Contacts of the strand formed by residues 562 - 567 (chain F) in PDB entry 2AS5
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 PHE 562 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F MG 2.5 28.8 - - - -
510F ALA* 3.6 39.0 - - + -
513F ILE* 3.6 23.1 - - + -
514F ARG* 3.8 17.5 - - + -
517F ILE* 4.4 4.9 - - + -
555F ASN 3.8 17.9 - - - -
556F LEU* 3.3 38.7 - - + +
559F HIS* 3.1 13.7 + + + +
560F LYS 2.9 2.8 - - - +
561F CYS* 1.3 94.1 - - - +
563F VAL* 1.3 62.2 + - - +
573F TRP* 3.7 3.5 - - - -
574F THR 3.4 9.9 - - - +
575F VAL* 4.1 17.7 - - + -
580F TYR* 5.0 1.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 563 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560F LYS 3.5 19.7 - - - +
561F CYS 4.8 2.5 - - - +
562F PHE* 1.3 74.3 - - - +
564F ARG* 1.3 63.0 + - - +
565F VAL* 3.5 7.6 + - + -
573F TRP* 3.7 3.1 - - - -
574F THR* 2.9 66.0 + - - +
575F VAL 5.2 4.3 - - - -
576F ASP* 5.0 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 564 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4012A T 5.0 0.6 + - - -
4013A G 2.7 49.5 + - - -
4014A T 4.6 7.5 + - - +
563F VAL* 1.3 71.0 - - - +
565F VAL* 1.3 62.7 + - - +
566F GLU* 2.8 35.9 + - - +
570F GLY 4.2 3.0 + - - -
571F ALA* 3.0 29.5 - - + +
572F VAL 3.6 7.2 - - - +
573F TRP* 3.6 30.7 - - + +
665N ARG* 4.2 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 565 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524F GLN* 5.0 3.1 - - - +
563F VAL* 3.5 7.2 + - + +
564F ARG* 1.3 71.4 - - - +
566F GLU* 1.3 70.5 + - - +
567F ASN* 3.7 4.4 + - + +
571F ALA* 4.5 0.7 - - - -
572F VAL* 2.9 47.3 + - + +
574F THR* 3.9 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 566 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564F ARG* 2.8 34.2 + - - +
565F VAL* 1.3 82.7 - - - +
567F ASN* 1.3 62.0 + - - +
570F GLY 3.3 19.7 - - - +
571F ALA* 4.2 3.3 - - - +
664N LYS* 2.8 30.1 + - - +
665N ARG* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 567 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565F VAL* 4.3 5.7 - - + +
566F GLU* 1.3 79.6 - - - +
568F VAL* 1.3 70.5 + - + +
569F LYS* 2.9 33.0 - - - +
570F GLY* 3.2 17.3 + - - +
571F ALA* 3.2 27.5 + - - -
572F VAL* 4.3 11.5 - - + +
538N LYS* 4.7 2.1 + - - -
665N ARG* 5.4 1.2 + - - -
667N ARG* 6.2 0.7 - - - -
----------------------------------------------------------
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