Contacts of the helix formed by residues 439 - 456 (chain A) in PDB entry 4UH6
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 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A CYS* 3.6 0.9 - - - -
438A THR* 1.3 94.0 + - - +
440A ALA* 1.3 60.2 + - - +
441A HIS* 3.6 12.0 + - - +
442A GLY* 2.9 34.7 + - - -
443A MET* 3.0 14.9 + - - +
531A ALA* 3.5 8.1 - - - -
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Residues in contact with ALA 440 (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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439A THR* 1.3 73.1 - - - +
441A HIS* 1.3 57.6 + - - +
443A MET* 3.1 10.4 + - - +
444A PHE* 2.9 28.1 + - - +
529A LEU* 3.6 26.2 - - + +
531A ALA* 3.5 14.1 - - + +
535A ASP 5.7 0.2 - - - +
537A GLU* 3.7 30.4 + - - +
539A PHE* 3.6 15.8 - - + -
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Residues in contact with HIS 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A THR* 3.2 9.1 + - - +
440A ALA* 1.3 78.4 + - - +
442A GLY* 1.3 63.1 + - - +
444A PHE* 3.3 8.0 + + - +
445A ASN* 3.0 22.5 + - - +
537A GLU* 3.6 21.6 + - - -
539A PHE* 3.7 24.9 - + - -
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Residues in contact with GLY 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A CYS* 3.5 13.9 - - - -
438A THR 5.6 0.4 - - - -
439A THR* 2.9 20.3 + - - -
441A HIS* 1.3 77.9 - - - +
443A MET* 1.3 61.2 + - - +
445A ASN* 3.2 9.4 + - - +
446A TYR* 3.0 28.8 + - - -
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Residues in contact with MET 443 (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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437A CYS* 3.4 12.1 - - - -
439A THR 3.0 14.8 + - - +
440A ALA* 3.3 9.9 - - - +
442A GLY* 1.3 76.6 - - - +
444A PHE* 1.3 57.2 - - - +
446A TYR* 3.2 2.6 + - - +
447A ILE* 2.9 34.9 + - + +
467A PHE* 3.7 31.9 - - + -
477A PHE* 3.8 9.6 - - + -
478A ARG 3.8 18.4 - - - +
479A VAL* 4.1 19.3 - - + -
529A LEU* 3.9 11.9 - - + -
530A GLN 3.1 41.5 - - - +
531A ALA* 3.8 9.6 - - - -
586A ALA* 4.7 1.1 - - + -
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Residues in contact with PHE 444 (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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440A ALA 2.9 12.9 + - - +
441A HIS* 3.5 11.4 - + - +
442A GLY 3.2 0.2 - - - -
443A MET* 1.3 76.3 - - - +
445A ASN* 1.3 60.1 - - + +
447A ILE* 3.2 3.6 + - - +
448A CYS* 2.8 56.5 + - - -
527A LEU* 4.0 14.8 - - + -
529A LEU* 3.5 12.3 - - + +
539A PHE* 3.4 40.6 - + + -
540A GLN 3.5 28.9 - - - -
541A ILE* 4.3 3.4 - - - -
542A PRO* 3.9 9.0 - - + -
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Residues in contact with ASN 445 (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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441A HIS 3.0 12.5 + - - +
442A GLY* 3.4 11.8 + - - +
444A PHE* 1.3 80.7 - - + +
446A TYR* 1.3 68.4 + - - +
448A CYS* 3.4 6.1 + - - +
449A ASN* 3.1 46.1 + - - +
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Residues in contact with TYR 446 (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 PHE* 5.3 8.2 - - + -
433A ASP 3.7 11.7 + - - -
434A ALA* 3.7 31.9 - - + -
436A ASP* 2.6 34.6 + - - -
437A CYS* 4.0 12.8 - - + -
442A GLY* 3.0 22.5 + - - -
443A MET 3.2 6.9 + - - +
445A ASN* 1.3 81.2 - - + +
447A ILE* 1.3 57.9 + - - +
449A ASN* 3.3 13.7 + - + +
450A HIS* 3.0 26.9 + - - +
465A THR* 4.2 11.4 + - + -
467A PHE* 3.8 18.8 - + + -
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Residues in contact with ILE 447 (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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443A MET* 2.9 21.7 + - + +
444A PHE 3.7 3.4 - - - +
446A TYR* 1.3 75.2 - - - +
448A CYS* 1.3 65.3 + - - +
450A HIS* 3.1 8.0 + - + +
451A VAL* 2.9 28.7 + - + +
465A THR* 5.6 0.9 - - + -
467A PHE* 4.0 16.6 - - + -
479A VAL* 3.9 18.2 - - + -
484A LEU* 4.0 33.4 - - + -
527A LEU* 3.6 23.6 - - + -
529A LEU* 3.7 32.5 - - + -
541A ILE* 5.5 0.7 - - + -
588A PRO* 4.7 5.6 - - + -
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Residues in contact with CYS 448 (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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444A PHE* 2.8 61.1 + - - +
445A ASN* 3.7 7.2 - - - +
447A ILE* 1.3 72.7 - - - +
449A ASN* 1.3 66.2 + - - +
451A VAL* 3.3 6.0 + - - +
452A LYS* 3.0 25.3 + - - +
527A LEU* 5.5 1.8 - - - -
541A ILE* 5.2 4.3 - - - -
542A PRO* 3.8 18.8 - - - -
545A LEU* 3.8 17.4 - - + +
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Residues in contact with ASN 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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432A PHE* 5.1 3.3 - - + -
445A ASN* 3.1 35.7 + - - +
446A TYR* 3.6 14.5 - - + +
447A ILE 3.3 0.2 - - - -
448A CYS* 1.3 79.0 - - - +
450A HIS* 1.3 62.1 + - - +
452A LYS* 3.9 7.0 - - - +
453A TYR* 3.0 25.6 + - - +
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Residues in contact with HIS 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A PHE* 4.3 13.6 - + + -
446A TYR 3.0 11.3 + - - +
447A ILE* 3.1 12.3 + - - +
449A ASN* 1.3 77.9 - - - +
451A VAL* 1.3 60.9 + - + +
453A TYR* 3.2 2.4 + - - +
454A ALA* 2.8 33.1 + - + -
463A ALA* 3.3 28.3 + - + +
464A ILE* 3.7 1.5 - - - -
465A THR* 2.8 32.2 + - - +
484A LEU* 4.7 14.4 - - + +
569A LEU* 5.1 0.7 - - + -
588A PRO* 3.3 29.4 + - - +
589A PHE* 4.2 0.7 - - - -
590A SER* 2.9 29.7 + - - -
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Residues in contact with VAL 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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447A ILE* 2.9 25.3 + - + +
448A CYS* 3.7 6.5 - - - +
450A HIS* 1.3 79.5 - - - +
452A LYS* 1.3 57.7 + - - +
454A ALA* 3.8 0.5 - - - +
455A THR* 2.8 40.6 + - - +
484A LEU* 4.1 26.7 - - + -
485A ILE* 4.5 12.8 - - + -
541A ILE* 5.2 11.7 - - + -
545A LEU* 3.3 36.6 - - + +
569A LEU* 4.2 15.9 - - + -
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Residues in contact with LYS 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 CYS 3.0 16.7 + - - +
449A ASN* 3.9 8.3 - - - +
451A VAL* 1.3 77.6 - - - +
453A TYR* 1.3 63.9 + - - +
455A THR* 3.9 4.0 - - - -
456A ASN* 3.1 21.0 + - - -
461A ARG* 4.9 0.3 + - - -
545A LEU* 3.6 29.0 - - + +
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Residues in contact with TYR 453 (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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430A GLN* 3.5 44.0 + - + +
432A PHE* 3.6 28.7 - + + -
449A ASN 3.0 18.7 + - - +
450A HIS 3.7 2.2 - - - +
452A LYS* 1.3 79.6 - - - +
454A ALA* 1.3 67.9 + - - +
456A ASN* 3.5 3.1 - - - +
461A ARG* 3.0 84.9 + - + +
462A SER 4.4 0.4 - - - -
463A ALA* 4.2 7.2 - - + -
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Residues in contact with ALA 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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450A HIS* 2.8 25.6 + - + +
451A VAL 4.1 1.3 - - - +
453A TYR* 1.3 77.0 - - - +
455A THR* 1.3 61.1 + - - +
460A LEU* 3.2 9.2 - - - +
461A ARG 3.0 44.5 + - - +
463A ALA* 4.5 3.8 - - + -
569A LEU* 3.8 13.3 - - + +
590A SER* 3.5 21.5 - - - +
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Residues in contact with THR 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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451A VAL* 2.8 34.4 + - - +
452A LYS* 3.9 4.0 - - - -
454A ALA* 1.3 75.6 - - - +
456A ASN* 1.3 71.3 + - - +
457A LYS* 3.9 8.1 - - - +
458A GLY 2.9 14.7 + - - -
459A ASN 3.6 1.4 + - - -
460A LEU* 3.2 18.7 - - + +
545A LEU 4.1 8.3 + - - +
547A LEU* 3.9 37.7 + - + +
569A LEU* 4.1 15.2 - - + +
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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 LYS 3.1 14.3 + - - -
453A TYR 3.5 14.1 - - - +
454A ALA 4.3 0.9 - - - +
455A THR* 1.3 77.1 - - - +
457A LYS* 1.3 70.6 + - - +
458A GLY 3.2 1.4 + - - -
459A ASN* 2.9 51.4 + - - +
461A ARG* 3.4 36.9 + - - +
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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
------------------------------------------------------------
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