Contacts of the helix formed by residues 365 - 377 (chain B) in PDB entry 2WO6
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 ASN 365 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321B PTR 5.1 1.1 - - - -
325B ARG* 3.8 16.3 - - - +
363B GLY 3.3 0.8 - - - -
364B ALA* 1.3 86.2 + - - +
366B GLU* 1.3 52.7 + - - +
367B VAL* 3.4 9.4 + - - +
368B ASP* 2.8 37.5 + - - +
369B GLN* 2.7 34.7 + - - +
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Residues in contact with GLU 366 (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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321B PTR 4.2 22.1 + - + +
325B ARG* 4.5 0.4 - - - +
328B ARG* 3.8 24.5 + - - +
332B VAL* 4.6 1.9 - - - +
333B LEU* 3.7 23.5 - - + +
365B ASN* 1.3 71.7 - - - +
367B VAL* 1.3 59.3 + - - +
369B GLN* 3.4 7.7 - - - +
370B MET* 2.8 26.7 + - - +
390B LYS* 3.0 29.0 + - - -
393B LYS* 2.4 43.9 + - - +
394B PHE* 3.3 16.8 - - + -
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Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B ASN* 3.4 7.7 + - - +
366B GLU* 1.3 74.9 - - - +
368B ASP* 1.3 58.9 + - - +
370B MET* 3.1 1.6 + - - +
371B ASN* 2.9 49.9 + - - +
393B LYS* 3.7 39.0 - - + +
394B PHE* 3.7 14.8 - - + -
406B LYS* 6.6 0.2 - - + -
415B TYR* 5.3 3.1 - - + +
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Residues in contact with ASP 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B GLY* 3.2 1.4 - - - -
364B ALA* 2.8 31.0 + - + +
365B ASN* 2.8 25.4 + - - +
367B VAL* 1.3 76.5 - - - +
369B GLN* 1.3 57.1 + - - +
371B ASN* 4.0 0.5 - - - +
372B LYS* 2.9 53.7 + - - +
415B TYR* 2.6 44.5 + - - +
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Residues in contact with GLN 369 (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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325B ARG* 3.0 39.1 + - + +
326B PHE* 3.5 6.7 + - - -
328B ARG 5.0 2.2 + - - +
333B LEU* 4.0 21.1 - - + -
361B PHE* 3.1 38.3 + - - +
363B GLY* 2.9 29.6 + - - +
365B ASN 2.7 21.7 + - - +
366B GLU* 3.4 10.1 - - - +
368B ASP* 1.3 71.5 - - - +
370B MET* 1.3 65.4 - - - +
372B LYS* 3.3 4.7 + - - +
373B ILE* 3.1 29.5 + - + +
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Residues in contact with MET 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B PRO* 4.4 10.3 - - + -
333B LEU* 3.8 36.5 - - + +
334B LEU* 4.0 18.4 - - + -
366B GLU 2.8 11.4 + - - +
367B VAL 3.6 1.3 - - - +
369B GLN* 1.3 72.2 - - - +
371B ASN* 1.3 59.8 + - - +
373B ILE* 3.0 15.6 + - - +
374B VAL* 2.9 37.0 + - + +
380B PRO* 4.9 5.4 - - + -
394B PHE* 3.4 42.4 - - + -
395B PHE* 3.5 35.7 - - + -
405B LEU* 5.7 0.7 - - + -
462B TYR* 5.4 0.4 - - - -
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Residues in contact with ASN 371 (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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367B VAL* 2.9 44.9 + - - +
368B ASP 4.0 0.4 - - - +
370B MET* 1.3 77.3 - - - +
372B LYS* 1.3 58.1 + - - +
374B VAL* 3.3 8.8 + - - +
375B GLU* 3.0 32.6 + - - +
394B PHE* 5.2 4.0 + - - +
405B LEU* 3.0 40.7 - - - +
415B TYR* 3.7 43.6 - - + +
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Residues in contact with LYS 372 (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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360B LEU 5.6 0.2 - - - +
361B PHE* 3.2 29.1 - - + -
362B SER* 2.8 45.3 + - - +
363B GLY 3.9 0.4 - - - +
364B ALA* 4.7 0.6 - - - +
368B ASP* 2.9 46.6 + - - +
369B GLN* 3.6 4.9 - - - +
370B MET 3.2 0.2 - - - -
371B ASN* 1.3 74.1 - - - +
373B ILE* 1.3 64.2 + - - +
375B GLU* 3.6 31.1 + - - +
376B VAL* 3.9 3.6 + - - +
415B TYR* 4.4 6.3 - - + -
421B ARG* 4.9 4.5 + - - +
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Residues in contact with ILE 373 (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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328B ARG 4.3 7.2 - - - +
330B PRO* 5.0 3.8 - - + -
333B LEU* 3.7 30.7 - - + -
345B TRP* 3.7 36.6 - - + -
361B PHE* 3.5 27.8 - - + -
369B GLN* 3.1 18.9 + - - +
370B MET* 3.0 13.7 + - - +
372B LYS* 1.3 74.6 - - - +
374B VAL* 1.3 58.0 - - - +
376B VAL* 3.1 6.6 + - - +
377B LEU* 3.0 31.2 + - + +
462B TYR* 3.5 22.7 - - + +
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Residues in contact with VAL 374 (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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370B MET* 2.9 23.1 + - - +
371B ASN* 3.3 9.1 + - - +
373B ILE* 1.3 74.5 - - - +
375B GLU* 1.3 64.8 + - - +
378B GLY 3.1 27.0 + - - +
379B ILE* 3.9 9.4 - - + -
380B PRO* 4.3 2.0 - - + -
395B PHE* 3.8 30.1 - - + -
405B LEU* 4.2 12.1 - - + -
418B PRO* 3.2 28.2 - - + +
419B GLY 2.9 17.0 + - - -
462B TYR* 3.9 6.1 - - - +
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Residues in contact with GLU 375 (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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371B ASN 3.0 17.4 + - - +
372B LYS* 3.8 27.8 - - - +
373B ILE 3.3 0.4 - - - -
374B VAL* 1.3 76.7 - - + +
376B VAL* 1.3 58.8 + - - +
414B GLU 4.8 0.2 - - - +
415B TYR* 3.3 21.4 - - + -
416B LYS* 2.7 53.1 + - + +
417B PRO 3.9 6.2 - - - +
418B PRO* 4.3 0.2 - - - -
419B GLY 3.1 13.0 + - - +
420B THR 3.1 1.2 + - - -
421B ARG* 3.0 46.8 + - + -
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Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU* 4.7 2.0 - - + -
361B PHE* 3.7 26.2 - - + -
372B LYS 3.9 3.8 - - - +
373B ILE 3.1 6.5 + - - +
375B GLU* 1.3 81.3 - - - +
377B LEU* 1.3 77.5 + - + +
378B GLY 3.6 0.7 - - - -
419B GLY* 3.8 10.3 - - - +
421B ARG* 3.4 49.0 - - - +
422B LYS* 5.1 4.0 - - - +
423B LEU* 4.3 21.8 - - + +
426B ILE* 4.0 9.4 - - + -
457B LEU* 5.7 0.4 - - + -
460B LEU* 5.9 1.1 - - + -
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Residues in contact with LEU 377 (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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345B TRP* 3.6 24.9 - - + -
361B PHE* 4.2 7.0 - - + -
373B ILE* 3.0 18.0 + - + +
376B VAL* 1.3 94.4 - - + +
378B GLY* 1.3 61.5 + - - +
379B ILE 4.9 0.5 - - - +
419B GLY* 4.4 2.0 - - - -
457B LEU* 3.9 28.9 - - + +
460B LEU* 3.5 36.8 - - + +
462B TYR* 3.6 28.2 - - + +
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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