + -
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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