Contacts of the helix formed by residues 439 - 456 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B CYS* 3.5 1.1 - - - -
438B THR* 1.3 95.7 + - - +
440B ALA* 1.3 59.3 + - - +
441B HIS* 3.5 12.1 + - - +
442B GLY* 3.0 21.0 + - - -
443B MET* 3.0 27.2 + - - +
531B ALA* 3.4 9.4 - - - +
537B GLU* 6.0 0.4 - - - -
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Residues in contact with ALA 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B THR* 1.3 73.8 - - - +
441B HIS* 1.3 57.8 + - - +
443B MET* 3.2 9.6 + - - +
444B PHE* 2.8 28.2 + - - +
529B LEU* 3.5 26.9 - - + +
531B ALA* 3.4 13.6 - - + +
535B ASP 5.8 0.2 - - - +
537B GLU* 3.7 29.1 + - - +
539B PHE* 3.6 16.6 - - + -
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Residues in contact with HIS 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B THR* 3.2 10.1 + - - +
440B ALA* 1.3 77.6 + - - +
442B GLY* 1.3 64.2 + - - +
444B PHE* 3.2 7.3 + + - +
445B ASN* 3.0 23.8 + - - +
537B GLU* 3.7 20.1 + - - -
539B PHE* 3.9 23.5 - + - -
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Residues in contact with GLY 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B CYS* 3.4 14.1 - - - -
439B THR* 3.0 16.6 + - - -
441B HIS* 1.3 80.8 - - - +
443B MET* 1.3 60.3 + - - +
445B ASN* 3.3 9.6 + - - +
446B TYR* 3.0 29.4 + - - -
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Residues in contact with MET 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B CYS* 3.5 12.6 - - - -
439B THR 3.0 14.9 + - - +
440B ALA* 3.5 9.9 - - - +
442B GLY* 1.3 75.4 - - - +
444B PHE* 1.3 58.5 + - - +
446B TYR* 3.3 1.7 + - - +
447B ILE* 2.9 34.7 + - + +
467B PHE* 3.6 32.5 - - + -
477B PHE* 3.9 8.3 - - + -
478B ARG 3.6 22.2 - - - +
479B VAL* 4.3 7.6 - - + -
529B LEU* 4.0 20.0 - - + -
530B GLN 3.2 42.0 - - - +
531B ALA* 3.7 12.1 - - - -
586B ALA* 4.7 0.7 - - + -
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Residues in contact with PHE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ALA 2.8 13.4 + - - +
441B HIS* 3.4 12.3 - + - +
443B MET* 1.3 76.5 - - - +
445B ASN* 1.3 60.4 - - + +
447B ILE* 3.4 2.0 + - - +
448B CYS* 2.9 57.2 + - - -
527B LEU* 4.0 12.8 - - + -
529B LEU* 3.6 8.9 - - + +
539B PHE* 3.3 47.6 - + + -
540B GLN 3.7 25.6 - - - -
541B ILE* 4.3 3.4 - - - -
542B PRO* 3.9 7.9 - - + -
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Residues in contact with ASN 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B HIS 3.0 12.4 + - - +
442B GLY* 3.4 12.0 + - - +
444B PHE* 1.3 83.4 - - + +
446B TYR* 1.3 69.1 + - - +
448B CYS* 3.3 5.1 + - - +
449B ASN* 3.1 40.0 + - - +
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Residues in contact with TYR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B PHE* 5.3 8.0 - - + -
433B ASP 3.7 20.5 + - - -
434B ALA* 3.7 24.2 - - + -
436B ASP* 2.6 36.2 + - - -
437B CYS* 4.1 11.9 - - + -
442B GLY* 3.0 26.3 + - - +
443B MET 3.3 3.8 + - - +
445B ASN* 1.3 83.1 - - - +
447B ILE* 1.3 58.5 + - - +
449B ASN* 3.4 11.6 + - + +
450B HIS* 2.9 27.5 + - - +
465B THR* 4.1 12.1 + - + -
467B PHE* 3.9 17.7 - + + -
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Residues in contact with ILE 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B MET* 2.9 22.3 + - + +
444B PHE 3.9 2.7 - - - +
446B TYR* 1.3 74.6 - - - +
448B CYS* 1.3 66.1 + - - +
450B HIS* 3.1 7.8 + - + +
451B VAL* 2.8 28.0 + - + +
465B THR* 5.5 1.1 - - + -
467B PHE* 3.9 18.8 - - + -
479B VAL* 4.1 15.7 - - + -
484B LEU* 4.0 27.4 - - + -
527B LEU* 3.6 24.5 - - + -
529B LEU* 3.6 34.3 - - + -
541B ILE* 5.6 0.7 - - + -
588B PRO* 4.4 10.1 - - + -
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Residues in contact with CYS 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B PHE* 2.9 61.5 + - - +
445B ASN* 3.7 6.3 - - - +
447B ILE* 1.3 74.7 - - - +
449B ASN* 1.3 61.1 + - - +
451B VAL* 3.3 5.2 + - - -
452B LYS* 3.0 30.2 + - - +
527B LEU* 5.5 2.0 - - - -
541B ILE* 5.1 4.5 - - - -
542B PRO* 3.8 18.8 - - - -
545B LEU* 3.7 17.1 - - + +
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Residues in contact with ASN 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B PHE* 5.1 4.4 - - + -
445B ASN* 3.1 38.8 + - - +
446B TYR* 3.7 11.3 - - + +
448B CYS* 1.3 75.2 - - - +
450B HIS* 1.3 65.8 + - - +
452B LYS* 3.4 9.6 + - - +
453B TYR* 3.0 24.9 + - - +
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Residues in contact with HIS 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B PHE* 4.2 12.8 - + - -
446B TYR 2.9 10.9 + - - +
447B ILE* 3.3 12.6 - - - +
449B ASN* 1.3 75.2 - - - +
451B VAL* 1.3 63.0 + - + +
453B TYR* 3.1 3.6 + - - +
454B ALA* 2.9 32.2 + - + +
463B ALA* 3.3 31.1 + - + +
464B ILE* 3.7 1.3 + - - -
465B THR* 2.8 31.6 + - - +
484B LEU* 4.6 13.3 - - + +
569B LEU* 5.2 1.1 - - + -
588B PRO* 3.2 30.8 + - + +
589B PHE* 4.2 0.4 - - - -
590B SER* 3.0 28.3 + - - -
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Residues in contact with VAL 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ILE* 2.8 28.8 + - + +
448B CYS* 3.8 7.0 - - - +
450B HIS* 1.3 74.3 - - - +
452B LYS* 1.3 57.5 + - - +
455B THR* 2.7 41.9 + - - +
484B LEU* 3.9 29.8 - - + -
485B ILE* 4.3 12.8 - - + -
541B ILE* 5.2 10.5 - - + -
545B LEU* 3.4 32.8 - - + +
569B LEU* 4.1 16.4 - - + -
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Residues in contact with LYS 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B CYS 3.0 17.6 + - - +
449B ASN* 3.8 9.4 - - - +
451B VAL* 1.3 76.9 - - - +
453B TYR* 1.3 64.3 - - - +
455B THR* 4.1 2.8 - - - -
456B ASN* 3.2 20.4 + - - -
461B ARG* 4.9 0.3 + - - -
545B LEU* 4.2 30.4 - - + +
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Residues in contact with TYR 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B GLN* 3.4 44.9 + - + +
432B PHE* 3.7 28.5 - + + -
449B ASN 3.0 17.5 + - - +
450B HIS 3.6 2.2 - - - +
452B LYS* 1.3 80.8 - - - +
454B ALA* 1.3 66.4 + - - +
456B ASN* 3.4 4.2 - - - +
461B ARG* 3.0 86.5 + - + +
462B SER 4.3 2.7 - - - -
463B ALA* 4.2 3.6 - - + -
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Residues in contact with ALA 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B HIS* 2.9 22.9 + - + +
451B VAL 4.2 1.3 - - - +
453B TYR* 1.3 78.3 - - - +
455B THR* 1.3 64.8 + - - +
460B LEU* 3.2 9.0 - - - +
461B ARG 2.9 44.6 + - - +
463B ALA* 4.4 4.0 - - + -
569B LEU* 3.8 12.1 - - + -
590B SER* 3.6 20.6 - - - +
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Residues in contact with THR 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B VAL* 2.7 34.5 + - - +
452B LYS* 4.1 2.9 - - - -
454B ALA* 1.3 77.3 - - - +
456B ASN* 1.3 67.8 + - - +
457B LYS* 4.0 8.1 - - - +
458B GLY 3.0 12.6 + - - -
459B ASN 3.5 2.3 + - - -
460B LEU* 3.2 19.1 - - + +
545B LEU 3.9 9.2 + - - +
547B LEU* 3.8 38.8 + - + +
569B LEU* 4.1 14.3 - - + +
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Residues in contact with ASN 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B LYS 3.2 13.0 + - - -
453B TYR 3.4 15.3 - - - +
454B ALA 4.2 0.9 - - - +
455B THR* 1.3 77.8 - - - +
457B LYS* 1.3 73.7 + - - +
459B ASN* 2.9 50.4 + - - +
461B ARG* 3.7 32.1 + - - +
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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
------------------------------------------------------------
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