Contacts of the helix formed by residues 338 - 364 (chain A) in PDB entry 5DKG
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 SER 338 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A PRO 4.4 0.2 + - - -
337A PHE* 1.3 72.8 - - - +
339A GLU* 1.3 64.1 + - - +
340A ALA* 3.2 11.8 + - - +
341A SER* 2.8 28.4 + - - -
342A MET* 3.0 24.6 + - - +
417A CYS* 4.3 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A SER* 1.3 74.5 - - - +
340A ALA* 1.3 60.4 + - - +
343A MET* 3.3 28.9 + - + +
417A CYS* 3.4 23.0 + - - +
418A VAL* 3.6 35.3 - - + +
419A GLU* 4.7 4.7 + - - +
528A MET* 5.2 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A SER* 3.1 8.8 + - - +
339A GLU* 1.3 78.9 - - - +
341A SER* 1.3 59.9 + - - +
343A MET* 3.8 2.3 - - - +
344A GLY* 2.8 25.8 + - - -
535A PRO* 6.0 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PHE* 3.3 15.0 - - - +
338A SER* 2.8 36.6 + - - -
340A ALA* 1.3 74.9 - - - +
342A MET* 1.3 61.8 + - - +
344A GLY* 3.4 1.9 - - - +
345A LEU* 2.8 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PHE* 3.5 41.3 - - + -
338A SER 3.0 16.6 + - - +
339A GLU 4.2 2.2 - - - +
341A SER* 1.3 82.9 + - - +
343A MET* 1.3 62.4 + - - +
345A LEU* 3.5 4.7 + - - +
346A LEU* 3.2 38.9 + - + +
408A LEU* 6.1 1.1 - - - -
410A LEU* 3.9 31.0 - - + -
414A GLN 3.3 24.0 - - - +
417A CYS* 4.4 7.4 - - - -
418A VAL* 4.3 3.8 - - + -
421A MET* 3.5 26.5 - - + +
425A PHE* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLU* 3.3 20.4 + - + +
340A ALA* 4.1 2.7 - - - +
342A MET* 1.3 77.5 - - - +
344A GLY* 1.3 59.0 + - - +
346A LEU* 4.1 6.4 - - - +
347A THR* 2.9 40.7 + - - +
418A VAL* 4.1 19.1 - - + -
421A MET* 3.8 27.1 - - - -
525A LEU* 4.5 3.4 - - + -
528A MET* 4.1 28.3 - - + -
536A LEU* 6.4 0.2 - - + -
601A 5C7 3.8 51.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ALA 2.8 19.4 + - - -
341A SER* 3.1 4.0 + - - -
343A MET* 1.3 78.1 - - - +
345A LEU* 1.3 62.6 + - - +
347A THR* 3.9 2.3 - - - -
348A ASN* 3.0 27.2 + - - +
535A PRO* 5.6 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER* 3.8 25.5 + - - +
330A GLU* 4.2 33.7 - - + +
332A ASP* 6.1 1.8 - - + +
337A PHE* 3.5 36.8 - - + -
341A SER* 2.8 20.2 + - - +
342A MET* 3.9 6.7 - - - +
344A GLY* 1.3 73.1 - - - +
346A LEU* 1.3 59.3 + - + +
348A ASN* 3.6 5.4 + - + +
349A LEU* 3.1 28.9 + - - +
352A ARG* 5.4 0.3 + - - -
408A LEU* 4.4 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A MET* 3.2 31.0 + - - +
343A MET* 4.1 6.3 - - - +
345A LEU* 1.3 73.0 - - + +
347A THR* 1.3 61.5 + - - +
349A LEU* 3.4 5.6 + - + +
350A ALA* 2.9 30.1 + - - +
404A PHE* 3.7 43.5 - - + -
408A LEU* 4.1 16.8 - - + -
410A LEU* 4.4 6.5 - - + -
421A MET* 4.2 14.6 - - + -
425A PHE* 4.9 0.4 - - + -
601A 5C7 3.8 45.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A MET* 2.9 27.3 + - - +
344A GLY* 3.9 3.8 - - - -
346A LEU* 1.3 74.9 - - - +
348A ASN* 1.3 67.4 + - - +
350A ALA* 3.3 1.8 + - - +
351A ASP* 2.9 25.4 + - + +
535A PRO 3.8 19.7 - - - +
536A LEU* 3.6 30.3 - - + +
537A SER* 4.7 2.9 - - - +
540A LEU* 3.7 11.0 - - + +
601A 5C7 2.9 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLU* 3.8 26.1 + - - +
344A GLY 3.0 18.4 + - - +
345A LEU* 3.8 5.8 - - - +
347A THR* 1.3 78.8 - - - +
349A LEU* 1.3 62.5 + - - +
351A ASP* 3.5 6.5 + - - +
352A ARG* 2.9 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 4.1 32.3 - - + +
328A TYR 4.3 7.0 - - - +
329A SER* 5.0 3.8 - - - +
345A LEU 3.1 19.1 + - - +
346A LEU* 3.6 4.5 - - - +
348A ASN* 1.3 77.0 + - - +
350A ALA* 1.3 58.4 + - - +
352A ARG* 3.2 23.4 + - - +
353A GLU* 2.9 49.9 + - + +
404A PHE* 3.4 43.5 - - + +
405A ALA* 4.6 3.6 - - + +
408A LEU* 5.1 5.4 - - + -
601A 5C7 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU 2.9 18.7 + - - +
347A THR 3.7 3.6 - - - +
349A LEU* 1.3 76.4 - - - +
351A ASP* 1.3 63.1 + - - +
353A GLU* 3.3 13.8 + - - +
354A LEU* 3.0 28.6 + - - +
387A LEU* 3.9 14.1 - - + +
540A LEU* 4.8 5.4 - - + -
601A 5C7 3.7 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A THR* 2.9 18.4 + - + +
348A ASN* 3.7 7.3 - - - +
350A ALA* 1.3 77.4 - - - +
352A ARG* 1.3 68.3 + - - +
354A LEU* 3.4 22.7 + - - +
355A VAL* 3.7 11.9 + - - +
537A SER* 2.5 38.1 + - - +
539A LEU* 4.0 17.2 - - - +
540A LEU* 4.5 5.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 3.7 31.0 - - + +
328A TYR 2.9 30.9 + - - +
329A SER* 4.1 10.1 - - - +
330A GLU* 4.9 2.8 - - - +
345A LEU 5.4 0.4 + - - -
348A ASN* 2.9 36.0 + - - +
349A LEU* 3.2 22.8 + - - +
351A ASP* 1.3 81.4 - - - +
353A GLU* 1.3 65.7 - - - +
355A VAL* 3.3 19.4 + - - +
356A HIS* 3.5 16.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PRO* 5.8 0.2 - - - +
325A PRO 5.9 1.1 - - - +
327A LEU* 3.7 18.6 - - + +
349A LEU* 2.9 32.2 + - + +
350A ALA* 3.3 8.5 + - - +
352A ARG* 1.3 76.8 - - - +
354A LEU* 1.3 57.5 + - - +
356A HIS* 3.1 7.8 + - - +
357A MET* 2.8 27.0 + - - +
387A LEU* 3.6 19.5 - - + +
394A ARG* 3.0 27.1 + - - -
601A 5C7 2.5 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ALA 3.0 18.9 + - - +
351A ASP* 3.5 13.0 - - - +
352A ARG 3.2 0.2 - - - -
353A GLU* 1.3 73.5 - - - +
355A VAL* 1.3 65.7 + - - +
357A MET* 3.2 29.5 + - + +
358A ILE* 3.1 35.1 + - + +
383A TRP* 3.9 29.2 - - + -
387A LEU* 4.7 3.1 - - + -
539A LEU* 4.0 24.0 - - + -
540A LEU* 3.7 30.3 - - + -
543A MET* 4.4 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ASP* 3.7 15.9 - - - +
352A ARG* 3.5 11.2 - - - +
353A GLU 3.3 0.6 - - - -
354A LEU* 1.3 77.4 - - - +
356A HIS* 1.3 63.1 + - + +
358A ILE* 3.6 9.6 + - - +
359A ASN* 2.7 38.7 + - - +
539A LEU* 4.7 11.2 - - + -
693C LEU* 5.0 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PRO* 4.1 19.9 - - + +
325A PRO* 3.5 27.2 - - + +
327A LEU* 3.7 31.7 - - + +
352A ARG* 3.5 18.1 + - + -
353A GLU* 3.1 8.8 + - - +
355A VAL* 1.3 82.3 - - + +
357A MET* 1.3 61.7 + - - +
358A ILE 3.2 0.2 - - - -
359A ASN* 3.3 8.7 + - + +
360A TRP* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PRO* 5.0 3.8 - - - +
353A GLU 2.8 11.4 + - - +
354A LEU* 3.5 23.8 - - + +
356A HIS* 1.3 78.0 - - - +
358A ILE* 1.3 58.5 + - - +
360A TRP* 3.1 18.4 + - + +
361A ALA* 2.8 26.2 + - - +
379A LEU* 4.2 15.3 - - + -
383A TRP* 3.3 38.8 - - - +
386A ILE* 3.7 35.0 - - + -
387A LEU* 3.5 27.6 - - + -
543A MET* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 3.1 23.2 + - + +
355A VAL* 3.9 5.4 - - - +
356A HIS 3.2 0.2 - - - -
357A MET* 1.3 81.0 - - + +
359A ASN* 1.3 61.2 + - - +
361A ALA* 3.5 7.5 + - - +
362A LYS* 3.3 23.1 + - + +
379A LEU* 4.0 11.2 - - + -
539A LEU* 4.9 7.4 - - + -
543A MET* 6.0 3.4 - - + -
690C LEU* 3.6 26.5 - - + -
693C LEU* 3.6 51.8 - - + +
694C LEU* 3.6 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A VAL* 2.7 33.7 + - - +
356A HIS* 3.3 10.8 + - + +
357A MET 3.3 0.4 - - - -
358A ILE* 1.3 78.4 - - - +
360A TRP* 1.3 66.2 + - - +
361A ALA 3.5 0.3 + - - -
362A LYS* 3.6 14.9 + - - +
363A ARG* 3.6 12.1 + - - +
693C LEU* 5.0 7.5 + - - +
696C ASP 4.3 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.8 7.2 + - + +
322A ALA* 3.2 41.4 - - + +
323A GLU* 4.0 10.9 + - - -
324A PRO* 3.8 18.2 - - + -
356A HIS 2.9 15.2 + - - +
357A MET* 3.3 30.7 - - + +
359A ASN* 1.3 77.0 - - - +
361A ALA* 1.3 69.2 + - + +
363A ARG* 3.0 15.9 + - - +
364A VAL* 3.2 28.4 + - + +
386A ILE* 4.0 24.0 - - + -
446A VAL* 5.2 2.9 + - - +
449A LYS* 3.7 46.6 - - + +
450A SER* 4.0 11.4 - - - -
453A LEU* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A MET 2.8 15.0 + - - +
358A ILE* 3.7 6.7 - - - +
359A ASN 3.3 0.4 - - - -
360A TRP* 1.3 85.9 - - + +
362A LYS* 1.3 60.9 + - - +
364A VAL* 3.0 17.0 + - - +
367A PHE* 3.1 42.8 - - + +
379A LEU* 4.1 15.5 - - + -
453A LEU* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ILE* 3.3 17.4 + - + +
359A ASN* 3.9 10.3 - - - +
360A TRP 3.3 1.0 - - - -
361A ALA* 1.3 75.8 - - - +
363A ARG* 1.3 58.0 + - - +
364A VAL 4.4 2.9 - - - +
367A PHE* 4.0 5.8 - - + -
368A VAL* 4.2 34.0 + - - +
372A LEU* 5.1 1.8 - - - +
375A GLN* 3.5 31.4 + - - +
693C LEU 5.6 0.9 - - - +
694C LEU* 3.2 46.2 + - + +
695C GLN* 5.2 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ALA* 4.9 4.9 - - - +
322A ALA* 3.6 27.2 - - + +
359A ASN 3.6 9.5 + - - +
360A TRP* 3.0 10.0 + - - +
361A ALA 3.0 0.8 - - - -
362A LYS* 1.3 77.6 - - - +
364A VAL* 1.3 64.1 + - - +
365A PRO* 3.2 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.4 8.5 - - + -
322A ALA* 5.6 0.4 - - + -
360A TRP* 3.2 46.9 + - + +
361A ALA* 3.0 11.0 + - - +
362A LYS 4.4 1.4 - - - +
363A ARG* 1.3 76.9 - - - +
365A PRO* 1.3 81.6 - - + +
366A GLY 3.2 0.3 + - - -
367A PHE* 3.0 24.2 + - + +
368A VAL* 4.3 2.1 + - - +
450A SER* 3.9 20.2 - - - -
453A LEU* 3.9 17.3 - - + -
454A LEU* 4.7 12.1 - - + -
482A ILE* 5.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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