Contacts of the helix formed by residues 386 - 404 (chain A) in PDB entry 5ULM
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 ALA 386 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLN 4.3 1.0 + - - -
385A VAL* 1.3 78.7 - - - +
387A SER* 1.3 67.9 + - - +
388A ASP* 3.3 7.4 - - + +
389A MET* 3.0 25.2 + - + +
390A TYR* 3.3 9.8 + - - -
426A GLU* 4.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL 3.8 1.6 + - - -
386A ALA* 1.3 71.8 - - - +
388A ASP* 1.3 55.4 + - - +
390A TYR* 3.0 13.0 + - - +
391A CYS* 2.8 51.1 + - - -
422A ALA* 4.4 7.5 - - - +
426A GLU* 4.2 37.2 + - - +
428A THR* 3.8 18.9 + - - +
430A GLN* 5.0 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A PHE* 3.5 28.0 - - + -
386A ALA* 3.3 5.8 - - + +
387A SER* 1.3 78.4 - - - +
389A MET* 1.3 59.5 + - + +
391A CYS* 3.8 6.1 - - - +
392A LEU* 2.9 22.9 + - - +
430A GLN* 4.2 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A HIS* 4.3 13.9 - - + +
350A HIS* 4.1 27.4 - - + +
353A PHE* 4.0 22.9 - - + -
375A MET* 3.8 26.7 - - + +
378A MET* 3.9 15.9 - - - +
379A VAL* 4.0 19.1 - - + -
385A VAL* 4.0 12.6 - - + -
386A ALA* 3.0 21.4 + - + +
388A ASP* 1.3 74.6 - - + +
390A TYR* 1.3 68.3 + - - +
391A CYS 3.4 0.2 + - - -
392A LEU 3.4 1.2 + - - -
393A VAL* 3.4 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A VAL* 3.3 19.9 - - + +
385A VAL* 3.2 43.5 + - + +
386A ALA 3.3 16.5 + - - -
387A SER* 3.0 7.6 + - - +
389A MET* 1.3 78.7 - - - +
391A CYS* 1.3 57.7 + - - +
393A VAL* 3.4 4.5 + - - +
394A GLY* 3.1 23.2 + - - -
418A TRP* 3.7 36.4 - + - +
421A LYS* 3.7 38.4 + - + -
422A ALA* 3.6 29.6 - - + -
425A SER* 4.1 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A SER* 2.8 37.2 + - - +
388A ASP* 3.9 4.9 - - - +
389A MET 3.2 0.2 - - - -
390A TYR* 1.3 72.0 - - - +
392A LEU* 1.3 59.4 + - - +
394A GLY 3.4 0.2 + - - -
395A ARG* 2.8 29.3 + - - +
419A PHE* 3.5 22.2 - - + -
422A ALA* 4.2 3.1 - - - -
430A GLN* 3.6 33.4 - - - +
431A SER* 3.8 26.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A PHE* 3.6 47.6 - - + +
356A ALA* 4.0 3.4 - - + -
357A PHE* 3.8 40.2 - - + +
360A ASN* 5.2 3.4 - - - +
375A MET* 3.8 17.7 - - + -
388A ASP 2.9 17.7 + - - +
389A MET 3.9 4.0 - - - +
390A TYR 3.4 0.4 - - - -
391A CYS* 1.3 73.1 - - - +
393A VAL* 1.3 66.2 + - - +
395A ARG* 3.1 14.5 + - + -
396A ILE* 2.9 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 4.0 9.0 - - + -
375A MET* 3.6 35.2 - - + -
376A ILE* 4.1 6.5 - - + -
379A VAL* 4.5 2.2 - - + -
389A MET 3.4 13.3 + - - +
390A TYR 3.6 6.3 - - - +
392A LEU* 1.3 76.6 - - - +
394A GLY* 1.3 62.6 + - - +
396A ILE* 3.2 20.0 + - - +
397A TYR* 3.3 28.2 + - + -
418A TRP* 3.5 45.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A TYR 3.1 13.1 + - - -
391A CYS 3.7 3.1 - - - -
393A VAL* 1.3 76.3 - - - +
395A ARG* 1.3 55.9 + - - +
397A TYR* 3.3 3.8 + - - +
398A LYS* 2.9 27.9 + - - +
415A GLY* 4.0 7.1 - - - -
418A TRP* 3.9 17.6 - - - +
419A PHE* 3.4 25.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A PHE* 3.3 37.9 - - - -
360A ASN* 4.4 5.1 - - - +
361A ARG* 3.6 24.9 - - - +
391A CYS 2.8 20.7 + - - +
392A LEU* 3.1 15.0 + - + +
394A GLY* 1.3 72.0 - - - +
396A ILE* 1.3 59.9 + - - +
398A LYS* 3.8 23.3 - - - +
399A ASP* 2.8 44.5 + - - +
419A PHE* 3.5 6.8 - - + -
509A TRP* 4.5 3.8 + - - -
512A LYS* 3.9 12.9 - - - +
513A SER* 3.6 26.2 - - - +
516A GLU* 3.1 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ALA 5.0 0.4 - - - +
360A ASN* 3.6 35.3 - - + +
368A ARG* 4.1 17.7 - - + +
371A ALA* 3.9 26.0 - - + +
372A LEU* 3.7 33.7 - - + -
375A MET* 4.5 5.6 - - + -
392A LEU* 2.9 34.0 + - + +
393A VAL* 3.2 15.4 + - - +
395A ARG* 1.3 76.5 - - - +
397A TYR* 1.3 59.2 + - - +
399A ASP* 3.7 1.9 - - - +
400A MET* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 3.8 25.0 - - + +
376A ILE* 3.7 18.8 - - + +
393A VAL* 3.3 39.2 + - + -
394A GLY 3.7 0.9 - - - +
396A ILE* 1.3 74.3 - - - +
398A LYS* 1.3 65.8 + - - +
400A MET* 3.1 21.3 + - + +
401A PHE* 2.9 23.0 + - - +
411A SER* 3.3 29.6 - - - +
414A HIS* 3.8 44.1 - + + +
415A GLY* 3.5 11.7 - - - +
418A TRP* 3.8 15.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLY 2.9 20.5 + - - +
395A ARG* 3.6 18.0 - - + +
397A TYR* 1.3 72.0 - - - +
399A ASP* 1.3 62.7 + - - +
401A PHE* 3.2 9.3 + - - +
402A LEU* 2.9 28.7 + - - +
411A SER 5.4 0.2 - - - -
415A GLY* 4.6 1.8 - - - -
419A PHE* 4.5 8.3 - - + -
434A ASN* 3.4 23.4 + - + +
437A VAL* 6.2 1.3 - - + -
438A LEU* 4.6 17.9 - - + -
513A SER* 3.3 22.4 + - - +
516A GLU* 2.8 43.5 + - - -
517A THR* 3.5 10.0 + - - +
520A ILE* 3.7 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ASN* 2.8 18.5 + - - +
361A ARG* 2.7 27.9 + - - -
368A ARG* 3.7 20.6 - - - +
395A ARG* 2.8 31.4 + - - +
396A ILE 3.7 3.4 - - - +
398A LYS* 1.3 75.0 - - - +
400A MET* 1.3 57.7 + - - +
402A LEU* 4.4 5.9 - - - +
403A ASP* 2.8 41.7 + - - +
516A GLU* 2.9 26.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ARG* 4.0 27.6 - - + +
372A LEU* 4.3 11.0 - - + -
396A ILE* 2.9 30.1 + - - +
397A TYR* 3.4 24.7 - - + +
399A ASP* 1.3 75.4 - - - +
401A PHE* 1.3 57.4 + - - +
403A ASP* 3.9 1.2 - - - +
404A SER* 3.0 31.2 + - - -
408A ASP* 4.1 9.9 - - - +
411A SER* 3.4 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A TYR 2.9 12.9 + - - +
398A LYS* 3.3 9.6 - - - +
400A MET* 1.3 73.9 - - - +
402A LEU* 1.3 64.3 + - - +
404A SER* 2.7 22.0 + - - -
406A PHE* 3.1 60.7 + + - -
408A ASP* 3.2 31.9 - - - +
409A THR* 4.6 4.3 - - + -
411A SER* 4.2 0.8 - - - -
412A ARG* 3.5 30.5 - - + +
438A LEU* 4.0 15.7 - - + -
441A ALA* 3.8 31.9 - - + -
520A ILE* 4.1 9.6 - - + -
524A PHE* 3.8 9.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LYS* 2.9 18.6 + - - +
399A ASP* 3.9 6.3 - - - +
401A PHE* 1.3 72.7 - - - +
403A ASP* 1.3 68.4 + - - +
405A ASN* 3.0 21.5 + - - -
406A PHE* 3.6 35.5 + - + -
512A LYS* 5.2 3.4 - - - +
516A GLU* 3.9 43.7 - - + +
519A LEU* 4.9 18.6 - - + -
520A ILE* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ARG* 5.0 4.3 + - - -
363A ASN* 4.1 7.6 + - - +
368A ARG* 2.8 38.0 + - - +
399A ASP* 2.8 23.7 + - - +
400A MET* 3.9 2.0 - - - +
402A LEU* 1.3 84.2 - - - +
404A SER* 1.3 54.5 + - - +
405A ASN* 3.2 4.1 + - - +
512A LYS* 5.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A MET 3.0 13.8 + - - -
401A PHE 2.7 19.9 + - - -
403A ASP* 1.3 74.2 - - - +
405A ASN* 1.3 64.9 + - - +
407A THR* 2.7 33.6 + - - +
408A ASP* 2.9 32.8 + - - +
----------------------------------------------------------
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