Contacts of the helix formed by residues 318 - 329 (chain A) in PDB entry 2WOK
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 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A PRO* 3.1 13.0 + - + +
316A PHE 3.1 1.2 - - - -
317A ASP* 1.3 82.8 - - - +
319A VAL* 1.3 67.3 + - - +
320A HIS* 2.8 45.1 + - - +
321A VAL* 3.1 18.2 + - + +
322A ARG* 3.3 14.1 + - - +
384A ALA 4.8 2.4 + - - -
385A ALA* 3.7 26.1 + - + +
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A ASP 3.6 4.4 + - - -
318A ASN* 1.3 72.8 + - - +
320A HIS* 1.3 81.8 + - + +
322A ARG* 3.2 29.6 + - - +
323A ARG* 2.8 59.9 + - + +
519A GLU 3.8 5.8 - - - +
520A HIS* 3.8 11.2 - - - +
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Residues in contact with HIS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ASN* 2.8 18.0 + - - +
319A VAL* 1.3 90.5 - - + +
321A VAL* 1.3 59.5 + - - +
323A ARG* 4.2 16.5 + - - -
324A ALA* 2.9 25.3 + - - +
381A GLU* 2.7 57.8 - - - +
384A ALA* 3.5 27.2 + - + +
385A ALA 3.9 3.1 - - - +
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A PRO* 3.5 23.8 - - + +
316A PHE* 3.6 23.6 - - + -
318A ASN* 3.1 14.7 + - + +
320A HIS* 1.3 77.7 - - - +
322A ARG* 1.3 61.6 + - - +
324A ALA* 3.2 8.7 + - - +
325A VAL* 3.1 22.2 + - - +
382A LEU* 4.8 3.1 - - + -
385A ALA* 3.6 22.4 - - + -
387A LEU* 4.0 19.3 - - + -
391A PHE* 3.5 29.6 - - + -
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A MET* 3.6 29.2 - - + +
311A PRO* 3.9 12.2 - - - +
316A PHE* 2.9 44.1 + - + +
317A ASP 3.3 20.8 + - - -
318A ASN 3.6 3.8 - - - +
319A VAL* 3.2 28.3 + - - +
321A VAL* 1.3 76.6 - - - +
323A ARG* 1.3 61.9 + - - +
325A VAL* 3.2 5.2 + - - +
326A GLN* 3.1 26.4 + - - +
520A HIS* 2.8 41.6 + - - +
521A ALA* 3.4 17.3 - - + +
522A VAL* 3.4 26.0 - - - +
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Residues in contact with ARG 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A VAL* 2.8 35.0 + - - +
320A HIS* 4.0 17.9 + - - +
322A ARG* 1.3 73.2 - - - +
324A ALA* 1.3 60.0 + - - +
326A GLN* 3.2 8.8 + - - +
327A TYR* 2.9 36.2 + - + -
365A TYR* 2.9 42.3 + - + -
381A GLU* 3.6 30.6 + - + +
519A GLU* 2.9 30.5 + - - +
521A ALA* 3.8 5.6 - - + -
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A HIS 2.9 19.6 + - - +
321A VAL 3.3 5.8 - - - +
323A ARG* 1.3 76.8 - - - +
325A VAL* 1.3 61.8 + - - +
327A TYR 3.3 0.2 + - - -
328A ALA* 2.9 27.1 + - - +
378A ALA* 3.5 28.5 - - + +
381A GLU* 3.7 8.9 - - + +
382A LEU* 3.7 24.9 - - + -
418A ILE* 4.7 5.2 - - + -
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Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A MET* 3.6 29.6 - - + -
316A PHE* 4.3 13.5 - - + -
321A VAL 3.1 12.8 + - - +
322A ARG 3.2 6.9 + - - +
324A ALA* 1.3 76.1 - - - +
326A GLN* 1.3 63.3 + - - +
328A ALA 3.2 3.1 + - - -
329A ALA* 3.2 21.0 + - - +
391A PHE* 4.9 2.0 - - + -
409A VAL* 5.5 1.3 - - + -
413A LEU* 3.8 38.3 - - + +
418A ILE* 4.0 13.9 - - + -
448A LEU* 4.0 9.6 - - + -
524A LEU* 4.2 13.2 - - + -
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Residues in contact with GLN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A MET* 3.9 4.4 - - + +
322A ARG 3.1 20.9 + - - +
323A ARG* 3.5 9.0 - - - +
325A VAL* 1.3 78.5 - - - +
327A TYR* 1.3 64.0 + - - +
329A ALA* 3.3 13.9 + - - +
365A TYR* 3.7 39.8 - - + +
367A THR* 3.8 10.2 - - - +
518A MET* 3.8 7.4 - - - +
521A ALA* 3.1 28.4 + - + +
523A LEU 2.9 28.8 + - - +
524A LEU* 3.5 35.4 - - + +
525A PRO* 4.2 1.0 - - - +
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Residues in contact with TYR 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A ARG* 2.9 27.8 + - + +
324A ALA 3.8 2.0 - - - +
326A GLN* 1.3 74.3 - - - +
328A ALA* 1.3 56.2 + - - +
329A ALA 3.2 1.3 + - - -
364A LEU 3.8 6.2 + - - -
365A TYR* 3.6 43.9 - + + -
366A PRO* 3.4 26.0 - - + +
367A THR* 3.9 6.7 - - - +
373A GLY* 3.4 5.7 - - - -
374A ASP* 2.9 41.1 + - + +
377A ALA* 3.6 27.1 - - + -
378A ALA 3.7 6.3 - - - +
381A GLU* 3.6 35.8 + - + -
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ALA 2.9 17.7 + - - +
325A VAL 3.2 2.0 + - - -
327A TYR* 1.3 75.5 - - - +
329A ALA* 1.3 59.1 + - - +
330A ASP 3.4 0.7 + - - -
375A LEU* 4.2 15.5 - - + -
378A ALA* 3.8 13.2 - - + -
412A SER* 3.4 12.5 - - - +
413A LEU* 3.7 19.7 - - + -
415A ARG* 2.8 23.1 + - - -
416A VAL* 4.0 15.3 - - + -
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A VAL 3.2 9.3 + - - +
326A GLN 3.5 13.2 - - - +
327A TYR 3.2 2.2 - - - -
328A ALA* 1.3 78.1 - - - +
330A ASP* 1.3 59.4 + - - +
331A LYS* 3.2 18.0 + - + -
334A LEU* 4.0 13.0 - - + -
367A THR* 3.5 17.5 - - - +
373A GLY* 3.7 6.1 + - - -
412A SER* 4.2 5.4 - - - -
413A LEU* 5.0 1.8 - - + -
415A ARG* 4.2 0.7 - - - -
524A LEU* 4.0 21.8 - - + -
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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
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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