Contacts of the helix formed by residues 542 - 550 (chain B) in PDB entry 2VF8
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 GLN 542 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B ARG* 3.9 14.0 + - - +
511B ASN* 3.6 13.7 - - - +
537B SER* 2.9 8.9 + - - +
538B THR* 3.1 30.8 - - - +
541B SER* 1.3 78.8 - - - +
543B ALA* 1.3 67.6 + - - +
544B LEU 3.4 0.9 - - - -
545B VAL 3.1 10.2 + - - -
546B ASP* 2.6 25.8 + - - +
569B HIS* 3.1 37.0 + - + +
570B THR* 3.6 21.8 - - - +
1844B ADP 3.8 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B LEU* 4.3 8.1 - - + -
508B VAL* 3.7 30.3 - - + -
510B ARG* 3.7 21.3 + - - +
538B THR 2.5 21.9 + - - +
539B LEU* 3.5 8.7 - - - +
542B GLN* 1.3 75.6 - - - +
544B LEU* 1.3 63.7 + - - +
546B ASP* 3.4 2.3 + - - +
547B ALA* 3.1 22.5 + - - +
574B ALA* 5.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B LEU* 3.9 24.0 - - + -
505B LEU* 3.8 23.8 - - + +
520B PHE* 4.3 17.3 - - + -
539B LEU 3.2 12.8 + - - +
540B VAL* 3.6 11.9 + - + +
542B GLN 3.2 0.6 + - - -
543B ALA* 1.3 78.8 - - - +
545B VAL* 1.3 58.2 + - - +
547B ALA* 3.4 5.0 - - + +
548B LEU* 3.0 51.9 + - + +
576B LEU* 6.5 0.7 - - + -
754B VAL* 5.7 0.9 - - + -
756B VAL* 3.9 28.3 - - + -
787B ILE* 4.7 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B VAL 2.9 21.3 - - - +
541B SER* 3.0 25.6 - - - +
542B GLN 3.1 1.4 + - - -
544B LEU* 1.3 74.0 - - - +
546B ASP* 1.3 57.0 + - - +
548B LEU* 3.0 1.4 + - - -
549B ALA* 2.6 40.6 + - + +
556B VAL* 5.6 3.1 - - + -
586B LEU* 3.3 27.5 - - + +
588B ARG* 4.4 26.5 - - + +
756B VAL* 4.2 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B ARG* 3.8 20.3 + - - +
541B SER 4.6 0.5 - - - +
542B GLN* 2.6 34.2 + - - +
543B ALA 4.0 2.2 - - - +
545B VAL* 1.3 76.4 - - - +
547B ALA* 1.3 56.3 + - - +
549B ALA* 4.1 7.4 - - - -
550B ALA* 2.8 38.5 + - + +
573B SER* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B LEU* 4.8 12.1 - - + -
543B ALA 3.1 19.2 + - - +
544B LEU* 3.4 11.0 - - + +
546B ASP* 1.3 77.7 - - - +
548B LEU* 1.3 60.6 + - + +
550B ALA* 4.9 1.9 - - - +
551B HIS* 3.5 20.2 + - - +
574B ALA* 4.3 17.9 - - + +
576B LEU* 3.6 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B LEU* 4.2 18.6 - - + -
544B LEU* 3.0 47.5 + - + +
545B VAL 3.7 2.7 - - - +
547B ALA* 1.3 77.5 - - + +
549B ALA* 1.3 66.0 + - - +
550B ALA 3.4 0.2 - - - -
551B HIS* 3.3 5.1 + - + +
552B PHE* 3.1 30.8 + - + -
576B LEU* 3.6 26.7 - - + -
583B ILE* 4.3 13.0 - - + -
586B LEU* 3.8 23.6 - - + -
754B VAL* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B VAL* 2.6 24.3 + - + +
546B ASP* 3.9 7.9 - - - +
548B LEU* 1.3 70.1 - - - +
550B ALA* 1.3 54.1 + - - +
552B PHE* 2.5 37.2 + - - +
553B GLY 4.3 0.2 - - - +
554B GLN 3.3 20.4 - - - +
555B PRO* 4.5 5.5 - - + +
556B VAL* 4.2 17.0 - - + +
586B LEU* 3.9 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ASP 2.8 21.5 + - - +
547B ALA* 4.9 2.7 - - - +
549B ALA* 1.3 73.2 - - - +
551B HIS* 1.3 60.8 + - - +
552B PHE 3.1 8.4 - - - +
555B PRO* 6.4 1.1 - - - -
----------------------------------------------------------
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