Contacts of the helix formed by residues 389 - 400 (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 389 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385B GLN 4.0 5.6 + - - +
386B SER* 3.6 7.4 + - - -
387B LYS 3.1 0.6 - - - -
388B ALA* 1.3 83.7 - - + +
390B ARG* 1.3 65.6 + - - +
391B ASP 3.3 2.7 - - - -
392B ARG* 3.1 39.3 + - + +
393B ASP* 2.8 43.6 + - - -
470B ASP 6.0 1.8 - - - +
471B GLN* 3.5 11.0 - - - +
545B ARG* 4.7 5.5 + - - -
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Residues in contact with ARG 390 (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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287B ASN* 2.5 40.2 + - - +
291B TRP* 3.3 68.1 - - + +
386B SER 3.4 10.6 + - - +
387B LYS* 3.2 48.8 + - - +
388B ALA 3.6 0.2 - - - -
389B THR* 1.3 78.5 - - - +
391B ASP* 1.3 70.7 + - - +
393B ASP* 3.8 5.0 - - - +
394B LEU* 3.0 32.7 + - - +
471B GLN* 3.9 0.4 - - - +
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Residues in contact with ASP 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TRP* 3.8 24.5 + - - -
387B LYS 5.0 0.9 - - - +
389B THR 3.3 0.4 - - - -
390B ARG* 1.3 86.1 + - - +
392B ARG* 1.3 66.6 + - - +
394B LEU* 4.8 0.2 - - - -
395B THR* 2.6 33.8 + - - +
467B LEU* 4.1 14.5 - - + +
468B PRO* 6.0 2.7 - - - -
471B GLN* 3.4 22.4 + - + +
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Residues in contact with ARG 392 (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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389B THR* 3.1 40.9 + - - +
391B ASP* 1.3 83.1 - - - +
393B ASP* 1.3 81.4 + - - +
395B THR* 3.8 1.2 - - - -
396B LEU* 2.9 36.0 + - + +
464B TYR* 6.2 0.7 - - + -
467B LEU* 4.4 5.7 - - + +
470B ASP 5.6 2.8 + - - -
471B GLN* 3.2 41.0 - - + +
472B ARG 4.2 7.7 + - - -
473B VAL* 4.1 25.4 - - + -
538B LEU* 3.5 32.1 - - - +
541B GLU* 4.2 8.3 + - - -
545B ARG* 5.8 1.8 - - - +
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Residues in contact with ASP 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B SER* 4.4 3.6 - - - +
389B THR* 2.8 40.5 + - - +
390B ARG* 3.8 5.1 - - - +
392B ARG* 1.3 107.1 + - - +
394B LEU* 1.3 57.3 + - - +
396B LEU* 4.0 5.0 - - - +
397B ALA* 3.0 31.6 + - - +
538B LEU* 4.4 8.2 - - - +
542B ARG* 6.4 2.2 - - - -
545B ARG* 4.6 9.2 + - - -
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TRP* 3.7 23.8 - - + -
295B THR* 3.8 24.9 - - + -
296B ILE* 4.0 29.2 - - + -
299B HIS* 4.3 8.7 - - + +
390B ARG 3.0 18.0 + - - +
391B ASP* 4.2 2.2 - - - +
393B ASP* 1.3 74.7 - - - +
395B THR* 1.3 60.7 + - - +
397B ALA* 3.3 6.6 + - + +
398B LEU* 2.9 55.9 + - + +
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Residues in contact with THR 395 (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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299B HIS* 5.0 6.9 + - - -
391B ASP* 2.6 24.8 + - - +
392B ARG 3.9 2.0 - - - -
394B LEU* 1.3 80.8 - - - +
396B LEU* 1.3 56.9 + - - +
398B LEU* 3.5 0.3 + - - -
399B PHE* 2.9 29.8 + - + +
460B TRP* 4.1 25.9 - - + +
463B GLU* 4.3 5.0 + - + +
464B TYR* 4.0 37.7 - - + +
467B LEU* 4.2 18.0 - - + +
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Residues in contact with LEU 396 (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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392B ARG* 2.9 19.8 + - + +
393B ASP* 4.0 4.0 - - - +
395B THR* 1.3 73.9 - - - +
397B ALA* 1.3 60.7 + - - +
399B PHE* 3.3 8.3 + - + +
400B ASN* 2.8 54.6 + - - +
464B TYR* 5.7 8.0 - - + -
473B VAL* 4.5 18.6 - - + -
476B VAL* 4.2 25.1 - - + -
527B TYR* 4.2 6.3 - - - +
531B VAL* 5.9 1.1 - - + -
534B THR* 5.3 1.6 - - + -
535B LEU* 3.7 20.9 - - + -
538B LEU* 3.7 31.0 - - + -
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Residues in contact with ALA 397 (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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393B ASP 3.0 19.1 + - - +
394B LEU* 3.5 9.9 - - + +
396B LEU* 1.3 78.9 - - - +
398B LEU* 1.3 63.7 + - + +
400B ASN* 3.5 6.0 + - - +
401B ASN* 3.2 24.9 + - - +
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Residues in contact with LEU 398 (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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296B ILE* 5.4 4.5 - - + -
299B HIS* 4.6 5.6 - - + +
300B TYR* 4.8 23.6 - - + +
394B LEU* 2.9 42.1 + - + +
397B ALA* 1.3 77.8 - - + +
399B PHE* 1.3 68.4 + - - +
400B ASN 3.2 0.2 - - - -
401B ASN* 3.1 31.0 + - + +
402B THR* 3.4 9.9 + - - +
460B TRP* 3.4 47.1 + - + -
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Residues in contact with PHE 399 (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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395B THR* 2.9 20.7 + - + +
396B LEU* 3.7 10.1 - - + +
398B LEU* 1.3 78.2 - - - +
400B ASN* 1.3 61.9 + - - +
401B ASN 3.2 0.7 + - - -
402B THR* 3.0 26.0 + - + +
405B LEU* 3.3 28.5 - - + +
457B GLN* 4.2 20.4 - - + -
460B TRP* 3.6 35.5 - - + +
461B LEU* 3.5 35.7 - - + -
464B TYR* 5.9 6.5 - + + -
476B VAL* 5.0 8.3 - - + -
479B TRP* 4.2 11.9 - + - -
495B LEU* 5.1 0.7 - - + -
527B TYR* 3.5 33.9 - + - -
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Residues in contact with ASN 400 (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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396B LEU* 2.8 39.5 + - - +
397B ALA* 3.7 5.8 - - - +
399B PHE* 1.3 78.2 - - - +
401B ASN* 1.3 57.3 + - - +
402B THR 3.5 0.7 - - - -
405B LEU* 3.6 5.7 - - - +
406B GLY* 3.0 29.6 + - - -
409B THR* 4.0 12.5 + - - +
527B TYR* 2.7 37.0 + - - -
531B VAL* 5.0 0.4 - - - +
535B LEU* 3.9 24.6 - - + +
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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
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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