Contacts of the helix formed by residues 333 - 349 (chain A) in PDB entry 4OG6
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 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A LEU* 5.9 1.2 - - - +
327A TYR* 4.8 5.1 - - - -
328A HIS* 2.8 42.2 + - - +
331A ASN* 3.8 25.4 - - - +
332A ARG* 1.3 72.0 - - - +
334A VAL* 1.3 58.3 + - - +
335A ARG 3.3 2.7 - - - -
336A GLU* 3.2 21.3 + - + +
337A ALA* 2.9 28.6 + - - +
608A DMS 4.2 2.9 - - - -
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Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A CYS* 6.3 0.2 - - - +
332A ARG* 4.3 6.3 - - + +
333A ASN* 1.3 71.9 - - - +
335A ARG* 1.4 64.0 + - - +
337A ALA* 3.3 6.1 + - - +
338A LEU* 2.9 39.1 + - + +
375A LEU* 4.4 36.6 - - + +
376A LEU* 4.2 17.0 - - + -
379A ALA* 4.9 6.5 - - + -
403A ALA* 3.6 20.4 - - + -
608A DMS 3.2 32.5 - - + +
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Residues in contact with ARG 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ASN 3.3 0.2 - - - -
334A VAL* 1.4 75.0 - - - +
336A GLU* 1.3 91.2 + - - +
338A LEU* 3.7 0.8 - - - +
339A GLN* 2.9 53.7 + - - +
406A ASP* 3.6 19.7 - - - +
408A GLU* 5.3 4.3 - - - -
409A CYS* 3.4 30.4 - - - -
412A HIS* 3.7 15.0 + - - +
608A DMS 3.0 15.0 + - - +
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Residues in contact with GLU 336 (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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328A HIS* 3.4 40.0 - - + +
333A ASN* 3.2 21.9 + - - +
335A ARG* 1.3 118.9 + - - +
337A ALA* 1.3 59.3 + - - +
339A GLN* 3.4 13.2 + - - +
340A ALA* 3.0 29.5 + - - +
608A DMS 4.7 1.6 + - - -
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Residues in contact with ALA 337 (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 ALA* 3.8 16.3 - - - +
328A HIS* 3.6 16.5 - - + +
329A CYS* 3.9 9.0 - - - +
333A ASN 2.9 16.3 + - - +
334A VAL* 3.7 7.2 - - - +
336A GLU* 1.3 74.3 - - - +
338A LEU* 1.3 65.5 + - - +
340A ALA* 3.2 2.4 + - - +
341A TRP* 2.9 49.3 + - + -
375A LEU* 4.5 1.6 - - + -
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A VAL* 2.9 39.8 + - + +
335A ARG 3.7 3.8 - - - +
337A ALA* 1.3 75.2 - - - +
339A GLN* 1.3 57.8 + - - +
341A TRP* 3.4 8.8 + - + +
342A ALA* 2.8 30.7 + - - +
372A ILE* 4.0 35.7 - - + -
375A LEU* 5.8 1.1 - - + -
376A LEU* 4.6 10.5 - - + -
403A ALA* 4.9 0.2 - - + -
409A CYS* 3.7 33.4 - - + +
412A HIS* 3.7 16.3 - - + +
413A LEU* 4.5 18.6 - - + -
416A PHE* 5.4 1.6 - - + +
447A PHE* 4.8 4.9 - - + -
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Residues in contact with GLN 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ARG* 2.9 38.1 + - - +
336A GLU* 3.6 12.8 + - - +
337A ALA 3.3 0.2 - - - -
338A LEU* 1.3 76.2 - - - +
340A ALA* 1.3 57.7 + - - +
342A ALA* 3.3 3.5 + - - +
343A ASP* 3.0 37.7 + - - +
412A HIS* 3.6 36.6 + - + +
415A ARG* 4.2 6.4 + - - +
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Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A TYR* 3.7 8.3 - - + +
324A LEU* 4.1 18.8 - - + -
325A ALA* 3.6 31.6 - - + +
336A GLU 3.0 17.5 + - - +
337A ALA 3.2 0.6 + - - +
339A GLN* 1.3 75.4 - - - +
341A TRP* 1.3 60.5 + - - +
343A ASP* 3.2 11.6 + - - +
344A THR* 3.0 31.0 + - - +
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Residues in contact with TRP 341 (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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322A MET* 4.0 17.9 - - + -
325A ALA* 3.2 17.4 - - + +
329A CYS* 3.9 16.6 - - + -
337A ALA* 2.9 33.5 + - + +
338A LEU* 3.9 10.3 - - + +
340A ALA* 1.3 72.9 - - - +
342A ALA* 1.3 66.3 + - - +
344A THR* 2.6 23.9 + - + -
345A ALA 3.0 4.5 + - - -
367A VAL* 3.6 23.1 - - + +
371A VAL* 3.5 33.7 - - + -
372A ILE* 3.6 25.6 - - + -
375A LEU* 3.6 26.0 - - + -
416A PHE* 3.4 24.1 - + + -
602A 2S9 3.2 28.6 + - - -
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Residues in contact with ALA 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU 2.8 18.8 + - - +
339A GLN 3.5 1.3 - - - +
341A TRP* 1.3 72.3 - - - +
343A ASP* 1.3 58.8 + - - +
345A ALA* 3.2 4.7 + - - +
346A THR* 2.9 30.0 + - - -
412A HIS* 3.5 26.0 - - - +
415A ARG* 3.3 36.2 - - + +
416A PHE* 4.1 11.8 - - - +
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Residues in contact with ASP 343 (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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321A TYR* 3.5 33.0 - - + -
324A LEU* 5.9 1.4 - - - +
339A GLN* 3.0 27.6 + - - +
340A ALA* 3.2 10.4 + - - +
342A ALA* 1.3 73.8 - - - +
344A THR* 1.4 64.7 + - - +
346A THR* 3.2 6.6 + - - +
347A VAL* 3.2 26.2 + - - +
415A ARG* 2.8 28.7 + - - +
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Residues in contact with THR 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE* 3.6 17.7 - - - +
321A TYR* 3.3 25.4 - - + +
322A MET* 3.6 31.6 - - + +
340A ALA 3.0 15.3 + - - +
341A TRP* 2.6 25.6 + - + +
343A ASP* 1.4 74.6 - - - +
345A ALA* 1.3 56.4 + - - +
347A VAL* 3.2 7.7 + - - +
348A ILE 3.0 21.5 + - - -
364A PHE* 3.2 26.0 - - - -
416A PHE* 4.4 0.3 - - - -
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Residues in contact with ALA 345 (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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341A TRP 3.0 4.3 + - - +
342A ALA 3.5 7.9 - - - +
344A THR* 1.3 81.9 + - - +
346A THR* 1.3 58.0 + - - +
348A ILE* 3.3 10.9 + - - +
349A GLN* 3.0 25.6 + - - +
364A PHE* 4.1 5.6 - - + -
415A ARG 4.1 0.9 - - - +
416A PHE* 3.2 41.5 - - + +
419A GLY* 3.5 19.7 - - - -
420A ILE* 4.3 0.9 - - + +
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Residues in contact with THR 346 (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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342A ALA 2.9 11.2 + - - -
343A ASP* 3.2 9.6 + - - +
345A ALA* 1.3 78.5 - - - +
347A VAL* 1.3 59.3 + - + +
349A GLN* 3.2 36.0 + - - +
350A ASP* 4.3 4.5 - - - +
415A ARG* 3.0 38.1 + - - +
419A GLY* 5.1 0.6 - - - -
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Residues in contact with VAL 347 (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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224A LYS* 5.2 0.3 + - - -
315A ASP* 3.7 18.4 - - - +
316A GLU* 3.6 31.9 - - + +
317A HIS 3.7 5.4 - - - +
318A ILE* 3.4 19.3 - - + -
321A TYR* 3.7 27.6 - - + -
343A ASP 3.2 14.3 + - - +
344A THR 3.2 6.3 + - - +
346A THR* 1.3 77.6 - - + +
348A ILE* 1.3 65.1 + - - +
349A GLN 3.1 3.5 + - - -
350A ASP* 3.4 13.0 + - - +
351A TYR* 3.6 11.5 - - + -
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Residues in contact with ILE 348 (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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220A TRP* 4.3 16.6 - - + -
318A ILE* 3.8 21.5 - - + -
344A THR 3.0 6.8 + - - +
345A ALA* 3.4 13.9 - - - +
347A VAL* 1.3 77.5 - - - +
349A GLN* 1.3 66.0 + - - +
351A TYR* 3.0 27.3 + - + +
360A ILE* 4.3 2.7 - - + -
364A PHE* 3.7 34.1 - - + -
419A GLY 4.0 12.8 - - - +
420A ILE* 4.7 0.9 - - - +
423A TRP* 3.3 55.5 - - + +
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Residues in contact with GLN 349 (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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345A ALA 3.0 12.4 + - - +
346A THR* 3.2 40.4 + - - +
347A VAL 3.1 1.4 - - - -
348A ILE* 1.3 77.4 - - - +
350A ASP* 1.3 74.7 + - - +
351A TYR 3.3 4.4 + - - +
418A ASP* 4.5 2.3 - - - +
419A GLY* 3.5 25.6 - - - +
422A LYS* 3.6 32.5 - - + +
423A TRP* 3.8 10.0 + - - +
554A GLN* 3.6 33.9 - - - +
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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
------------------------------------------------------------
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