Contacts of the helix formed by residues 407 - 422 (chain A) in PDB entry 3MTC
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 GLU 407 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ALA* 4.6 4.9 - - + -
403A ALA 3.3 25.6 - - - +
404A HIS* 3.1 16.9 + - + -
406A GLU* 1.3 91.8 - - + +
408A TYR* 1.3 62.4 + - - +
409A GLU 3.2 3.6 - - - +
410A ARG* 3.0 29.7 + - + +
411A ARG* 3.1 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A ILE 3.9 5.2 - - - -
406A GLU* 3.5 12.3 + - - -
407A GLU* 1.3 76.8 - - - +
409A GLU* 1.3 96.5 + - + +
411A ARG* 3.3 25.8 + - - +
412A ASN* 3.0 32.4 + - - +
450A TYR* 4.2 8.0 - - + -
453A GLU* 3.8 14.8 - - - -
477A GLN* 3.9 26.9 - - + +
481A GLN* 3.9 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLU 5.1 1.0 + - - +
407A GLU 3.2 0.6 - - - -
408A TYR* 1.3 105.1 + - + +
410A ARG* 1.3 58.7 + - - +
412A ASN* 3.3 13.7 + - - +
413A GLN* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A THR 2.9 23.4 + - - -
372A GLY* 3.1 19.2 + - - -
375A GLY* 4.2 7.9 - - - -
402A ALA* 3.5 21.1 - - + -
407A GLU* 3.0 25.9 + - + +
409A GLU* 1.3 76.3 - - - +
411A ARG* 1.3 54.0 + - - +
413A GLN* 3.2 12.6 + - - +
414A ASP* 2.7 54.8 + - - +
574A GOL 3.0 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LEU* 3.9 7.2 - - + +
402A ALA 2.7 52.6 + - - +
403A ALA 3.5 8.7 + - - -
404A HIS 2.9 30.5 + - - -
405A ILE* 3.2 11.9 + - - +
407A GLU 3.1 10.7 + - - +
408A TYR* 3.4 19.8 - - - +
410A ARG* 1.3 73.8 - - - +
412A ASN* 1.3 66.2 + - - +
414A ASP* 3.1 10.3 + - - +
415A TYR* 2.9 23.4 + - - +
448A LEU 3.1 25.4 - - - +
449A ASN 3.4 18.3 + - - -
450A TYR* 3.4 34.2 + - + +
477A GLN* 2.9 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TYR* 3.0 19.6 + - - +
409A GLU* 3.5 17.4 - - - +
410A ARG 3.3 0.2 - - - -
411A ARG* 1.3 75.0 - - - +
413A GLN* 1.3 58.6 + - - +
415A TYR* 3.2 4.3 + - - +
416A LYS* 3.0 38.4 + - - +
450A TYR* 2.8 30.3 + - - -
481A GLN* 2.9 32.7 + - - +
486A THR* 3.2 16.4 + - - +
487A VAL* 3.4 22.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
409A GLU 2.9 14.9 + - - +
410A ARG* 3.5 18.2 - - - +
412A ASN* 1.3 74.3 - - - +
414A ASP* 1.3 60.1 + - - +
416A LYS* 3.3 25.6 + - - +
417A ASP* 2.8 68.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A THR* 3.3 31.7 + - + +
380A LYS* 5.0 1.7 - - - +
401A LEU* 3.6 16.7 - - + -
402A ALA* 3.1 35.0 + - - +
410A ARG* 2.7 43.6 + - - +
411A ARG* 3.5 6.7 - - - +
413A GLN* 1.3 71.7 - - - +
415A TYR* 1.3 58.4 + - - +
417A ASP* 3.2 8.4 + - - +
418A ILE* 2.9 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LEU* 4.1 11.3 - - + +
411A ARG 2.9 11.8 + - - +
412A ASN 3.4 7.9 - - - +
414A ASP* 1.3 76.3 - - - +
416A LYS* 1.3 72.4 + - + +
418A ILE* 3.2 10.5 + - - +
419A CYS* 3.0 41.7 + - - -
444A TRP* 3.6 37.7 - + - -
486A THR 5.1 0.9 - - - -
487A VAL* 4.0 24.7 - - + -
488A PHE* 3.4 58.4 - + + -
489A GLU 4.1 3.0 + - - -
491A PHE* 3.7 15.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ASN* 3.0 27.2 + - - +
413A GLN* 3.7 30.7 - - - +
415A TYR* 1.3 87.7 - - + +
417A ASP* 1.3 58.9 + - - +
419A CYS* 3.2 6.0 + - - +
420A SER* 3.0 30.9 + - - -
486A THR* 2.9 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A VAL* 4.1 1.1 - - - +
371A THR* 4.3 15.2 - - + +
375A GLY* 5.4 3.3 - - - +
413A GLN* 2.8 54.7 + - - +
414A ASP* 3.7 7.4 - - - +
415A TYR 3.2 0.2 - - - -
416A LYS* 1.3 70.6 - - - +
418A ILE* 1.3 64.2 + - - +
420A SER* 3.5 7.1 + - - -
421A ARG* 3.0 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A VAL* 4.2 9.9 - - + -
371A THR* 4.0 14.4 - - + -
381A GLY* 3.7 25.8 - - - +
382A GLY* 3.8 8.5 - - - +
397A VAL* 4.5 4.9 - - + -
399A SER* 4.0 9.9 - - - -
401A LEU* 3.9 19.3 - - + -
414A ASP 2.9 21.4 + - - +
415A TYR 3.2 3.8 + - - +
417A ASP* 1.3 75.2 - - - +
419A CYS* 1.3 62.2 + - - +
422A MET* 3.1 57.2 + - + +
436A ILE* 4.0 4.9 - - + -
444A TRP* 4.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A TYR* 3.0 54.0 + - + +
416A LYS* 3.6 9.9 - - - +
418A ILE* 1.3 78.7 - - - +
420A SER* 1.3 61.8 + - - +
422A MET* 4.2 9.9 + - - +
435A THR* 4.7 11.8 - - - +
436A ILE* 4.3 14.7 + - + +
444A TRP* 3.9 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LYS 3.0 16.5 + - - -
417A ASP* 3.5 12.3 + - - -
419A CYS* 1.3 77.2 - - - +
421A ARG* 1.3 69.1 + - - +
422A MET 3.6 2.3 - - - +
423A GLN* 4.7 10.0 + - - +
435A THR* 5.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A VAL* 3.4 30.0 - - + +
370A GLY 2.9 32.7 + - - +
371A THR* 4.3 5.1 - - - +
375A GLY 3.4 15.0 + - - -
376A ARG* 4.9 13.1 + - - +
417A ASP* 3.0 34.2 + - - +
420A SER* 1.3 82.0 - - - +
422A MET* 1.3 64.4 + - - +
423A GLN* 3.2 13.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
367A GLU* 3.6 38.1 - - - +
368A THR 4.0 0.7 - - - -
369A VAL* 3.7 14.0 - - + +
382A GLY 3.9 20.0 - - - +
383A VAL 4.1 4.0 - - - +
384A ALA* 3.9 21.3 - - + -
397A VAL* 5.1 0.9 - - + -
418A ILE* 3.1 42.8 + - + +
419A CYS 4.2 4.6 - - - +
420A SER 3.6 0.9 - - - +
421A ARG* 1.3 74.0 - - - +
423A GLN* 1.3 62.7 + - - +
424A PHE* 3.8 18.4 - - + -
435A THR* 3.8 22.0 - - - +
436A ILE* 3.7 19.5 + - + -
----------------------------------------------------------
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