Contacts of the helix formed by residues 451 - 465 (chain B) in PDB entry 5J3V
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 LYS 451 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B GLY* 3.4 33.7 + - - -
411B TRP* 3.5 54.1 - - + +
449B ASP* 2.8 17.3 + - - +
450B LYS* 1.3 79.3 - - + +
452B ALA* 1.3 65.6 + - - +
453B LEU* 4.5 1.6 - - + +
454B VAL* 3.3 19.0 + - + +
455B ARG* 3.2 20.4 + - - -
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Residues in contact with ALA 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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319B LYS 6.1 1.1 - - - +
450B LYS 3.5 3.0 + - - -
451B LYS* 1.3 72.1 - - - +
453B LEU* 1.3 69.8 + - + +
455B ARG* 3.2 28.7 + - - +
456B SER* 3.1 22.0 + - - -
493B ASN* 3.7 31.9 - - - +
495B ARG* 6.6 0.2 - - - -
496B VAL* 3.5 7.1 - - + +
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B TYR* 4.2 28.9 + - + +
315B ILE* 4.9 5.2 - - + -
318B LEU* 3.9 44.4 - - + +
319B LYS 5.7 0.2 - - - +
320B GLY* 4.6 12.6 - - - -
411B TRP* 3.7 37.0 - - + -
415B GLU* 3.7 5.7 - - + +
451B LYS* 3.3 1.4 - - + +
452B ALA* 1.3 80.4 - - + +
454B VAL* 1.3 59.8 + - - +
456B SER* 3.2 19.3 + - - +
457B ILE* 3.3 15.9 - - - +
495B ARG* 4.9 13.7 - - + -
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Residues in contact with VAL 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B TRP* 4.0 31.9 - - + +
414B LYS* 4.1 12.6 - - - -
415B GLU* 4.3 5.8 - - + -
418B ILE* 4.1 21.3 - - + -
446B CYS* 4.2 4.7 - - + +
449B ASP* 3.7 26.7 - - + +
451B LYS* 3.3 26.9 + - + +
452B ALA 3.2 0.6 - - - -
453B LEU* 1.3 76.9 - - - +
455B ARG* 1.3 56.8 + - - +
457B ILE* 3.3 6.9 - - - +
458B THR* 2.3 37.8 + - - +
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Residues in contact with ARG 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B CYS 4.1 6.1 - - - +
447B LEU* 3.4 30.3 - - - +
448B SER 4.8 1.1 - - - -
449B ASP 3.3 28.3 + - - +
450B LYS* 3.7 12.2 + - - -
451B LYS 3.2 2.6 + - - +
452B ALA* 3.2 36.9 + - - +
454B VAL* 1.3 80.6 - - - +
456B SER* 1.3 61.5 + - - +
458B THR* 3.5 3.5 + - - -
459B CYS* 3.3 26.1 + - - -
488B ARG* 4.2 7.0 - - - +
491B ASP* 2.7 44.5 + - - -
492B SER* 4.6 7.1 + - - -
493B ASN* 4.5 3.6 - - - +
496B VAL* 4.0 13.2 - - + -
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Residues in contact with SER 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B ALA 3.1 12.5 + - - -
453B LEU* 3.2 18.7 + - - +
455B ARG* 1.3 72.5 - - - +
457B ILE* 1.3 70.5 + - - +
458B THR 3.1 4.5 - - - -
459B CYS* 3.1 21.7 + - - +
460B TRP* 3.5 5.7 + - - +
495B ARG* 4.0 17.5 - - - +
496B VAL* 4.2 7.8 - - - +
499B ALA* 3.5 26.4 - - - +
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Residues in contact with ILE 457 (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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376B ARG* 4.4 4.9 - - - +
415B GLU* 3.3 37.5 - - + +
418B ILE* 4.3 9.6 - - + -
419B LEU* 3.7 44.0 - - + +
453B LEU 3.3 16.4 - - - +
454B VAL* 3.3 10.1 - - - +
456B SER* 1.3 82.1 + - - +
458B THR* 1.3 63.7 + - - +
460B TRP* 3.6 18.5 + - + +
461B THR* 3.0 28.1 + - - +
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Residues in contact with THR 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ILE* 3.7 19.8 - - - +
443B LEU* 3.1 40.2 - - + +
446B CYS* 3.8 14.9 + - + +
447B LEU* 3.7 12.8 - - + -
454B VAL 2.3 27.9 + - - -
455B ARG 3.5 5.8 - - - -
456B SER 3.1 0.8 - - - -
457B ILE* 1.3 76.7 - - - +
459B CYS* 1.3 64.4 + - - +
461B THR* 3.4 1.2 + - - -
462B LEU* 3.0 30.3 + - + +
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Residues in contact with CYS 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LEU* 3.8 17.3 - - - -
455B ARG 3.3 17.5 - - - -
456B SER* 3.1 10.6 + - - +
458B THR* 1.3 79.7 - - - +
460B TRP* 1.3 62.1 + - - +
462B LEU* 3.4 4.3 + - - +
463B SER 3.1 17.3 + - - -
485B LEU* 3.9 10.6 - - + +
488B ARG* 4.7 6.1 - - - -
496B VAL* 4.8 2.5 - - - -
499B ALA 3.8 18.8 - - - +
500B ALA* 3.7 28.0 - - - -
503B ALA* 3.2 18.1 - - + +
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Residues in contact with TRP 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ASP* 6.4 0.7 - - - -
419B LEU* 3.9 21.8 - - + -
422B GLY* 3.3 37.9 - - - -
423B ALA* 3.8 9.2 - - + -
456B SER 3.5 7.8 + - - +
457B ILE* 3.9 22.4 - - + +
458B THR 3.3 0.4 - - - -
459B CYS* 1.3 77.2 - - - +
461B THR* 1.3 81.3 + - - +
463B SER* 2.5 27.0 + - - -
464B ARG* 3.1 43.0 + - + +
499B ALA* 5.0 4.0 + - + -
503B ALA* 4.7 2.2 - - - -
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Residues in contact with THR 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ILE* 2.8 36.9 + - + +
421B LEU* 4.0 6.1 - - + -
422B GLY* 3.6 15.7 - - - +
443B LEU* 3.9 20.9 - - + -
457B ILE 3.0 17.0 + - - -
458B THR 3.4 2.9 + - - -
460B TRP* 1.3 90.7 - - - +
462B LEU* 1.3 61.6 + - - +
464B ARG* 3.1 10.7 + - - +
465B TYR* 3.1 34.5 - - + -
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ILE* 4.3 26.0 - - + +
443B LEU* 3.6 34.1 - - + +
444B ILE* 4.4 1.3 - - + +
447B LEU* 3.8 20.9 - - + -
458B THR* 3.0 36.8 + - + +
459B CYS* 3.7 5.6 - - - +
461B THR* 1.3 77.5 - - - +
463B SER* 1.3 60.2 - - - +
464B ARG 3.2 0.7 + - - -
465B TYR* 3.4 13.8 + - - +
466B ALA* 3.6 10.2 + - - +
469B VAL* 4.9 1.8 - - + +
481B LEU* 3.6 41.7 - - + +
485B LEU* 5.4 4.0 - - + -
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Residues in contact with SER 463 (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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459B CYS 3.1 11.9 + - - -
460B TRP* 2.5 34.0 + - - -
462B LEU* 1.3 74.4 - - - +
464B ARG* 1.3 61.5 + - - +
465B TYR 3.3 0.4 - - - -
466B ALA* 3.5 14.3 - - - +
485B LEU* 6.4 0.4 - - - -
503B ALA* 3.7 31.2 - - - +
506B THR* 3.3 28.9 + - - +
507B LEU* 5.7 1.3 - - - +
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Residues in contact with ARG 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ASP* 3.3 29.1 + - - -
422B GLY* 2.9 26.9 + - - +
423B ALA* 4.0 1.6 + - - +
425B ALA* 3.6 15.8 - - + +
426B GLU* 3.3 38.6 + - - +
429B MET* 3.5 19.2 - - - +
460B TRP* 3.1 48.8 + - + +
461B THR* 3.1 12.5 + - - +
463B SER* 1.3 81.1 - - - +
465B TYR* 1.3 57.5 + - + +
466B ALA 3.4 1.5 + - - -
467B HIS* 5.3 0.7 + - - +
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Residues in contact with TYR 465 (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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421B LEU* 2.3 50.5 + - + +
424B ILE* 4.3 1.0 - - - +
425B ALA* 3.6 26.0 + - + -
429B MET* 3.7 29.4 - - + -
432B MET* 4.1 18.9 - - + +
436B LEU* 3.7 29.4 - - + -
440B ILE* 4.1 23.8 - - + -
443B LEU* 5.3 0.4 - - + -
461B THR* 3.1 36.1 - - + -
462B LEU* 3.4 7.2 + - - +
463B SER 3.3 0.4 - - - -
464B ARG* 1.3 76.9 - - - +
466B ALA* 1.3 61.3 + - - +
467B HIS 3.2 3.1 - - - +
468B TRP* 3.3 11.6 + - + +
469B VAL* 3.2 16.3 + - - +
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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