Contacts of the strand formed by residues 615 - 621 (chain B) in PDB entry 1FO4
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 615 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ARG* 4.1 8.3 - - + -
614B HIS* 1.3 78.4 - - - +
616B LYS* 1.3 65.7 + - - +
659B THR* 3.2 4.9 - - - -
660B VAL* 2.9 33.6 + - + +
689B TYR* 3.9 15.5 - - + -
690B GLU 3.3 17.3 - - - +
691B ASP* 3.5 16.6 - - - +
692B LEU* 3.8 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B ALA* 1.3 75.6 - - - +
617B ILE* 1.3 62.5 + - - +
618B LYS* 3.4 22.8 + - + +
658B ASP 3.3 9.4 - - - +
659B THR* 3.7 8.3 - - + -
689B TYR* 3.3 7.8 - - - +
690B GLU* 2.8 61.0 + - - +
692B LEU* 3.9 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 617 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B LYS* 1.3 72.8 - - - +
618B LYS* 1.3 63.2 + - - +
619B SER 4.3 6.1 - - - +
620B ILE* 3.8 31.6 - - + -
656B ALA* 4.2 17.5 - - + +
658B ASP* 2.6 28.4 + - - +
659B THR* 4.2 7.4 - - - +
660B VAL* 3.5 33.9 - - + -
667B ILE* 4.0 24.0 - - + -
687B VAL* 4.4 5.4 - - + -
688B THR 3.9 2.9 - - - -
689B TYR* 4.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 618 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B LYS* 4.1 21.7 - - + +
617B ILE* 1.3 75.2 - - - +
619B SER* 1.3 61.4 + - - +
688B THR* 2.8 26.2 + - + +
689B TYR 3.9 9.4 - - - +
690B GLU* 3.5 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 619 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B ILE* 3.6 1.6 - - - +
618B LYS* 1.3 81.7 - - - +
620B ILE* 1.3 75.2 + - - +
621B ASP* 4.4 5.0 + - - +
686B LYS 5.0 0.3 + - - -
687B VAL* 3.5 2.0 - - - +
688B THR* 2.8 50.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 620 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B ILE* 3.8 24.0 - - + -
619B SER* 1.3 84.2 + - - +
621B ASP* 1.3 60.6 + - - +
622B VAL* 4.1 6.9 + - + +
634B PHE* 4.2 30.3 - - + -
636B SER* 5.6 5.4 - - - -
667B ILE* 3.9 23.8 - - + -
685B VAL* 4.3 14.6 - - + -
686B LYS 3.5 4.0 - - - +
687B VAL* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 621 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619B SER* 4.3 5.8 + - - +
620B ILE* 1.3 72.7 - - - +
622B VAL* 1.3 61.1 + - - +
623B SER* 2.7 40.8 + - - -
624B GLU* 4.7 6.9 + - - +
684B VAL 4.3 1.4 - - - +
685B VAL* 3.7 3.8 - - - -
686B LYS* 2.7 61.6 + - + +
----------------------------------------------------------
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