Contacts of the strand formed by residues 535 - 540 (chain A) in PDB entry 3F6K
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 TYR 535 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A SER 5.9 0.4 - - - -
508A SER 3.5 26.0 - - - -
509A ARG 4.4 2.2 - - - -
510A PRO* 3.5 34.0 - - + +
533A PRO 6.0 0.2 - - - -
534A ILE* 1.3 68.8 - - - +
536A PHE* 1.3 62.5 + - - +
554A GLY* 3.0 5.9 - - - -
555A PHE* 2.8 83.0 + + + +
557A GLU* 3.8 36.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A TYR* 3.2 49.7 + + + -
504A ILE* 3.9 24.7 - - + -
505A GLU 4.8 3.4 - - - +
509A ARG 5.7 0.4 + - - -
511A ILE* 3.8 21.5 - - + +
534A ILE* 3.3 6.7 + - + -
535A TYR* 1.3 71.5 - - - +
537A THR* 1.3 59.8 + - - +
538A GLY 3.4 39.9 - - - -
539A LEU* 3.7 17.3 - - + -
552A ILE* 3.5 27.8 - - + -
553A TRP 3.5 10.1 - - - -
554A GLY* 4.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A TYR* 4.5 12.8 + - - -
535A TYR 3.6 1.5 + - - +
536A PHE* 1.3 81.3 - - - +
538A GLY* 1.3 55.4 + - - +
553A TRP* 2.8 35.5 + - - +
554A GLY* 3.4 2.8 - - - -
555A PHE* 3.9 32.8 - - + -
564A TRP* 3.9 20.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A TYR* 5.2 4.3 - - - -
536A PHE* 3.4 19.8 - - - -
537A THR* 1.3 80.5 + - - +
539A LEU* 1.3 58.4 - - - -
553A TRP* 2.7 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A MET* 4.4 8.0 - - + +
491A TYR* 3.9 26.7 - - + +
492A TYR* 3.9 13.9 - - - +
493A THR* 3.3 27.6 - - - +
502A VAL* 5.1 3.8 - - + +
504A ILE* 4.0 20.6 - - + -
514A ILE* 5.1 2.5 - - + -
536A PHE* 3.7 13.7 - - + -
538A GLY* 1.3 72.1 - - - -
540A ALA* 1.3 59.8 + - - +
550A ILE* 3.9 19.7 - - + -
551A SER 3.2 11.0 - - - +
552A ILE* 4.2 11.2 - - + -
553A TRP* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 3.6 30.5 - - + -
83A TRP* 4.3 16.4 - - + +
91A ILE* 5.9 1.3 - - + -
538A GLY 4.2 0.6 - - - -
539A LEU* 1.3 73.8 - - - +
541A SER* 1.3 60.7 + - - +
550A ILE* 3.4 2.1 - - - +
551A SER* 2.8 46.5 + - - -
553A TRP* 4.3 10.6 - - + +
----------------------------------------------------------
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