Contacts of the strand formed by residues 516 - 521 (chain A) in PDB entry 4BL8
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 HIS 516 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A VAL 3.9 5.8 - - - +
502A SER* 3.5 0.4 - - - -
503A TRP* 3.1 20.9 + - - -
504A HIS* 3.3 45.1 + + - -
507A LEU* 3.6 3.8 - - - +
514A ILE 3.7 0.4 - - - -
515A GLN* 1.3 87.6 + - - +
517A MET* 1.3 75.2 + - - +
542A GLY* 3.3 5.7 - - - -
543A VAL* 3.1 34.6 + - + -
545A THR* 3.3 50.6 - - + +
548A LEU* 3.0 32.2 - - + +
549A HIS* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 4.3 11.9 - - + -
484A LEU* 4.0 19.5 - - + -
500A HIS* 3.6 2.9 - - - +
501A VAL* 2.9 49.8 + - + +
503A TRP* 3.4 48.9 - - + -
507A LEU* 3.8 16.4 - - + -
516A HIS* 1.3 91.0 - - - +
518A LEU* 1.3 69.1 + - - +
519A LEU* 5.4 2.9 - - + -
540A ILE* 3.4 32.3 - - + -
541A VAL 3.4 5.8 - - - +
543A VAL* 3.7 1.5 - - - +
548A LEU* 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A GLY 5.2 3.6 - - - +
499A ASP 3.6 5.6 - - - +
500A HIS* 3.4 28.9 - - + -
517A MET* 1.3 76.9 - - - +
519A LEU* 1.3 66.7 + - - +
539A GLN 3.7 0.2 - - - +
540A ILE* 3.7 0.9 - - - -
541A VAL* 2.9 36.3 + - + +
543A VAL* 3.9 25.4 - - + -
547A GLU 5.2 1.3 - - - +
548A LEU* 4.6 7.4 - - + -
551A ALA* 3.7 17.7 - - + -
556A GLY* 4.7 2.5 - - - +
559A ILE* 3.9 32.1 - - + -
560A LEU* 4.0 24.2 - - + -
563A LEU* 4.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 4.8 7.0 - - + -
484A LEU* 4.5 9.9 - - + -
495A PHE* 3.4 49.1 - - + -
496A CYS 4.0 9.6 - - - +
497A SER* 4.4 0.4 - - - -
498A GLY* 2.8 26.1 + - - -
499A ASP* 2.9 21.5 + - + +
501A VAL* 4.6 10.5 - - + -
517A MET* 5.4 3.1 - - + -
518A LEU* 1.3 81.3 - - - +
520A THR* 1.3 64.3 + - - +
538A LEU* 4.1 13.9 - - + -
539A GLN 3.5 11.9 - - - +
540A ILE* 3.9 22.7 - - + -
560A LEU* 3.5 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A SER* 3.4 12.8 + - - -
519A LEU* 1.3 76.4 - - - +
521A GLU* 1.3 68.4 + - - +
523A PRO* 6.1 0.4 - - + -
538A LEU* 4.1 6.2 - - - +
539A GLN* 2.7 37.5 + - + +
541A VAL* 3.7 19.7 - - + -
557A GLN* 5.0 1.9 + - - -
560A LEU* 3.7 16.1 - - + +
564A ARG* 3.4 20.8 + - - -
574A LEU* 3.5 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A SER* 3.3 26.1 + - - -
520A THR* 1.3 81.8 + - - +
522A ASP* 1.3 68.6 + - - +
523A PRO* 3.2 6.9 - - - +
536A THR* 6.5 1.6 - - - -
537A PHE 3.7 9.0 - - - +
538A LEU* 4.7 4.5 - - + -
557A GLN* 5.6 0.2 + - - -
564A ARG* 5.2 2.9 + - - -
574A LEU* 5.8 0.5 - - - +
----------------------------------------------------------
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