Contacts of the strand formed by residues 563 - 570 (chain F) in PDB entry 2HDX
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 GLU 563 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B TYR* 3.8 6.8 + - - -
557F SER* 2.9 26.7 + - - -
560F ARG* 3.3 29.3 + - + +
561F ARG 3.2 7.9 - - - +
562F GLY* 1.3 83.9 - - - +
564F CYS* 1.3 67.9 + - - +
578F ARG* 2.8 53.9 + - - +
579F LEU 3.2 15.0 - - - +
580F SER* 4.0 13.6 - - - +
581F LEU* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 564 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522F LEU* 4.6 7.4 - - - -
528F PHE* 4.8 1.3 - - - -
554F VAL* 4.2 8.3 - - + -
555F ARG 3.2 14.8 - - - +
556F GLN* 3.9 18.6 - - - -
557F SER 4.0 1.3 - - - +
563F GLU* 1.3 80.8 - - - +
565F VAL* 1.3 65.4 + - - +
578F ARG* 3.7 1.7 - - - +
579F LEU* 2.7 51.8 + - + +
581F LEU* 3.8 25.9 - - + +
597F ILE* 4.6 7.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
554F VAL* 3.3 7.3 - - - +
555F ARG* 2.7 81.8 + - + +
557F SER* 4.7 11.0 - - - -
564F CYS* 1.3 80.8 - - - +
566F LEU* 1.3 63.4 + - - +
567F THR* 3.7 8.4 + - - +
576F HIS* 3.9 16.6 - - + -
577F LEU 3.5 13.5 - - - +
578F ARG* 5.0 3.1 - - + -
579F LEU* 4.1 4.3 - - - -
813L PTR 3.8 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 566 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552F PHE* 4.0 23.1 - - + -
553F LEU 3.8 12.8 - - - +
554F VAL* 3.8 15.0 - - + -
565F VAL* 1.3 73.1 - - - +
567F THR* 1.3 58.1 + - - +
568F PHE* 3.6 20.8 - - + -
576F HIS* 3.6 0.2 - - - -
577F LEU* 2.7 64.5 + - + +
579F LEU* 4.0 14.8 - - + +
600F MET* 4.1 20.2 - - + -
601F LEU* 4.1 8.3 - - + -
604F PHE* 4.6 0.9 - - + -
609F ILE* 4.3 12.1 - - + -
621F LEU* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 567 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537F ALA* 3.8 31.2 - - - +
538F ALA* 4.2 0.7 - - - +
541F VAL* 3.7 13.7 - - + +
552F PHE* 3.1 3.5 - - - +
553F LEU* 3.0 39.5 + - - +
555F ARG* 2.9 28.1 + - - -
565F VAL* 3.7 1.2 + - - +
566F LEU* 1.3 71.8 - - - +
568F PHE* 1.3 64.1 + - - +
574F ALA* 4.9 1.3 - - + -
575F LYS 3.2 5.6 - - - +
576F HIS* 3.0 31.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 568 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541F VAL* 3.8 6.5 - - - -
550F GLY* 5.3 1.6 - - - -
551F VAL 3.1 11.9 - - - +
552F PHE* 3.7 11.4 - - + +
566F LEU* 3.6 29.6 - - + -
567F THR* 1.3 76.9 - - - +
569F ASN* 1.3 71.7 + - - +
570F PHE* 4.3 4.9 - - + -
573F LYS 3.6 0.5 - - - +
574F ALA* 3.6 1.4 - - - -
575F LYS* 2.8 63.9 + - + -
577F LEU* 4.1 16.8 - - + -
609F ILE* 4.0 28.5 - - + -
611F LEU* 4.1 27.8 - - + -
619F VAL* 4.3 10.3 - - + -
621F LEU* 4.4 5.4 - - + -
814L GLU* 4.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 569 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541F VAL* 2.9 32.4 + - - +
542F LEU* 3.7 16.9 - - - +
545F GLY 3.1 23.6 + - - -
548F SER* 3.4 23.4 - - - +
549F HIS* 3.3 8.8 + - - -
550F GLY* 2.9 26.5 + - - -
551F VAL 2.7 12.5 + - - +
568F PHE* 1.3 75.2 - - - +
570F PHE* 1.3 59.1 + - - +
572F GLY* 2.9 24.3 + - - -
573F LYS 3.6 3.8 - - - -
619F VAL* 4.2 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 570 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549F HIS* 3.8 8.7 - + - -
568F PHE* 3.6 3.1 + + + -
569F ASN* 1.3 71.9 + - - +
571F GLN* 1.3 80.9 + - + +
572F GLY 3.0 0.2 - - - -
573F LYS* 2.7 29.9 + - + +
575F LYS* 3.5 37.9 - - + -
611F LEU* 4.0 15.9 - - + -
613F SER 4.5 16.6 - - - -
618F ASP* 4.1 22.4 - - - -
619F VAL* 3.6 40.2 - - + -
----------------------------------------------------------
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