Contacts of the helix formed by residues 438 - 443 (chain B) in PDB entry 4IDT
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 ALA 438 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ALA* 3.7 24.7 - - + +
358B LYS* 4.2 10.8 - - + -
361B ALA* 3.9 11.2 - - + +
436B PHE* 3.6 14.8 - - - -
437B ARG* 1.3 71.6 - - - +
439B GLU* 1.3 57.4 + - - +
440B GLU 3.0 0.2 - - - -
441B LEU* 2.8 27.9 + - - +
442B MET* 2.9 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ARG* 3.4 33.3 + - - +
438B ALA* 1.3 78.5 + - - +
440B GLU* 1.3 62.4 + - - +
441B LEU 2.9 7.0 + - - -
442B MET* 3.6 28.9 - - + +
443B ALA* 3.1 26.8 + - - +
535B PHE 4.0 3.2 - - - +
538B ALA* 3.5 27.6 - - + +
539B VAL* 4.3 11.6 - - - +
540B CYS* 4.3 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B PHE* 4.2 17.2 - - - +
429B LYS* 2.4 36.7 + - - +
431B VAL* 4.5 6.6 - - - +
436B PHE* 4.2 7.3 - - + -
437B ARG* 3.0 25.5 + - + +
439B GLU* 1.3 79.4 - - - +
441B LEU* 1.3 59.9 + - - +
444B CYS* 3.4 17.7 - - - -
467B ILE* 3.2 26.9 - - + +
534B ASP* 3.2 0.7 - - - +
535B PHE* 3.7 20.3 + - - +
536B GLY* 3.1 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU* 3.9 18.2 - - + -
354B THR* 4.7 2.2 - - - +
357B ALA* 3.8 25.4 - - + -
360B TRP* 4.2 2.2 - - + -
436B PHE* 3.9 18.2 - - + -
438B ALA 2.8 7.5 + - - +
440B GLU* 1.3 86.4 - - - +
442B MET* 1.3 59.1 + - - +
443B ALA 3.1 2.4 + - - -
444B CYS* 3.9 2.9 - - - -
445B ALA* 2.8 37.0 + - + +
455B LEU* 3.8 22.4 - - + -
458B ALA* 3.6 24.9 - - + -
467B ILE* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B THR* 3.8 31.9 - - + +
357B ALA* 5.5 0.4 - - + -
358B LYS* 4.5 25.8 - - - -
438B ALA* 2.9 26.7 + - + +
439B GLU* 3.6 39.7 - - + +
441B LEU* 1.3 76.2 - - + +
443B ALA* 1.3 59.1 + - - +
444B CYS 3.6 0.2 + - - -
445B ALA* 4.4 6.0 + - - +
447B LEU* 5.7 1.6 - - - +
511B ILE* 4.4 6.9 - - - +
540B CYS* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B GLU 3.1 18.0 + - - +
442B MET* 1.3 78.4 - - - +
444B CYS* 1.3 57.8 + - - +
447B LEU* 3.0 20.1 - - - +
506B LEU* 3.7 0.2 - - - +
511B ILE* 3.5 28.9 - - + +
535B PHE* 3.3 33.2 - - + -
538B ALA* 3.7 11.0 - - + -
540B CYS* 4.7 5.2 - - - -
----------------------------------------------------------
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