Contacts of the helix formed by residues 404 - 425 (chain A) in PDB entry 5MQI
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 404 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A SER 4.3 6.5 - - - -
401A GLU 4.2 4.0 + - - -
402A THR 3.8 1.6 + - - -
403A LEU* 1.3 77.3 - - - +
405A VAL* 1.4 64.7 + - - +
406A ARG* 3.5 14.8 + - - +
407A THR* 3.0 26.3 + - - -
408A PHE* 3.2 29.2 + - - -
1600A SO4 3.5 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A SER* 1.4 70.3 - - - +
406A ARG* 1.3 66.2 + - - +
408A PHE* 3.1 12.5 + - + +
409A HIS* 2.9 24.7 + - + +
1600A SO4 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LYS* 3.8 14.7 + - - +
400A SER 5.9 0.2 + - - -
401A GLU* 5.4 8.3 + - - -
404A SER* 3.8 14.7 - - - +
405A VAL* 1.3 78.0 - - - +
407A THR* 1.3 57.2 + - - +
409A HIS* 3.4 8.0 + - - +
410A PHE* 3.0 28.2 + - - +
1600A SO4 2.6 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LYS* 4.6 5.4 + - - +
378A TYR* 4.6 8.9 + - - +
382A LEU* 3.8 24.9 - - + -
401A GLU 3.4 5.5 + - - -
402A THR* 3.3 37.9 - - - +
404A SER* 3.0 23.0 + - - -
406A ARG* 1.3 74.1 - - - +
408A PHE* 1.4 66.4 + - - +
410A PHE* 3.2 6.6 + - + +
411A ILE* 2.9 26.2 + - + +
446A LEU* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU* 5.3 1.8 - - + -
404A SER 3.2 28.0 + - - -
405A VAL* 3.1 13.6 + - + +
407A THR* 1.4 77.7 - - - +
409A HIS* 1.3 59.0 + - - +
411A ILE* 3.4 1.4 + - - +
412A GLU* 2.9 44.5 + - - +
443A TYR* 3.8 23.3 - + - -
446A LEU* 3.8 40.4 - - + -
447A LEU* 3.9 24.7 - - + -
450A VAL* 3.9 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A VAL* 2.9 19.9 + - + +
406A ARG* 3.6 8.7 - - - +
407A THR 3.2 0.2 - - - -
408A PHE* 1.3 76.5 - - - +
410A PHE* 1.4 59.5 + - - +
412A GLU* 3.3 15.4 + - - +
413A GLN* 2.9 72.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LYS* 3.8 31.2 - - + +
365A LEU* 4.3 23.3 - - + -
366A LEU* 3.9 27.6 - - + -
369A LYS* 5.8 2.9 - - - -
375A GLU* 5.7 1.3 - - + -
378A TYR* 3.7 41.1 - + - -
379A MET* 4.6 4.3 - - + -
406A ARG 3.0 17.3 + - - +
407A THR* 3.6 4.9 - - - +
409A HIS* 1.4 75.3 - - + +
411A ILE* 1.3 69.9 + - + +
413A GLN* 3.3 18.3 + - + +
414A ASN* 2.8 55.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A TYR* 4.3 3.4 - - + -
379A MET* 3.5 30.7 - - + -
382A LEU* 4.0 18.4 - - + -
407A THR* 2.9 25.7 + - + +
408A PHE 4.0 2.0 - - - +
410A PHE* 1.3 82.0 - - + +
412A GLU* 1.3 58.0 + - - +
414A ASN* 3.2 4.7 + - - +
415A LEU* 2.8 29.3 + - + +
439A ALA* 3.5 29.3 - - + +
442A ALA* 4.4 2.7 - - + -
443A TYR* 3.7 29.4 - - + +
446A LEU* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PHE* 2.9 33.4 + - - +
409A HIS* 3.5 16.2 + - - +
411A ILE* 1.3 78.1 - - - +
413A GLN* 1.3 56.4 + - - +
415A LEU* 3.3 9.8 + - + +
416A THR* 2.9 35.2 + - - +
443A TYR* 2.6 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LEU* 5.5 3.6 - - - +
409A HIS* 2.9 55.4 + - + +
410A PHE* 3.6 21.9 - - + +
411A ILE 3.3 0.2 - - - -
412A GLU* 1.3 76.4 - - + +
414A ASN* 1.3 60.2 + - - +
416A THR* 3.5 6.1 + - - -
417A ASN* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 3.9 11.6 - - - +
379A MET* 3.5 25.0 - - + +
410A PHE* 2.8 62.5 + - - +
411A ILE 3.7 2.7 - - - +
413A GLN* 1.3 77.6 - - - +
415A LEU* 1.3 59.5 + - - +
417A ASN* 3.3 6.0 + - - +
418A TYR* 2.9 58.5 + - + -
439A ALA* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ILE* 2.8 18.8 + - + +
412A GLU* 3.8 8.7 - - + +
414A ASN* 1.3 76.4 - - - +
416A THR* 1.3 62.6 + - - +
418A TYR* 3.5 1.9 + - - +
419A TYR* 3.1 27.0 + - + +
436A MET* 3.7 49.1 - - + +
439A ALA* 4.1 13.4 - - + +
440A LEU* 4.1 27.6 - - + +
443A TYR* 5.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A GLU* 2.9 18.9 + - - +
413A GLN* 3.7 7.4 - - - +
415A LEU* 1.3 73.8 - - - +
417A ASN* 1.3 59.9 + - - +
419A TYR* 3.4 6.5 + - - +
420A GLU* 2.9 58.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 5.5 0.8 + - - -
413A GLN 3.0 18.3 + - - +
414A ASN* 3.3 7.7 + - - +
416A THR* 1.3 78.7 - - - +
418A TYR* 1.3 80.6 + - - +
420A GLU* 3.7 11.0 - - - +
421A MET* 2.9 35.0 + - - +
432A TRP* 4.5 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 2.5 47.2 + - - +
376A THR* 4.8 3.7 - - + +
379A MET* 4.2 7.4 - - + +
414A ASN* 2.9 35.9 + - + +
415A LEU* 3.9 3.1 - - - +
417A ASN* 1.3 83.4 - - - +
419A TYR* 1.3 57.4 + - - +
421A MET* 3.3 2.1 + - - +
422A MET* 2.9 28.9 + - - +
432A TRP* 3.7 37.1 - + - +
435A ARG* 3.3 44.1 - - + +
436A MET* 3.7 18.4 - - + +
439A ALA* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LEU* 3.1 19.9 + - + +
416A THR* 3.7 6.3 - - - +
418A TYR* 1.3 76.1 - - - +
420A GLU* 1.3 68.3 + - + +
422A MET* 3.1 27.6 + - + +
423A LEU* 3.2 37.4 + - + +
436A MET* 3.8 34.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A THR* 2.9 42.3 + - + +
417A ASN* 3.7 10.4 - - - +
419A TYR* 1.3 80.5 - - + +
421A MET* 1.3 62.2 + - + +
423A LEU* 3.2 7.6 + - - +
424A THR* 2.9 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ASN* 2.9 34.9 + - - +
418A TYR 3.7 1.1 - - - +
420A GLU* 1.3 75.0 - - - +
422A MET* 1.3 62.3 + - - +
424A THR* 3.6 10.3 - - - -
425A ASP* 2.7 53.5 + - + +
432A TRP* 3.3 54.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A TYR 2.9 14.4 + - - +
419A TYR* 3.1 36.9 + - + +
421A MET* 1.3 77.1 - - - +
423A LEU* 1.3 67.7 + - + +
426A ARG* 2.9 32.1 + - - +
429A ALA* 3.6 27.1 - - + +
432A TRP* 3.6 14.1 - - + +
433A ALA* 3.6 29.2 - - - +
436A MET* 4.0 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A TYR* 3.2 51.2 + - + +
420A GLU* 3.8 7.2 - - + +
421A MET 3.1 0.6 - - - -
422A MET* 1.3 90.4 - - + +
424A THR* 1.3 62.8 + - + +
426A ARG* 3.5 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A GLU* 2.9 24.0 + - + +
421A MET* 3.6 15.1 - - - +
423A LEU* 1.3 85.6 - - + +
425A ASP* 1.3 62.1 + - - +
426A ARG* 3.2 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A MET* 2.7 41.2 + - + +
424A THR* 1.3 70.0 + - - +
426A ARG* 1.3 57.3 + - - +
427A LYS* 4.2 7.4 + - - +
428A GLU* 2.9 39.9 + - - +
429A ALA* 3.4 7.4 + - - -
432A TRP* 2.8 27.2 + - - +
----------------------------------------------------------
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