Contacts of the helix formed by residues 403 - 411 (chain A) in PDB entry 3PEI
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 HIS 403 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A PRO* 3.1 21.9 + - + +
402A LEU* 1.3 67.4 - - - +
404A LYS* 1.3 66.7 + - - +
405A PRO* 3.4 30.6 - - + +
406A TYR* 2.9 59.1 + + + +
429A ILE* 4.1 5.8 - - + +
433A LEU* 3.2 12.0 - - - +
493A EDO 5.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LEU* 3.2 14.9 + - + +
403A HIS* 1.3 70.5 - - - +
405A PRO* 1.3 71.6 - - + +
406A TYR 2.9 1.4 + - - -
407A LEU* 2.9 36.8 + - + +
408A LYS* 5.1 0.7 + - - +
433A LEU* 4.2 11.7 - - + -
440A GLU* 5.9 3.4 - - - -
506A EDO 4.0 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A HIS* 3.3 36.3 - - + +
404A LYS* 1.3 93.6 - - + +
406A TYR* 1.3 57.6 + - - +
407A LEU 3.1 0.2 - - - -
408A LYS* 2.8 31.1 + - + +
493A EDO 3.1 19.1 - - - -
506A EDO 3.8 30.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A HIS* 2.9 37.5 + + + +
405A PRO* 1.3 73.5 - - - +
407A LEU* 1.3 61.0 + - - +
408A LYS 3.0 1.6 - - - -
409A LYS* 2.8 47.7 + - + +
410A ILE* 4.2 1.7 + - - +
426A ALA* 3.6 25.4 - - + +
429A ILE* 3.7 29.6 - - + -
430A VAL* 4.4 7.7 - - + +
433A LEU* 3.5 12.1 - - + -
493A EDO 3.5 32.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LYS* 2.9 38.9 + - + +
406A TYR* 1.3 77.5 - - - +
408A LYS* 1.3 63.9 + - + +
410A ILE* 3.0 20.0 + - + +
411A GLU* 4.8 0.7 - - - -
417A MSE 4.5 12.3 - - + -
433A LEU* 3.6 42.8 - - + +
434A PHE 4.7 0.2 - - - +
436A SER* 5.3 1.6 - - - +
437A LYS* 4.3 27.8 - - + +
509A FMT 3.3 31.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LYS 5.1 1.0 + - - +
405A PRO* 2.8 26.5 + - + +
406A TYR 3.0 1.6 - - - -
407A LEU* 1.3 80.3 - - - +
409A LYS* 1.3 57.6 + - - +
410A ILE 3.0 4.7 + - - -
411A GLU* 3.2 42.7 + - - +
493A EDO 3.9 18.2 - - - +
506A EDO 2.9 44.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TYR* 2.8 41.9 + - + +
408A LYS* 1.3 77.0 - - - +
410A ILE* 1.3 57.7 + - - +
411A GLU 3.6 2.1 - - - +
418A ASP* 5.2 0.3 - - - +
420A CYS 4.2 0.9 - - - +
421A GLY* 3.5 25.6 - - - -
422A ARG* 4.4 9.7 + - - +
423A ASP* 4.4 7.7 + - - -
425A SER* 3.4 31.2 + - - +
426A ALA* 4.6 3.6 - - + -
430A VAL* 3.7 28.7 - - + -
493A EDO 3.7 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TYR 5.1 0.4 - - - +
407A LEU* 3.0 19.7 + - + +
408A LYS 3.0 1.0 - - - -
409A LYS* 1.3 79.6 - - - +
411A GLU* 1.3 60.9 + - - +
417A MSE 3.4 28.0 - - + -
418A ASP* 2.6 66.9 + - + +
419A ASN 3.7 16.4 - - - +
420A CYS 3.7 12.6 - - - +
430A VAL* 4.0 19.7 - - + +
433A LEU* 6.2 0.2 - - + -
434A PHE* 3.8 25.4 - - + +
509A FMT 3.9 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A LEU* 3.6 0.8 + - - +
408A LYS* 3.2 45.6 + - - +
409A LYS 3.6 2.1 - - - +
410A ILE* 1.3 83.3 - - - +
412A SER* 1.3 62.8 + - - +
416A ASP 5.2 1.6 - - - +
417A MSE 5.0 0.9 - - - +
418A ASP* 3.8 5.0 - - - +
422A ARG* 3.8 17.1 + - - -
509A FMT 3.3 22.8 - - - +
----------------------------------------------------------
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