Contacts of the strand formed by residues 562 - 569 (chain A) in PDB entry 5FS9
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 LYS 562 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A PHE* 3.3 7.3 - - - +
509A ALA* 2.9 37.7 + - - +
510A LYS 3.4 20.2 - - - +
511A ALA* 4.2 2.9 - - + -
512A THR* 4.7 7.1 - - - +
515A ASP* 3.2 35.4 + - - +
561A GLY* 1.3 79.1 - - - +
563A GLY* 1.3 60.5 + - - +
579A TRP* 3.2 26.0 - - - +
580A ASN* 3.7 8.5 - - + +
581A ILE* 4.1 9.4 - - + +
608A PHE 5.0 1.6 + - - -
609A ASN* 3.5 32.5 + - - +
610A ILE* 3.7 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A VAL 3.2 11.4 - - - -
508A PHE* 3.7 11.2 - - - -
562A LYS* 1.3 78.3 - - - +
564A VAL* 1.3 62.5 + - - -
565A ILE* 5.5 0.6 - - - +
577A VAL 4.1 0.2 - - - +
578A LEU* 3.6 1.0 - - - -
579A TRP* 2.9 37.0 + - - +
581A ILE* 3.5 16.4 - - - +
610A ILE* 4.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A VAL 4.0 0.9 - - - +
506A GLY* 3.3 2.1 - - - -
507A VAL* 2.8 42.7 + - + +
508A PHE* 4.8 0.5 - - - -
563A GLY* 1.3 77.1 - - - +
565A ILE* 1.3 66.7 + - - +
566A PHE* 3.8 37.2 - - + -
576A ILE* 3.9 12.8 - - + -
577A VAL 3.5 4.5 - - - +
578A LEU* 3.7 25.6 - - + -
581A ILE* 4.6 1.1 - - + -
605A ALA* 3.9 22.2 - - + -
608A PHE* 4.1 10.8 - - + -
610A ILE* 4.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PRO* 3.6 28.0 - - + -
347A TYR* 4.4 3.4 - - - +
348A LEU* 3.5 31.9 - - + -
504A THR* 3.9 23.3 - - - -
505A VAL 3.6 5.4 - - - +
506A GLY* 4.3 2.7 - - - -
508A PHE* 4.1 17.9 - - + -
563A GLY 5.5 0.9 - - - +
564A VAL* 1.3 79.5 - - - +
566A PHE* 1.3 63.1 + - - +
567A TYR* 3.6 20.9 - - + -
576A ILE* 3.3 6.9 - - - +
577A VAL* 2.8 51.0 + - + +
579A TRP* 5.6 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A PRO 3.8 0.2 - - - +
504A THR* 3.1 8.3 - - - -
505A VAL* 2.9 41.9 + - + +
507A VAL* 4.3 6.1 - - + -
564A VAL* 3.8 37.0 - - + -
565A ILE* 1.3 74.4 - - - +
567A TYR* 1.3 60.8 + - - +
568A LEU* 4.0 3.9 + - + +
573A VAL* 4.0 24.9 - - + -
575A GLY 3.7 2.5 - - - -
576A ILE* 4.0 20.6 - - + -
591A ILE* 4.7 0.4 - - + -
601A LEU* 3.7 44.0 - - + -
604A VAL* 3.6 35.7 - - + -
605A ALA* 4.0 5.4 - - - -
608A PHE* 4.2 8.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ILE 2.6 28.3 + - - -
344A LEU* 3.8 0.9 - - - +
345A PRO* 3.7 14.8 - - + +
497A LEU 3.5 18.4 - - - +
498A VAL* 3.6 11.3 - - + +
499A ASP 3.3 39.5 - - - -
500A SER* 4.3 0.9 - - - -
502A LEU* 4.1 8.1 - - + -
503A PRO 3.5 2.7 - - - -
504A THR* 3.5 18.6 - - + -
565A ILE* 3.6 24.5 - - + +
566A PHE* 1.3 75.2 - - - +
568A LEU* 1.3 60.2 + - - +
573A VAL* 3.6 2.3 - - - -
574A VAL* 2.9 28.1 + - - +
575A GLY 2.8 25.9 + - - +
577A VAL* 3.6 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LEU* 3.8 7.7 - - - +
503A PRO* 3.0 52.4 + - + +
505A VAL* 3.8 28.7 - - + -
566A PHE* 4.3 6.1 - - + +
567A TYR* 1.3 75.5 - - - +
569A ARG* 1.3 61.9 + - - +
571A LYS* 4.4 27.4 - - + +
572A VAL 3.3 10.5 - - - +
573A VAL* 3.8 29.4 - - + -
574A VAL* 4.1 2.2 - - - -
601A LEU* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A LYS 4.7 3.6 + - - -
447A LEU* 3.3 30.7 + - - +
497A LEU* 3.3 28.4 - - - +
502A LEU* 4.8 12.6 - - + -
503A PRO* 5.8 0.4 - - - -
568A LEU* 1.3 75.2 - - - +
570A ASP* 1.3 85.6 + - - +
572A VAL* 2.9 23.6 + - - +
574A VAL* 3.8 25.4 - - + +
----------------------------------------------------------
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