Contacts of the helix formed by residues 412 - 423 (chain A) in PDB entry 4EG8
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 PHE 412 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ASP* 3.4 29.8 - - - -
407A PHE* 3.5 24.0 - + - -
408A ARG 3.2 25.8 - - - -
409A LEU 2.9 9.8 + - - +
411A ALA* 1.3 81.9 - - + +
413A ARG* 1.3 65.0 + - - +
414A GLU 3.5 2.0 - - - -
415A ARG* 3.3 42.4 + - - +
416A LEU* 3.0 32.3 + - + +
529A ALA* 3.7 18.8 - - + -
532A LEU* 3.7 17.9 - - + -
533A SER* 3.6 31.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LEU 3.9 1.8 + - - -
410A SER 3.7 12.9 + - - +
411A ALA 3.5 1.6 - - - -
412A PHE* 1.3 78.3 - - - +
414A GLU* 1.3 82.5 + - + +
416A LEU* 3.3 2.3 + - - +
417A LEU* 3.0 41.9 + - + +
440A VAL* 3.3 30.1 + - + +
441A GLU* 2.6 45.5 + - - -
443A GLY* 3.9 16.9 - - - -
444A LEU* 4.5 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ALA 5.0 2.3 + - - +
412A PHE 3.5 0.2 - - - -
413A ARG* 1.3 97.2 + - + +
415A ARG* 1.3 58.5 + - + +
417A LEU* 3.4 9.9 + - + +
418A GLU* 3.0 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LYS* 5.6 7.9 - - - +
353A ASP* 5.8 0.6 + - - -
411A ALA* 3.6 22.6 + - - +
412A PHE* 3.3 46.8 + - - +
413A ARG 3.3 0.6 - - - -
414A GLU* 1.3 79.6 - - + +
416A LEU* 1.3 57.6 + - - +
418A GLU* 3.4 20.4 + - - +
419A TRP* 3.1 27.2 + - - +
532A LEU* 4.0 35.5 + - + +
533A SER* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LEU* 4.8 0.2 - - + -
412A PHE* 3.0 31.3 + - + +
413A ARG 3.7 3.4 - - - +
415A ARG* 1.3 74.9 - - - +
417A LEU* 1.3 59.5 + - - +
419A TRP* 3.2 8.8 + - + +
420A TYR* 2.9 58.5 + - + +
440A VAL* 4.5 2.7 - - + -
444A LEU* 4.0 25.6 - - + -
525A ILE* 3.8 20.0 - - + +
528A PRO* 3.5 37.9 - - + -
529A ALA* 4.1 7.2 - - + +
532A LEU* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ARG* 3.0 46.9 + - + +
414A GLU* 3.7 8.5 - - + +
415A ARG 3.4 0.2 - - - -
416A LEU* 1.3 74.7 - - - +
418A GLU* 1.3 64.1 + - + +
420A TYR* 3.4 11.3 + - + -
421A HIS* 2.9 36.7 + - + +
437A ILE* 4.1 27.1 - - + +
440A VAL* 4.1 15.7 - - + -
441A GLU* 3.8 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLU* 3.0 35.0 + - - +
415A ARG* 3.6 23.5 - - - +
416A LEU 3.3 0.2 - - - -
417A LEU* 1.3 75.1 - - - +
419A TRP* 1.3 57.3 + - - +
421A HIS* 3.9 3.0 - - - +
422A ALA* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ARG 3.1 15.4 + - - +
416A LEU* 3.2 10.7 + - + +
418A GLU* 1.3 77.2 - - - +
420A TYR* 1.3 97.3 + + - +
422A ALA* 4.7 0.4 - - - -
423A ASN* 3.1 55.7 + - - +
426A CYS* 4.1 24.2 - - + -
427A ILE* 5.0 1.3 - - + -
524A ALA 4.2 2.0 - - - -
528A PRO* 3.9 24.9 - - + -
532A LEU* 5.7 0.9 - - + -
538A LEU* 3.3 40.4 - - + +
539A PRO* 3.4 30.2 + - + -
540A LYS 5.6 0.2 - - - -
542A ILE* 4.4 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 2.9 39.0 + - + +
417A LEU* 3.8 11.7 - - + +
418A GLU 3.3 0.2 - - - -
419A TRP* 1.3 99.5 - + - +
421A HIS* 1.3 62.9 + - - +
423A ASN 3.3 18.9 - - - +
426A CYS* 4.2 6.7 - - - -
427A ILE* 3.7 24.0 - - + -
433A ARG* 3.6 16.5 + - - +
436A VAL* 3.4 15.3 - - + +
437A ILE* 3.7 33.2 - - + -
440A VAL* 3.7 24.4 - - + +
524A ALA 2.6 30.5 + - - -
525A ILE* 3.6 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 2.9 35.7 + - + +
418A GLU* 4.1 3.4 - - - +
420A TYR* 1.3 76.5 - - - +
422A ALA* 1.3 65.3 + - - +
423A ASN 3.1 0.8 + - - -
424A PRO* 3.7 16.5 - - - +
433A ARG* 4.4 3.8 + - - +
437A ILE* 4.0 32.4 - - + +
441A GLU* 4.6 8.4 + - - -
690B THR* 3.8 21.5 + - - +
691B ASP* 3.2 36.7 + - + +
693B GLU* 5.1 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLU* 2.9 20.1 + - + +
419A TRP* 4.7 0.7 - - - -
421A HIS* 1.3 77.3 - - - +
423A ASN* 1.3 75.3 + - - +
424A PRO* 3.5 6.8 - - - +
693B GLU* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A TRP* 3.1 46.0 + - - +
420A TYR 3.3 4.3 - - - +
422A ALA* 1.3 94.6 - - - +
424A PRO* 1.3 58.0 - - - +
425A GLY 3.1 4.9 - - - -
426A CYS* 2.9 42.8 + - + +
540A LYS* 5.7 1.8 + - - +
----------------------------------------------------------
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