Contacts of the helix formed by residues 326 - 342 (chain X) in PDB entry 3FEW
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 GLY 326 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322X GLY* 2.7 27.9 + - - +
323X ASP 4.7 1.0 + - - -
325X LEU* 1.3 76.2 - - - +
327X ASP* 1.3 57.8 + - - -
328X ALA* 3.2 9.4 + - - -
329X TYR* 3.5 8.3 + - - +
330X LYS* 3.5 7.7 + - - -
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Residues in contact with ASP 327 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326X GLY* 1.3 69.5 - - - -
328X ALA* 1.3 61.2 + - - +
329X TYR 3.4 0.2 - - - -
330X LYS* 3.7 27.3 - - + +
331X SER* 3.1 25.1 + - - -
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Residues in contact with ALA 328 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325X LEU 5.3 2.7 - - - +
326X GLY* 3.2 2.2 - - - -
327X ASP* 1.3 81.0 + - - +
329X TYR* 1.3 59.8 + - - +
331X SER* 3.5 6.6 - - - -
332X LEU* 3.1 25.3 + - - +
493X GLU* 3.8 26.4 - - + +
494X ILE* 3.9 11.8 - - + +
496X LYS* 6.3 1.6 - - - -
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Residues in contact with TYR 329 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317X ILE* 3.7 15.5 - - - +
318X GLY* 4.1 17.7 - - - -
321X VAL* 3.5 27.1 - - + -
322X GLY 4.0 7.2 - - - -
325X LEU* 3.7 31.3 + - + +
326X GLY 3.5 9.6 + - - +
328X ALA* 1.3 77.1 - - - +
330X LYS* 1.3 60.4 + - - +
332X LEU* 3.7 12.7 - - + +
333X ALA* 2.8 35.5 + - + +
471X GLY* 2.6 44.8 + - - -
472X ILE* 4.2 7.6 - - + -
474X LEU* 4.7 2.8 - - - +
475X ALA* 4.1 18.2 + - + +
490X LEU* 5.0 0.4 - - + -
494X ILE* 3.9 13.3 - - + +
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Residues in contact with LYS 330 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318X GLY* 3.2 27.7 - - - +
319X ASN* 4.7 14.1 - - - +
322X GLY* 3.8 15.5 - - - -
323X ASP* 3.8 23.0 + - - -
326X GLY 3.5 2.9 + - - +
327X ASP* 3.7 28.5 - - + +
329X TYR* 1.3 77.8 - - - +
331X SER* 1.3 63.0 + - - +
333X ALA* 3.4 3.4 + - - +
334X ARG* 3.2 32.9 + - + +
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Residues in contact with SER 331 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327X ASP 3.1 16.8 + - - -
328X ALA* 3.5 8.3 - - - -
330X LYS* 1.3 78.8 - - - +
332X LEU* 1.3 62.7 + - - +
334X ARG* 3.1 17.1 + - - +
335X GLU* 3.1 16.6 + - - +
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Residues in contact with LEU 332 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328X ALA 3.1 13.6 + - - +
329X TYR* 3.2 13.4 + - + +
331X SER* 1.3 76.1 - - - +
333X ALA* 1.3 66.3 + - - +
335X GLU* 3.0 18.5 + - + +
336X ILE* 3.1 20.0 + - + +
475X ALA* 4.3 10.5 - - + -
486X PHE* 3.6 25.4 - - + +
489X ALA* 3.5 27.1 - - + -
490X LEU* 3.4 42.0 - - + +
494X ILE* 4.7 7.9 - - + -
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Residues in contact with ALA 333 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314X ILE* 3.6 18.0 - - + +
315X SER* 5.3 0.9 - - - +
317X ILE* 6.0 0.4 - - + -
318X GLY* 3.5 31.2 - - - +
329X TYR* 2.8 30.7 + - + +
330X LYS 3.6 3.1 - - - +
332X LEU* 1.3 73.4 - - - +
334X ARG* 1.3 59.2 + - + +
336X ILE* 3.6 7.6 + - - -
337X ALA* 3.1 28.4 + - - +
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Residues in contact with ARG 334 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315X SER* 3.1 35.4 + - - +
318X GLY* 6.0 1.0 - - - -
319X ASN* 3.3 31.6 + - - +
330X LYS* 3.2 17.7 + - - +
331X SER* 3.1 10.9 + - - +
332X LEU 3.0 1.0 - - - -
333X ALA* 1.3 79.6 - - + +
335X GLU* 1.3 58.1 + - - +
337X ALA* 4.0 4.2 - - - +
338X ASP* 2.7 43.8 + - - +
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Residues in contact with GLU 335 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331X SER* 3.1 13.1 + - - +
332X LEU* 3.0 15.3 + - + +
334X ARG* 1.3 75.8 - - - +
336X ILE* 1.3 57.7 + - - +
338X ASP* 3.4 6.2 + - - +
339X ASP* 3.0 37.9 + - - +
485X LYS* 3.8 27.9 + - - +
486X PHE* 3.7 14.0 - - + -
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Residues in contact with ILE 336 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314X ILE* 4.1 11.9 - - + -
332X LEU* 3.1 20.1 + - + +
333X ALA* 3.9 9.9 - - - +
335X GLU* 1.3 73.6 - - - +
337X ALA* 1.3 60.5 + - - +
339X ASP* 3.2 2.8 + - - +
340X VAL* 2.8 30.9 + - + +
474X LEU* 6.2 0.7 - - + -
475X ALA* 3.9 42.0 - - + +
478X VAL* 3.9 19.7 - - + -
479X GLY* 4.6 1.8 - - - +
482X LEU* 3.7 20.0 - - + -
486X PHE* 3.5 33.2 - - + -
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Residues in contact with ALA 337 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311X ALA* 3.4 36.8 - - + +
314X ILE* 3.9 13.1 - - + +
315X SER* 4.0 13.7 - - - +
333X ALA 3.1 18.5 + - - +
334X ARG* 4.2 6.5 - - - +
336X ILE* 1.3 74.0 - - - +
338X ASP* 1.3 59.5 + - - +
340X VAL* 3.2 5.2 + - - +
341X LYS* 2.9 25.6 + - - +
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Residues in contact with ASP 338 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334X ARG* 2.7 30.0 + - - +
335X GLU* 3.6 8.9 - - - +
337X ALA* 1.3 79.8 - - - +
339X ASP* 1.3 60.3 + - - +
341X LYS* 3.3 24.0 + - - +
342X ASN* 2.8 38.6 + - - +
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Residues in contact with ASP 339 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335X GLU* 3.0 21.8 + - - +
336X ILE 3.7 3.6 - - - +
338X ASP* 1.3 76.5 - - - +
340X VAL* 1.3 64.6 + - - +
342X ASN* 3.6 5.7 + - - +
343X PHE* 3.3 27.9 + - - +
346X LYS* 5.8 0.3 - - - +
482X LEU* 4.4 10.7 - - + +
483X ASP* 4.6 5.9 - - - +
485X LYS* 3.7 28.0 + - - -
486X PHE* 3.9 14.3 - - + -
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Residues in contact with VAL 340 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307X LEU* 3.4 19.9 - - + +
310X ALA* 3.7 30.7 - - + -
311X ALA* 3.9 5.6 - - - +
314X ILE* 4.8 7.9 - - + -
336X ILE* 2.8 23.5 + - + +
337X ALA* 3.5 10.3 - - - +
339X ASP* 1.3 76.2 - - - +
341X LYS* 1.3 62.8 + - - +
343X PHE* 3.1 23.2 - - - +
446X LEU* 3.9 24.7 - - + -
450X SER* 5.1 1.6 - - - +
478X VAL* 4.9 3.6 - - + -
482X LEU* 3.8 18.8 - - + -
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Residues in contact with LYS 341 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303X GLN* 3.0 32.3 + - - +
307X LEU* 4.2 9.6 - - - +
308X ASN* 3.6 26.0 - - - +
311X ALA* 3.9 14.3 - - + +
337X ALA 2.9 16.1 + - - +
338X ASP* 3.3 27.6 + - - +
340X VAL* 1.3 77.6 - - - +
342X ASN* 1.3 68.8 + - - +
343X PHE 3.3 1.9 + - - -
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Residues in contact with ASN 342 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338X ASP* 2.8 29.4 + - - +
339X ASP* 3.6 7.2 - - - +
340X VAL 3.2 0.4 - - - -
341X LYS* 1.3 92.1 + - - +
343X PHE* 1.3 58.0 + - - +
344X GLN* 2.9 33.9 + - - +
346X LYS* 3.3 10.0 + - - -
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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