Contacts of the helix formed by residues 402 - 418 (chain B) in PDB entry 3WOO
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 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B GLN* 5.8 0.7 - - - +
398B LEU 3.4 7.3 + - - +
399B PHE* 3.0 18.4 + - - +
401B ASN* 1.3 79.1 - - - +
403B ALA* 1.3 57.4 + - - +
404B MET 3.4 1.0 + - - -
405B LEU* 3.8 19.6 + - - +
406B GLY* 2.8 30.3 + - - -
453B ASP* 3.7 11.0 - - - -
456B LEU* 4.3 9.6 - - + -
457B GLN* 4.0 27.6 - - - +
460B TRP* 4.0 21.3 - - + +
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Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B TYR* 5.7 0.7 - - - +
401B ASN 4.4 2.0 - - - -
402B THR* 1.3 74.8 - - - +
404B MET* 1.3 64.0 + - + +
406B GLY* 4.1 0.4 - - - -
407B SER* 2.9 33.3 + - - -
444B LEU* 3.9 22.5 - - + +
447B ARG 5.6 0.9 - - - +
448B TYR* 3.4 32.5 - - + -
453B ASP* 3.1 12.5 + - - +
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Residues in contact with MET 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B THR* 3.4 0.4 + - - -
403B ALA* 1.3 84.4 - - + +
405B LEU* 1.3 63.6 + - + +
407B SER* 3.5 4.9 + - - +
408B ALA* 3.0 29.5 + - - +
444B LEU* 4.0 13.2 - - + -
448B TYR* 3.6 41.7 - - + +
453B ASP* 3.9 10.5 + - - +
457B GLN* 4.3 14.8 - - - +
495B LEU* 6.5 0.2 - - + -
498B THR* 3.9 20.2 - - + -
500B LEU* 3.3 48.8 - - + +
501B GLY* 3.4 9.0 - - - -
506B ARG* 4.2 1.1 - - - +
524B ALA* 4.0 8.7 - - + +
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B PHE* 3.3 52.0 - - + +
400B ASN* 3.6 8.3 - - - -
402B THR* 3.5 17.3 + - - +
403B ALA 3.5 0.2 - - - -
404B MET* 1.3 78.9 - - + +
406B GLY* 1.3 54.0 + - - +
408B ALA* 4.1 1.7 - - - +
409B THR* 2.6 41.5 + - - +
457B GLN* 4.7 8.3 - - + +
495B LEU* 4.1 31.0 - - + -
524B ALA* 4.3 11.7 - - + +
527B TYR* 3.8 29.2 - - + -
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Residues in contact with GLY 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ASN 3.0 19.6 + - - -
401B ASN* 4.7 3.1 - - - -
402B THR 2.8 17.2 + - - -
403B ALA 4.1 0.4 - - - -
405B LEU* 1.3 75.9 - - - +
407B SER* 1.3 61.6 + - - -
409B THR* 3.1 3.3 + - - -
410B GLN* 2.9 28.0 + - - +
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Residues in contact with SER 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ALA 2.9 23.4 + - - -
404B MET* 3.8 6.3 - - - -
405B LEU 3.3 0.2 - - - -
406B GLY* 1.3 75.1 - - - +
408B ALA* 1.3 63.6 + - - +
410B GLN* 3.9 4.2 - - - +
411B LEU* 3.0 35.4 + - - +
441B LEU* 4.2 13.1 - - - +
444B LEU* 3.5 21.0 - - - +
500B LEU* 4.5 9.6 - - - -
506B ARG* 3.7 16.7 - - - -
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Residues in contact with ALA 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B MET 3.0 18.5 + - - +
405B LEU* 4.1 3.1 - - - +
406B GLY 3.2 0.2 - - - -
407B SER* 1.3 76.5 - - - +
409B THR* 1.3 58.3 + - - +
411B LEU* 3.9 3.0 - - - +
412B TYR* 2.9 33.1 + - - +
500B LEU* 3.7 19.0 - - + +
517B PHE* 4.6 1.8 - - - -
524B ALA* 3.5 29.8 - - + +
525B ILE* 3.9 7.0 - - + +
528B ALA* 3.6 7.1 - - + +
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Residues in contact with THR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ASN* 4.0 12.4 + - - +
405B LEU 2.6 24.7 + - - +
406B GLY* 3.1 14.2 + - - -
408B ALA* 1.3 73.6 - - - +
410B GLN* 1.4 57.8 + - - +
413B ARG* 2.9 33.0 + - - +
527B TYR* 4.4 15.0 - - + -
528B ALA* 3.8 24.2 - - + -
531B VAL* 4.4 0.2 - - + -
532B MET* 3.5 12.1 - - + +
535B LEU* 4.2 22.7 - - + -
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Residues in contact with GLN 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLY 2.9 21.7 + - - +
407B SER* 3.9 3.6 - - - +
409B THR* 1.4 73.4 + - - +
411B LEU* 1.3 60.2 + - + +
414B LEU* 2.9 27.3 + - + +
428B GLY 5.5 0.8 + - - -
429B TYR* 3.6 30.0 + - + +
437B ILE* 3.8 44.0 - - + +
441B LEU* 4.2 16.5 - - - +
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B SER* 3.0 28.1 + - - +
408B ALA* 3.9 2.7 - - - +
410B GLN* 1.3 74.1 - - + +
412B TYR* 1.3 66.1 + - - +
414B LEU* 3.3 7.9 + - + +
415B SER* 3.1 16.8 + - - -
437B ILE* 4.6 8.1 - - + -
441B LEU* 3.6 38.6 - - + -
500B LEU* 5.2 5.4 - - + -
506B ARG* 3.8 24.5 - - + +
509B TRP* 4.1 13.2 - - + +
510B PHE* 3.7 25.6 - - + -
517B PHE* 3.4 25.1 - - + -
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Residues in contact with TYR 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ALA 2.9 19.9 + - - +
409B THR 3.9 2.5 - - - +
411B LEU* 1.3 73.4 - - - +
413B ARG* 1.3 64.7 + - - +
415B SER* 2.6 34.3 + - - -
416B ILE* 3.0 24.2 + - + +
514B ARG* 4.1 8.0 + - + -
517B PHE* 3.5 37.0 - + + -
518B GLU* 2.7 34.3 + - + +
528B ALA* 3.9 7.9 - - + -
529B VAL* 3.6 34.9 + - + +
532B MET* 3.5 40.2 - - + -
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Residues in contact with ARG 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B THR 2.9 22.7 + - - +
410B GLN 3.7 3.6 - - - +
412B TYR* 1.3 72.9 - - - +
414B LEU* 1.3 56.7 + - - +
416B ILE* 3.1 14.4 + - - +
417B GLU* 2.6 54.3 + - - +
420B LYS* 5.5 0.8 - - - +
426B GLU* 3.6 20.4 + - - +
429B TYR* 3.5 32.4 + - + +
532B MET* 4.1 16.9 - - + +
535B LEU* 5.9 2.0 + - - +
536B LEU* 3.4 28.8 - - - +
539B GLU* 2.9 41.4 + - - -
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B GLN* 2.9 18.1 + - + +
411B LEU* 3.6 11.4 - - + +
412B TYR 3.2 0.4 - - - -
413B ARG* 1.3 75.5 - - - +
415B SER* 1.3 54.7 + - - +
417B GLU* 3.1 2.3 + - - +
418B ARG* 2.8 74.4 + - + +
429B TYR* 3.7 35.0 - - + +
434B LEU* 3.8 22.0 - - + -
437B ILE* 4.3 13.2 - - + -
510B PHE* 3.7 28.7 - - + +
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Residues in contact with SER 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU 3.1 2.8 + - - -
412B TYR* 2.6 34.3 + - - -
414B LEU* 1.3 79.6 - - - +
416B ILE* 1.3 60.5 + - - +
418B ARG* 3.7 16.0 + - - +
419B GLU* 3.9 9.0 - - - +
512B ALA 3.9 8.1 - - - -
513B ASP* 5.3 0.8 - - - +
514B ARG* 3.5 31.6 + - - +
517B PHE* 3.6 28.2 - - - -
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Residues in contact with ILE 416 (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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412B TYR* 3.0 40.2 + - + +
413B ARG* 3.4 13.0 - - - +
415B SER* 1.3 79.4 + - - +
417B GLU* 1.3 77.0 + - - +
418B ARG 3.2 0.7 + - - -
419B GLU* 3.2 19.6 + - - +
420B LYS* 4.3 12.0 + - - -
514B ARG* 3.9 40.6 - - - +
532B MET* 3.7 24.2 - - + -
536B LEU* 5.0 13.0 - - + -
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ARG* 2.6 55.0 + - - +
414B LEU 3.7 5.2 - - - +
416B ILE* 1.3 76.3 - - - +
418B ARG* 1.3 58.7 + - - +
419B GLU 2.9 5.9 + - - -
420B LYS* 3.0 43.7 + - - +
425B ARG* 3.1 28.8 - - + +
426B GLU* 2.9 27.7 + - - +
429B TYR* 3.6 32.8 - - + +
536B LEU* 5.0 1.2 - - - +
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Residues in contact with ARG 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LEU* 2.8 53.5 + - + +
415B SER* 3.9 12.7 - - - +
416B ILE 3.2 0.8 - - - -
417B GLU* 1.3 71.5 - - - +
419B GLU* 1.3 61.0 + - + +
420B LYS 3.2 1.1 - - - +
425B ARG* 3.3 31.9 + - - +
434B LEU* 4.2 20.3 - - + +
510B PHE* 2.7 48.6 + - - -
511B ALA* 4.5 7.7 + - - +
512B ALA 5.0 7.6 + - - -
513B ASP* 6.4 0.7 - - - +
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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