Contacts of the helix formed by residues 448 - 464 (chain A) in PDB entry 4Y5U
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 TRP 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A VAL 3.6 2.2 + - - -
447A PRO* 1.3 72.6 - - - +
449A GLU* 1.3 62.2 + - - +
451A MET* 3.7 25.4 - - + -
452A CYS* 3.0 43.6 + - - -
455A LEU* 4.5 11.2 - - + -
474A PHE* 3.6 12.1 + - - +
477A LEU* 3.9 25.6 - - + -
478A ALA* 3.5 34.2 - - + +
481A ILE* 4.0 17.7 - - + -
482A PHE* 4.0 15.0 - + + -
492A PHE* 3.4 27.9 + - + +
493A GLN* 5.3 1.8 - - - +
495A ARG 3.1 24.3 + - - +
497A VAL* 3.6 18.8 - - + +
514A PHE* 4.9 1.6 - + - -
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Residues in contact with GLU 449 (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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447A PRO* 4.2 8.1 - - + +
448A TRP* 1.3 79.1 - - - +
450A LYS* 1.3 81.2 + - - +
452A CYS* 3.4 9.1 - - - +
453A GLU* 3.3 23.1 + - - +
493A GLN* 4.7 14.0 + - - +
495A ARG 4.9 0.2 + - - -
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Residues in contact with LYS 450 (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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431A ALA 5.9 2.2 - - - -
432A PHE* 4.2 18.9 - - + -
446A VAL* 5.3 0.2 - - + -
447A PRO* 3.1 28.1 + - + +
449A GLU* 1.3 93.7 - - - +
451A MET* 1.3 59.9 - - - +
452A CYS 3.3 0.2 - - - -
453A GLU* 3.3 30.6 + - - +
454A THR* 2.9 25.7 + - - -
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Residues in contact with MET 451 (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 LEU* 4.3 6.1 - - + -
428A TRP* 4.5 7.4 - - - -
432A PHE* 4.3 20.6 - - + -
447A PRO 3.1 4.8 + - - +
448A TRP* 3.5 31.2 - - + +
450A LYS* 1.3 73.2 - - - +
452A CYS* 1.3 58.8 + - - +
454A THR* 3.1 21.9 + - + -
455A LEU* 2.9 54.8 + - + +
481A ILE* 5.5 0.2 - - + -
497A VAL* 3.8 24.9 - - + -
502A PHE* 3.9 28.9 - - + -
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Residues in contact with CYS 452 (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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448A TRP* 3.0 52.7 + - - +
449A GLU* 3.4 9.0 - - - +
451A MET* 1.3 74.1 - - - +
453A GLU* 1.3 64.8 + - - +
455A LEU* 4.5 3.8 - - - +
456A ASN* 3.2 17.7 + - - +
474A PHE* 3.3 56.7 - - + -
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Residues in contact with GLU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLU* 3.3 10.6 + - - +
450A LYS* 3.3 43.8 + - - +
452A CYS* 1.3 78.7 - - - +
454A THR* 1.3 63.2 + - - +
456A ASN* 3.7 7.0 + - - +
457A LEU* 3.4 36.7 + - + +
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Residues in contact with THR 454 (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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210A LEU* 6.1 0.2 - - - +
213A ASN* 4.3 10.3 - - + +
427A LEU* 4.0 20.6 - - + -
431A ALA* 3.8 31.6 - - + +
432A PHE* 3.9 4.2 - - + -
450A LYS 2.9 13.6 + - - -
451A MET* 3.1 25.9 + - + -
453A GLU* 1.3 78.7 - - - +
455A LEU* 1.3 61.2 + - - +
457A LEU* 3.7 5.5 + - - +
458A LYS* 3.2 22.2 + - - +
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Residues in contact with LEU 455 (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 LEU* 5.1 4.9 - - + -
448A TRP* 4.5 7.9 - - + -
451A MET* 2.9 48.4 + - + +
452A CYS* 4.0 7.6 - - - +
453A GLU 3.4 0.2 - - - -
454A THR* 1.3 76.9 - - - +
456A ASN* 1.3 59.1 + - - +
458A LYS* 3.4 5.2 + - + +
459A PHE* 2.9 30.3 + - - +
469A LEU* 4.3 6.3 - - + -
474A PHE* 4.9 0.9 - - + -
477A LEU* 4.3 15.7 - - + -
502A PHE* 4.5 12.6 - - + -
514A PHE* 4.3 21.3 - - + -
515A TRP* 5.2 1.3 - - + -
518A PHE* 3.7 36.7 - - + -
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Residues in contact with ASN 456 (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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452A CYS 3.2 16.8 + - - +
453A GLU* 4.0 6.3 + - - +
454A THR 3.3 0.2 - - - -
455A LEU* 1.3 74.8 - - - +
457A LEU* 1.3 74.9 + - - +
459A PHE* 3.5 3.2 + - - +
460A MET* 3.3 38.5 + - - +
468A GLY* 3.4 11.3 - - - -
469A LEU* 2.9 41.3 + - - +
474A PHE* 4.0 11.7 - - + -
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Residues in contact with LEU 457 (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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210A LEU* 5.6 3.6 - - + +
213A ASN* 3.6 11.1 - - + +
214A GLY 3.7 17.3 - - - +
215A ALA* 4.0 22.2 - - + +
216A PRO* 4.4 12.1 - - + -
453A GLU* 3.4 31.2 + - + +
454A THR* 4.1 5.2 - - - +
455A LEU 3.4 0.2 - - - -
456A ASN* 1.3 84.2 - - - +
458A LYS* 1.3 60.5 + - - +
460A MET* 3.7 23.5 + - + +
461A ALA* 3.3 25.3 + - - +
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Residues in contact with LYS 458 (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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212A GLY 5.1 7.5 + - - -
213A ASN* 3.6 17.3 + - - +
423A LYS* 5.7 8.9 - - - +
427A LEU* 3.5 32.0 - - + +
454A THR 3.2 17.2 + - - +
455A LEU* 3.6 7.2 - - + +
456A ASN 3.3 0.2 - - - -
457A LEU* 1.3 78.2 - - - +
459A PHE* 1.3 64.6 + - - +
461A ALA* 4.7 1.6 - - + -
462A GLU* 3.0 60.6 + - + +
515A TRP* 4.4 15.7 - - + -
518A PHE* 5.0 4.3 - - + -
522A LEU* 4.4 14.4 - - + -
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Residues in contact with PHE 459 (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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455A LEU 2.9 17.3 + - - +
456A ASN 3.8 4.9 - - - +
457A LEU 3.4 0.2 - - - -
458A LYS* 1.3 76.4 - - - +
460A MET* 1.3 58.8 + - + +
463A VAL* 2.9 47.9 + - + +
465A THR* 4.1 5.2 - - + -
467A ARG 4.5 3.8 - - - -
468A GLY* 5.1 0.4 - - - -
469A LEU* 3.8 22.0 - - + -
518A PHE* 4.3 10.5 - + + -
521A VAL* 4.2 12.8 - - + -
522A LEU* 3.6 22.9 - - + +
525A THR* 4.6 7.9 - - + -
533A TRP* 3.5 52.9 - + - -
541A PHE* 4.0 19.5 - + - -
563A PHE* 5.2 1.1 - + - -
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Residues in contact with MET 460 (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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214A GLY 5.7 1.6 - - - +
456A ASN* 3.3 36.8 + - - +
457A LEU* 3.8 23.3 - - + +
458A LYS 3.2 0.2 - - - -
459A PHE* 1.3 75.9 - - - +
461A ALA* 1.3 65.2 + - - +
464A GLY* 3.1 4.0 + - - -
465A THR* 3.0 42.5 + - - +
466A ASN* 3.6 25.1 - - - +
467A ARG 3.8 14.1 - - - +
468A GLY* 3.9 13.9 - - - -
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Residues in contact with ALA 461 (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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213A ASN 4.5 1.6 - - - +
214A GLY* 3.5 26.2 + - - +
457A LEU 3.3 15.5 + - - +
458A LYS* 4.1 2.7 - - + +
460A MET* 1.3 81.4 - - - +
462A GLU* 1.3 63.7 + - + +
464A GLY* 3.9 5.7 + - - -
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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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423A LYS* 5.7 5.2 + - - +
458A LYS* 3.0 45.2 + - + +
459A PHE 4.6 0.4 - - - +
461A ALA* 1.3 81.7 - - - +
463A VAL* 1.3 61.4 + - - +
464A GLY 3.3 0.2 - - - -
519A ASP* 5.8 0.9 - - - +
522A LEU* 4.4 25.4 - - + +
526A LYS* 3.2 44.8 + - - +
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Residues in contact with VAL 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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459A PHE* 2.9 36.2 + - + +
462A GLU* 1.3 76.9 - - - +
464A GLY* 1.3 58.9 + - - +
465A THR* 3.6 20.4 - - + -
522A LEU* 3.8 31.6 - - + +
525A THR* 4.0 36.1 - - + +
526A LYS* 4.0 14.8 - - - +
530A ARG* 3.8 21.7 + - + -
533A TRP* 5.1 1.3 - - + -
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Residues in contact with GLY 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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460A MET 3.1 8.5 + - - -
461A ALA 3.9 5.2 + - - -
462A GLU 3.3 3.2 - - - -
463A VAL* 1.3 76.6 - - - +
465A THR* 1.3 60.5 + - - +
530A ARG* 2.7 43.9 + - - -
534A SER* 5.1 0.9 + - - -
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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