Contacts of the helix formed by residues 449 - 466 (chain B) in PDB entry 3WOR
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 VAL 449 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B ASN* 5.4 1.8 - - - +
316B ASP* 4.0 9.6 - - - +
317B ILE* 3.9 37.7 - - + -
320B LYS* 3.4 22.9 - - + -
321B TYR* 3.1 20.3 + - + -
448B TYR* 1.3 83.5 - - - +
450B ALA* 1.3 67.8 + - - +
451B ALA* 3.8 13.5 - - + +
452B MET* 3.0 2.4 + - + +
453B ASP* 3.0 20.1 + - - +
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Residues in contact with ALA 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B TYR* 3.5 31.1 - - + +
449B VAL* 1.3 74.2 - - - +
451B ALA* 1.3 58.2 + - - +
453B ASP* 3.8 0.7 - - - +
454B ARG* 2.9 32.2 + - - +
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Residues in contact with ALA 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ILE* 5.2 6.7 - - + -
449B VAL* 3.3 10.5 - - + +
450B ALA* 1.3 78.7 - - - +
452B MET* 1.3 60.9 + - - +
454B ARG* 3.8 9.1 + - - +
455B GLN* 3.5 24.6 + - - +
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Residues in contact with MET 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B MET* 4.5 2.5 - - - +
307B VAL* 3.7 37.5 - - + -
310B ALA* 3.0 28.7 - - + -
317B ILE* 2.7 44.8 - - + +
321B TYR* 3.7 32.5 - - + -
449B VAL* 3.0 11.2 + - + +
451B ALA* 1.3 78.2 - - - +
453B ASP* 1.3 65.2 + - - +
455B GLN* 3.1 27.7 + - - +
456B LEU* 3.2 13.8 + - + +
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Residues in contact with ASP 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B TYR* 3.8 6.5 + - - +
402B THR* 3.8 9.7 - - - +
403B ALA* 3.3 27.3 + - - +
404B MET* 3.9 10.2 + - - +
448B TYR* 3.5 36.5 + - + +
449B VAL 3.0 7.9 + - - +
450B ALA 3.8 2.5 - - - +
452B MET* 1.3 74.8 - - - +
454B ARG* 1.3 65.0 + - - +
456B LEU* 3.0 13.0 + - - +
457B GLN* 2.9 44.1 + - - +
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Residues in contact with ARG 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ALA 2.9 18.2 + - - +
451B ALA* 3.9 8.3 - - - +
452B MET 3.2 0.2 - - - -
453B ASP* 1.3 76.0 - - - +
455B GLN* 1.3 60.3 + - + +
457B GLN* 3.4 15.3 + - - +
458B GLU* 2.9 29.4 + - - +
489B LYS* 4.3 9.3 + - - +
492B LEU* 3.6 55.8 + - + +
493B ASP* 3.1 30.1 + - - -
496B ALA* 3.9 16.4 - - + +
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Residues in contact with GLN 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B MET* 3.1 41.3 + - + +
310B ALA* 4.3 10.9 - - - +
451B ALA 3.5 17.0 + - - +
452B MET* 3.1 22.8 + - - +
454B ARG* 1.3 79.1 - - + +
456B LEU* 1.3 56.7 + - - +
458B GLU* 3.4 16.7 + - - +
459B TYR 3.0 21.1 + - - -
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Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLN* 3.8 35.7 - - + +
306B MET* 3.6 21.8 - - + -
307B VAL* 4.4 14.1 - - + -
321B TYR* 4.3 21.8 - - + -
324B THR* 6.2 0.4 - - + -
328B TRP* 4.2 17.3 - - + -
402B THR* 4.2 13.5 - - + -
452B MET 3.2 12.7 + - - +
453B ASP* 3.0 16.1 + - - +
455B GLN* 1.3 74.2 - - - +
457B GLN* 1.3 60.7 + - - +
459B TYR* 3.4 2.7 + - + +
460B TRP* 3.0 37.1 + - - -
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Residues in contact with GLN 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B PHE* 4.2 12.9 - - + -
402B THR* 4.1 22.4 + - - +
404B MET* 4.3 16.6 - - - +
405B LEU* 4.6 7.6 - - + +
453B ASP* 2.9 30.6 + - - +
454B ARG* 3.5 19.4 - - - +
456B LEU* 1.3 74.8 - - - +
458B GLU* 1.3 63.8 + - - +
460B TRP* 3.2 2.5 + - - +
461B LEU* 2.9 28.1 + - + +
492B LEU* 3.7 19.5 - - + +
495B LEU* 3.9 36.1 + - + +
496B ALA 5.6 0.3 + - - -
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Residues in contact with GLU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ARG* 2.9 21.4 + - - +
455B GLN* 3.4 18.8 + - - +
457B GLN* 1.3 69.7 - - - +
459B TYR* 1.3 66.9 + - - +
461B LEU* 3.1 6.4 + - - +
462B ASN* 2.8 42.9 + - - +
488B VAL* 4.7 7.3 - - + +
492B LEU* 3.7 30.9 - - + +
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Residues in contact with TYR 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG* 4.1 0.2 + - - -
299B HIS* 2.8 33.1 + - - -
302B ASN* 2.8 43.0 + - + +
303B GLN* 4.3 11.7 - - + -
306B MET* 3.9 25.4 - - + -
455B GLN 3.0 11.2 + - - +
456B LEU* 3.5 9.0 - - + +
458B GLU* 1.3 80.1 - - - +
460B TRP* 1.3 93.2 + + - +
462B ASN* 3.3 7.6 + - + +
463B GLU* 3.1 50.6 + - + +
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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
----------------------------------------------------------
299B HIS* 3.5 39.7 - + + -
303B GLN* 3.1 37.3 - - - +
394B LEU* 4.6 0.2 - - + -
395B THR* 4.3 28.7 - - + +
398B LEU* 3.3 50.4 + - + +
399B PHE* 3.7 29.5 - - + +
402B THR* 4.0 18.1 - - + +
456B LEU 3.0 29.2 + - - +
457B GLN 3.2 0.8 + - - +
459B TYR* 1.3 89.4 - + - +
461B LEU* 1.3 57.9 + - - +
463B GLU* 3.3 11.3 + - + +
464B TYR* 2.9 26.5 + - - +
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Residues in contact with LEU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B PHE* 3.6 33.2 - - + -
457B GLN* 2.9 20.6 + - + +
458B GLU 3.7 3.1 - - - +
460B TRP* 1.3 73.0 - - - +
462B ASN* 1.3 67.0 + - - +
463B GLU 3.1 0.2 - - - -
464B TYR* 3.1 10.3 + - + +
465B ILE* 2.9 30.1 + - - +
476B VAL* 5.5 1.3 - - + -
479B TRP* 4.2 15.3 - - + -
480B LEU* 4.4 18.2 - - + -
488B VAL* 4.3 20.6 - - + -
491B ALA* 4.1 20.0 - - + -
492B LEU* 4.0 23.6 - - + +
495B LEU* 5.5 1.8 - - + -
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Residues in contact with ASN 462 (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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458B GLU* 2.8 37.0 + - - +
459B TYR* 3.5 8.7 - - + +
461B LEU* 1.3 77.2 - - - +
463B GLU* 1.3 66.5 + - - +
465B ILE* 3.5 13.2 - - - +
466B LYS* 3.3 30.5 + - - +
485B ALA* 5.7 2.1 - - - -
488B VAL* 3.9 21.4 - - - +
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Residues in contact with GLU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG* 3.1 22.7 + - - -
299B HIS* 3.4 10.9 - - + -
302B ASN* 5.4 0.2 + - - -
395B THR* 4.4 5.6 - - + +
459B TYR* 3.1 56.3 + - + +
460B TRP* 3.6 17.7 - - + +
462B ASN* 1.3 78.5 - - - +
464B TYR* 1.3 66.3 + - - +
466B LYS* 3.3 44.4 + - - +
467B LEU* 3.6 13.2 + - - +
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Residues in contact with TYR 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ARG* 6.0 0.9 - - + -
395B THR* 3.9 16.6 - - + +
396B LEU* 5.5 8.7 - - + -
399B PHE* 6.0 7.4 - + + -
460B TRP 2.9 16.9 + - - +
461B LEU* 3.1 11.6 + - + +
463B GLU* 1.3 77.2 - - - +
465B ILE* 1.3 68.4 + - + +
467B LEU* 2.9 38.5 + - + +
471B GLN 4.9 0.4 - - - -
472B ARG* 3.5 25.0 + - - -
473B VAL* 3.0 39.2 + - + -
476B VAL* 3.6 30.1 - - + +
477B ASP* 2.7 28.8 + - - -
480B LEU* 4.5 11.2 - - + -
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Residues in contact with ILE 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B LEU 2.9 16.9 + - - +
462B ASN* 3.5 20.4 - - - +
464B TYR* 1.3 79.8 - - + +
466B LYS* 1.3 62.9 + - + +
467B LEU 3.1 0.7 - - - +
472B ARG* 2.9 26.6 + - - +
480B LEU* 3.8 28.5 - - + -
483B ASN* 4.2 19.3 - - + +
484B ASP* 4.2 21.8 - - - +
485B ALA 4.8 0.7 - - - +
488B VAL* 3.9 23.1 - - + -
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Residues in contact with LYS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG* 5.1 4.9 - - - +
462B ASN* 3.3 19.1 + - - +
463B GLU* 3.3 41.5 + - - +
464B TYR 3.1 0.6 - - - -
465B ILE* 1.3 79.8 - - + +
467B LEU* 1.3 65.3 + - + +
468B PRO* 3.7 2.8 - - - +
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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
------------------------------------------------------------
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