Contacts of the helix formed by residues 566 - 572 (chain B) in PDB entry 1IVV
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 GLY 566 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B PRO 3.3 14.1 - - - -
554B THR* 4.0 0.7 - - - -
555B GLY* 3.9 14.4 - - - +
565B ALA* 1.3 77.2 - - - +
567B LEU* 1.3 59.4 + - - -
569B SER* 2.8 23.4 + - - -
570B TYR* 3.1 36.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 567 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B SER* 5.2 0.2 - - - +
536B PHE* 3.7 14.1 - - + -
542B TRP* 3.7 41.1 - - + -
544B THR* 3.7 17.9 - - + -
553B PRO* 3.0 40.1 + - + +
566B GLY* 1.3 69.0 - - - -
568B PRO* 1.3 69.3 - - + +
569B SER 3.0 0.3 + - - -
570B TYR* 3.1 9.2 + - + +
571B ILE* 2.9 30.5 + - + +
585B TRP* 3.7 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 568 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ALA* 3.6 31.6 - - + -
536B PHE 5.2 0.4 - - - +
542B TRP* 4.5 13.9 - - + -
553B PRO 4.6 3.4 - - - +
564B GLY 6.4 0.2 - - - +
565B ALA 3.9 8.7 - - - +
566B GLY* 3.6 3.6 - - - -
567B LEU* 1.3 93.0 - - + +
569B SER* 1.3 59.6 + - - +
571B ILE* 4.1 7.8 - - + +
572B ALA* 3.7 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 569 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B GLY 3.8 23.1 + - - -
565B ALA* 3.9 8.5 + - - -
566B GLY 2.8 11.3 + - - -
568B PRO* 1.3 79.3 - - - +
570B TYR* 1.3 75.0 + - - +
572B ALA* 3.5 16.5 + - - +
573B GLN* 4.2 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 570 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B GLU* 3.6 4.7 - - - +
544B THR* 4.3 7.9 - - + -
549B ASP 4.1 6.1 + - - -
550B GLU* 3.6 61.4 - - + +
551B ARG 4.2 1.6 + - - -
552B TYR 3.2 28.1 + - - -
555B GLY* 3.9 13.5 - - - -
556B ASP 5.1 0.3 + - - -
566B GLY* 3.1 27.5 + - - -
567B LEU* 3.1 19.3 + - + +
569B SER* 1.3 81.8 - - - +
571B ILE* 1.3 61.7 + - - +
573B GLN* 3.0 33.9 + - - +
575B ARG* 3.7 4.7 + - - +
585B TRP* 4.4 9.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 571 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B GLU* 3.6 36.4 - - + +
481B SER* 4.4 7.4 + - - +
484B VAL* 4.0 18.2 - - + -
542B TRP* 3.7 26.0 - - + -
543B VAL 3.8 22.4 - - - +
544B THR* 4.0 13.2 - - + -
567B LEU 2.9 20.2 + - - +
568B PRO* 4.1 7.6 - - + +
570B TYR* 1.3 77.5 - - - +
572B ALA* 1.3 58.2 + - - +
574B ASP* 2.8 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 572 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B PRO 3.7 10.5 + - - +
569B SER* 3.5 13.4 + - - +
570B TYR 3.2 1.0 + - - -
571B ILE* 1.3 80.9 - - - +
573B GLN* 1.3 59.9 + - + +
574B ASP* 3.0 7.6 + - - +
----------------------------------------------------------
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