Contacts of the helix formed by residues 332 - 353 (chain A) in PDB entry 1U6G
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 LEU 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A TYR* 3.6 44.6 - - + +
325A VAL* 3.5 16.8 + - + +
326A SER* 4.0 20.2 - - - +
328A ILE 4.2 1.2 + - - +
330A ASP* 3.1 1.9 - - - -
331A GLY* 1.3 74.0 - - - +
333A GLY* 1.3 64.4 + - - +
335A LEU* 3.4 32.5 - - + +
336A LYS* 3.7 21.6 + - + +
387A ASP* 4.2 9.0 - - - +
390A PHE* 3.9 11.4 - - + -
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Residues in contact with GLY 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ASP* 3.0 12.7 + - - -
331A GLY 3.0 5.5 - - - -
332A LEU* 1.3 74.1 - - - +
334A GLU* 1.3 52.0 + - - -
335A LEU 2.9 4.3 - - - -
336A LYS* 2.8 42.9 + - - +
337A LYS* 3.3 6.9 + - - +
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Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A HIS* 3.8 31.8 + - + +
330A ASP 4.6 1.2 + - - -
331A GLY 4.0 4.2 + - - +
333A GLY* 1.3 72.4 - - - +
335A LEU* 1.3 61.5 - - - +
337A LYS* 3.1 43.5 + - + +
338A LEU* 3.1 59.8 + - - +
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A HIS* 3.8 27.4 - - + +
306A PHE* 3.3 54.5 - - + -
321A MET* 4.7 8.1 - - + +
322A TYR* 4.6 10.8 - - + -
325A VAL* 4.0 23.3 - - + -
331A GLY 4.5 2.1 + - - +
332A LEU* 3.4 38.0 - - + +
333A GLY 2.8 0.6 + - - -
334A GLU* 1.3 77.7 - - - +
336A LYS* 1.3 64.0 + - - +
338A LEU* 3.3 1.5 + - + -
339A LEU* 3.0 19.9 + - - +
384A PHE* 5.7 0.2 - - + -
390A PHE* 4.2 10.5 - - + -
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 3.7 14.8 - - + +
333A GLY* 2.8 13.2 + - - +
335A LEU* 1.3 75.9 - - - +
337A LYS* 1.3 66.5 + - + +
339A LEU* 3.0 17.5 + - - +
340A GLU* 3.0 15.1 + - - +
387A ASP* 5.4 0.9 - - - +
389A GLY* 3.6 39.7 - - - +
390A PHE* 3.7 29.6 - - + -
392A ALA* 5.9 0.2 - - - -
393A ALA* 3.9 6.7 - - + +
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Residues in contact with LYS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLY 3.3 8.4 + - - +
334A GLU* 3.1 36.7 + - + +
335A LEU 3.3 0.2 - - - -
336A LYS* 1.3 80.4 - - - +
338A LEU* 1.3 68.0 + - + +
339A LEU 3.1 0.3 + - - -
340A GLU* 3.2 9.6 + - - +
341A THR* 3.1 24.0 + - - -
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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
----------------------------------------------------------
303A HIS* 4.3 28.0 - - + +
306A PHE* 3.9 22.7 - - + -
307A GLN* 5.3 13.0 + - + +
310A LEU* 6.2 0.2 - - + -
334A GLU* 3.1 45.2 + - - +
335A LEU 3.6 4.5 - - - +
337A LYS* 1.3 83.1 - - + +
339A LEU* 1.3 57.0 + - - +
341A THR* 3.6 8.9 + - - +
342A HIS* 3.0 28.2 + - - +
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Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 4.1 7.2 - - + -
310A LEU* 4.1 29.6 - - + -
335A LEU 3.0 12.4 + - - +
336A LYS* 3.0 10.8 + - - +
338A LEU* 1.3 74.3 - - - +
340A GLU* 1.3 60.4 + - - +
342A HIS* 2.9 4.8 + - + -
343A ILE* 2.7 45.7 + - + +
376A TYR* 4.8 9.9 - - + -
379A LEU* 5.3 0.2 - - + -
380A VAL* 4.1 16.8 - - + -
384A PHE* 3.9 18.6 - - + -
390A PHE* 3.7 27.4 - - + +
393A ALA* 4.2 12.1 - - + -
394A LEU* 5.1 1.8 - - + +
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Residues in contact with GLU 340 (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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336A LYS 3.0 11.4 + - - +
337A LYS* 3.6 11.6 - - - +
339A LEU* 1.3 76.6 - - - +
341A THR* 1.3 69.4 + - - +
343A ILE* 3.9 4.5 - - - -
344A HIS* 3.0 22.9 + - - +
393A ALA* 3.4 34.4 - - + +
396A LYS* 3.3 32.5 - - + +
397A ALA* 3.5 7.8 - - + +
400A ARG* 3.7 24.9 + - - -
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Residues in contact with THR 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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337A LYS 3.1 10.9 + - - -
338A LEU* 3.7 14.1 - - + +
340A GLU* 1.3 82.6 + - - +
342A HIS* 1.3 64.3 + - - +
344A HIS* 3.4 5.4 - - + +
345A ASN* 3.0 46.8 + - - +
400A ARG* 5.2 6.2 + - - +
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Residues in contact with HIS 342 (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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307A GLN* 3.1 28.0 + - - +
310A LEU* 3.4 48.8 + - + +
311A ASP* 4.2 8.7 - - - -
338A LEU 3.0 16.4 + - - +
339A LEU* 2.9 12.0 + - + +
341A THR* 1.3 72.7 - - - +
343A ILE* 1.3 55.6 + - - +
344A HIS 2.9 2.0 + - - -
345A ASN* 3.0 5.7 + - - +
346A GLN* 2.7 47.4 + - + +
376A TYR* 2.9 45.9 + + - -
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Residues in contact with ILE 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 2.7 35.7 + - + +
340A GLU* 3.6 7.9 - - - +
342A HIS* 1.3 77.0 - - - +
344A HIS* 1.3 53.6 + - - +
346A GLN* 3.5 7.2 - - - +
347A GLY* 3.0 22.5 + - - -
372A VAL* 3.4 29.6 - - + +
376A TYR* 3.5 33.4 - - + -
394A LEU* 3.9 28.9 - - + +
397A ALA* 3.7 18.6 - - + -
398A CYS* 4.7 2.9 - - - -
401A PHE* 4.2 6.5 - - + -
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Residues in contact with HIS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLU 3.0 18.6 + - - +
341A THR* 3.4 5.4 - - - +
342A HIS 2.9 1.2 + - - -
343A ILE* 1.3 74.2 - - - +
345A ASN* 1.3 75.2 + - - +
347A GLY* 2.7 12.6 + - - -
348A LEU* 3.0 48.8 + - + +
397A ALA* 3.7 13.0 + - + +
400A ARG* 3.1 63.5 + - + +
401A PHE* 3.7 20.1 + - + +
404A ASN 5.3 1.3 - - - -
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Residues in contact with ASN 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 THR* 3.0 41.0 + - - +
342A HIS* 3.8 4.0 - - - +
344A HIS* 1.3 86.3 - - - +
346A GLN* 1.3 63.2 + - - +
347A GLY 3.0 0.5 + - - -
348A LEU* 3.0 16.8 + - - +
349A ALA* 3.0 26.7 + - - +
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Residues in contact with GLN 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 HIS* 2.7 33.9 + - + +
343A ILE* 3.5 11.2 - - - +
345A ASN* 1.3 74.0 - - - +
347A GLY* 1.3 58.1 + - - +
349A ALA* 4.0 7.6 - - - +
350A ALA* 3.5 20.1 + - - +
372A VAL* 4.1 7.7 - - + +
375A LYS* 4.6 8.7 - - - +
376A TYR* 3.1 36.8 + - + +
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Residues in contact with GLY 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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343A ILE 3.0 9.6 + - - -
344A HIS 2.7 10.5 + - - -
346A GLN* 1.3 76.6 - - - +
348A LEU* 1.3 63.1 + - - -
349A ALA 3.3 0.7 + - - -
350A ALA* 3.4 4.5 + - - +
351A ILE* 3.3 25.3 + - - +
372A VAL* 4.0 16.6 - - - -
401A PHE* 4.0 21.3 - - - -
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Residues in contact with LEU 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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344A HIS* 3.0 63.2 + - + +
345A ASN* 3.0 13.8 + - - +
347A GLY* 1.3 76.0 - - - +
349A ALA* 1.3 58.1 + - - +
351A ILE* 3.5 8.1 + - - +
352A GLU* 2.9 34.4 + - + +
401A PHE* 3.9 9.8 - - + +
404A ASN 3.8 22.4 - - - +
405A ASN* 4.4 11.9 - - - -
406A ALA* 4.9 3.3 - - - +
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Residues in contact with ALA 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 ASN 3.0 16.7 + - - +
346A GLN* 4.0 11.2 - - - +
348A LEU* 1.3 75.2 - - - +
350A ALA* 1.3 67.9 + - - +
352A GLU* 2.8 19.6 + - - +
353A LYS* 2.9 25.2 + - + +
533C TYR* 5.6 0.4 - - - -
534C LYS* 4.5 20.0 - - - +
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Residues in contact with ALA 350 (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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346A GLN* 3.5 7.6 + - - +
347A GLY 3.4 10.5 + - - +
349A ALA* 1.3 80.4 - - - +
351A ILE* 1.3 62.0 + - - +
353A LYS* 3.4 17.4 + - - +
354A CYS* 3.5 17.0 + - - -
368A THR* 3.4 22.6 - - + +
372A VAL* 3.7 20.6 - - + -
492C ASN* 5.2 0.5 + - - +
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Residues in contact with ILE 351 (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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347A GLY 3.3 12.9 + - - +
348A LEU 3.8 6.7 - - - +
349A ALA 3.2 0.4 - - - -
350A ALA* 1.3 72.8 - - - +
352A GLU* 1.3 68.6 + - - +
354A CYS* 2.9 20.3 + - - +
355A GLY* 3.8 3.3 + - - +
358A ALA* 4.7 2.7 - - + +
365A TYR* 3.9 14.4 - - + -
368A THR* 4.3 16.8 - - + -
369A VAL* 4.1 13.2 - - + +
372A VAL* 6.4 0.2 - - + -
401A PHE* 4.0 16.8 - - + -
405A ASN* 3.4 30.7 - - + +
406A ALA* 4.0 14.7 - - + +
407A VAL* 3.2 33.4 - - + +
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Residues in contact with GLU 352 (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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348A LEU* 2.9 20.6 + - + +
349A ALA* 2.8 17.2 + - - +
351A ILE* 1.3 71.1 - - - +
353A LYS* 1.3 58.6 + - + +
354A CYS 2.9 6.1 + - - -
355A GLY* 2.9 17.8 + - - -
406A ALA* 3.8 23.0 - - + +
532C PHE* 3.5 27.4 - - + -
533C TYR* 3.0 41.3 + - - +
534C LYS* 4.9 1.6 - - + -
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Residues in contact with LYS 353 (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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349A ALA* 2.9 25.7 + - + +
350A ALA* 3.7 12.1 - - - +
351A ILE 3.2 0.2 - - - -
352A GLU* 1.3 72.9 - - - +
354A CYS* 1.3 55.7 + - - +
490C SER* 4.9 0.3 - - - -
491C SER* 2.4 27.7 + - - +
492C ASN* 3.0 41.2 + - - +
495C ILE* 4.2 29.0 - - + +
496C ASP* 5.3 3.8 + - - -
532C PHE* 3.8 5.2 - - + -
534C LYS* 3.8 28.3 - - + +
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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