Contacts of the helix formed by residues 429 - 443 (chain A) in PDB entry 4MVY
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 PRO 429 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE 3.8 0.3 - - - +
428A VAL* 1.3 100.1 - - + +
430A GLU* 1.3 67.3 + - - +
431A PHE* 3.3 13.9 - - + -
432A ARG* 3.1 35.7 + - + +
433A ARG 3.3 8.1 + - - -
544A ALA 3.3 20.4 - - - +
587A PHE* 4.3 6.1 - - + -
588A SER* 3.6 31.2 - - - +
637B GLU* 6.0 1.1 - - - +
681B ASP* 5.1 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A PRO 3.9 6.4 - - - +
427A ILE 4.5 2.5 + - - +
428A VAL* 4.3 0.2 - - - +
429A PRO* 1.3 74.8 - - - +
431A PHE* 1.3 62.8 + - - +
433A ARG* 2.9 48.4 + - - +
434A ARG* 3.0 46.4 + - - +
637B GLU* 5.1 4.5 + - - +
681B ASP* 3.4 33.1 + - - +
682B MET* 3.3 34.4 - - + +
687B LEU* 5.1 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A PRO* 3.3 17.0 - - + -
430A GLU* 1.3 78.2 - - - +
432A ARG* 1.3 94.2 + - + +
434A ARG* 3.4 31.4 + - - +
435A GLU* 3.0 50.7 + - - +
438A ARG* 4.7 0.9 + - - -
588A SER* 3.8 35.7 - - - -
681B ASP* 4.9 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 4.0 7.6 - - + -
428A VAL 4.9 0.2 - - - +
429A PRO* 3.1 26.3 + - + +
431A PHE* 1.3 105.5 - - + +
433A ARG* 1.3 64.1 - - - +
435A GLU* 3.2 14.9 + - - +
436A VAL* 3.0 27.5 + - - +
517A LYS* 3.3 42.3 - - - +
520A LEU* 3.8 17.8 - - + +
544A ALA* 2.7 49.5 + - + -
545A HIS 3.9 2.6 + - - -
546A GLY* 4.5 3.4 - - - -
587A PHE 2.7 22.0 + - - -
588A SER 4.2 6.1 + - - -
590A ASP* 5.3 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A TYR* 3.4 25.0 + - + +
421A HIS* 4.5 2.0 - - - +
423A ASN 4.4 1.0 + - - -
424A PRO* 3.5 44.8 + - - +
426A CYS* 5.2 0.7 - - - -
427A ILE* 3.6 49.8 - - + +
429A PRO 3.3 3.2 + - - -
430A GLU* 2.9 43.6 + - - +
432A ARG* 1.3 77.7 - - - +
434A ARG* 1.3 65.3 + - - +
436A VAL* 3.2 4.0 + - - +
437A ILE* 3.0 45.7 + - + +
687B LEU* 5.7 3.2 - - - +
691B ASP* 4.1 16.0 + - - -
694B ARG* 5.0 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A GLU* 3.0 37.1 + - - +
431A PHE* 3.6 31.5 - - - +
432A ARG 3.3 0.2 - - - -
433A ARG* 1.3 79.4 - - - +
435A GLU* 1.3 63.2 + - - +
437A ILE* 3.3 9.2 + - + +
438A ARG* 3.0 49.5 + - + +
680B THR 5.2 1.8 + - - -
681B ASP 3.0 26.3 + - - -
682B MET 3.9 13.8 + - - -
683B ALA* 3.9 17.2 - - - +
686B LYS* 4.4 25.3 - - - +
687B LEU* 5.1 11.0 - - + -
690B THR* 5.7 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 3.0 41.7 + - - +
432A ARG* 3.4 21.5 + - - +
433A ARG 3.2 0.4 - - - -
434A ARG* 1.3 75.8 - - - +
436A VAL* 1.3 63.0 + - + +
438A ARG* 3.3 26.9 + - - +
439A ALA* 3.1 23.9 + - - +
520A LEU* 4.8 6.0 - - + +
805A DMS 4.1 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A TYR* 3.4 39.5 - - + +
427A ILE* 4.3 7.4 - - + -
432A ARG 3.0 14.1 + - - +
433A ARG 3.2 6.9 + - - +
435A GLU* 1.3 75.9 - - - +
437A ILE* 1.3 63.4 + - - +
439A ALA* 3.2 3.8 + - - +
440A VAL* 3.0 22.0 + - - +
520A LEU* 3.6 30.7 - - + -
524A ALA* 3.9 17.7 - - + -
525A ILE* 4.0 9.2 - - + -
805A DMS 3.8 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 4.1 8.0 - - + +
420A TYR* 3.7 35.4 - - + -
421A HIS* 6.1 0.2 - - - -
433A ARG* 3.0 55.7 + - + +
434A ARG* 3.9 8.3 - - + +
436A VAL* 1.3 75.8 - - + +
438A ARG* 1.3 59.3 + - + +
440A VAL* 3.2 2.1 + - - +
441A GLU* 2.8 53.9 + - + +
690B THR* 5.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE 4.7 1.4 + - - -
434A ARG* 3.0 43.5 + - - +
435A GLU* 3.3 35.8 + - - +
437A ILE* 1.3 77.0 - - + +
439A ALA* 1.3 62.5 + - - +
441A GLU* 3.5 9.6 + - - +
442A LYS* 3.4 26.9 + - - +
686B LYS* 4.7 15.9 - - - +
690B THR* 5.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A GLU 3.1 17.4 + - - +
436A VAL 3.6 4.5 - - - +
438A ARG* 1.3 75.8 - - - +
440A VAL* 1.3 63.6 + - - +
442A LYS* 3.4 22.2 + - - +
443A GLY 3.8 9.2 - - - +
444A LEU* 4.5 3.1 - - - +
525A ILE* 4.7 2.9 - - + -
804A DMS 4.6 21.0 - - + +
805A DMS 4.3 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ARG* 3.2 29.5 + - + +
416A LEU* 4.3 3.6 - - + -
417A LEU* 3.9 21.5 - - + -
420A TYR* 3.6 26.7 - - + +
436A VAL 3.0 16.2 + - - +
437A ILE 3.9 2.5 - - - +
439A ALA* 1.3 73.5 - - - +
441A GLU* 1.3 66.8 + - - +
443A GLY* 3.2 8.3 + - - -
444A LEU* 4.1 26.0 - - + -
525A ILE* 3.6 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ARG* 2.8 40.6 + - - +
417A LEU* 3.8 21.7 - - + +
437A ILE* 2.8 40.2 + - + +
438A ARG* 3.5 10.1 - - - +
440A VAL* 1.3 77.2 - - - +
442A LYS* 1.3 60.4 + - + +
690B THR 5.6 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ARG* 4.7 0.2 - - - -
438A ARG 3.4 14.0 + - - +
439A ALA* 3.5 13.7 - - - +
440A VAL 3.2 1.0 - - - -
441A GLU* 1.3 79.2 - - + +
443A GLY* 1.3 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ARG* 4.0 12.8 - - - -
439A ALA 3.8 6.1 + - - +
440A VAL 3.2 10.5 + - - -
441A GLU 3.2 0.6 - - - -
442A LYS* 1.3 81.6 - - - +
444A LEU* 1.3 70.2 + - - +
445A PRO* 4.3 3.2 - - - +
804A DMS 4.9 3.8 - - - +
----------------------------------------------------------
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