Contacts of the strand formed by residues 549 - 556 (chain A) in PDB entry 4BI2
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 ILE 549 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A LEU* 3.8 13.7 - - + -
541A GLN* 3.7 39.7 - - + +
542A VAL 3.2 13.5 - - - +
543A LEU* 3.8 8.0 - - + +
548A GLN* 1.3 72.9 - - - +
550A TYR* 1.3 69.0 + - - +
603A GLU* 5.6 0.2 - - - -
604A CYS* 4.5 15.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A TYR* 3.8 21.8 - + - -
541A GLN* 3.4 9.4 - - - +
542A VAL* 2.8 45.4 + - + -
544A ASN* 3.5 25.7 + - - -
548A GLN* 3.4 46.4 + - + -
549A ILE* 1.3 76.0 - - - +
551A ALA* 1.3 59.0 + - - +
589A TYR* 3.6 39.7 - + + -
601A VAL* 4.1 15.5 - - + -
602A MET 3.7 14.6 - - - +
603A GLU* 4.9 1.1 - - - -
604A CYS* 3.8 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A ILE* 4.3 3.8 - - + -
539A VAL* 4.6 2.7 - - + -
540A PHE 3.2 8.7 - - - +
550A TYR* 1.3 72.4 - - - +
552A ILE* 1.3 63.3 + - - +
600A MET 3.3 2.1 - - - +
601A VAL 3.9 0.3 - - - -
602A MET* 2.9 36.3 + - - +
603A GLU 3.7 10.1 - - - +
604A CYS* 4.0 8.5 - - + +
1797A ZO8 3.7 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A MET* 3.9 25.8 - - + -
520A VAL* 3.8 20.0 - - + -
525A TYR* 3.4 42.6 - - + -
538A LYS 3.7 1.2 - - - +
539A VAL* 3.4 3.5 - - - -
540A PHE* 2.8 40.3 + - + -
542A VAL* 3.6 20.6 - - + +
550A TYR 4.1 0.4 - - - -
551A ALA* 1.3 73.8 - - - +
553A LYS* 1.3 73.3 + - - +
554A TYR 4.7 0.2 - - - +
599A TYR* 4.4 5.2 - - + -
600A MET 3.1 16.4 - - - +
601A VAL* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A SER* 4.5 5.6 - - - -
538A LYS 3.7 1.8 - - - -
539A VAL* 4.1 14.1 - - + +
551A ALA 4.0 0.4 + - - -
552A ILE* 1.3 76.1 - - - +
554A TYR* 1.3 65.3 + - - +
555A VAL* 4.2 9.7 - - + +
598A ILE 3.2 9.2 - - - +
599A TYR* 3.2 3.1 - - - -
600A MET* 2.9 40.6 + - + +
602A MET* 3.8 18.4 - - + -
1796A 7PE 3.1 104.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A MET* 5.7 1.6 - - + -
536A SER 4.4 5.8 - - - -
537A SER* 3.2 7.1 - - - -
538A LYS* 2.8 46.4 + - + +
540A PHE* 4.2 14.4 - + + -
552A ILE* 3.9 1.7 + - + +
553A LYS* 1.3 74.6 - - - +
555A VAL* 1.3 81.6 + - - +
556A ASN* 3.4 37.6 + - + +
596A GLN 4.8 1.6 + - - -
597A TYR* 3.7 17.6 - + + +
598A ILE 3.5 2.7 - - - -
599A TYR* 3.1 37.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A SER* 4.0 6.3 - - - +
537A SER* 3.8 10.3 - - - +
553A LYS* 4.2 13.5 - - + +
554A TYR* 1.3 85.0 - - - +
556A ASN* 1.3 63.5 + - - +
557A LEU* 4.1 11.4 - - + -
568A TYR* 3.9 29.2 - - + +
597A TYR* 3.3 12.6 - - - +
598A ILE* 3.0 48.2 + - + +
1796A 7PE 3.7 31.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A SER* 3.2 35.9 + - - +
554A TYR* 3.4 26.6 + - + +
555A VAL* 1.3 75.8 - - - +
557A LEU* 1.4 62.1 + - - +
558A GLU* 3.0 39.8 + - - +
559A GLU* 4.0 6.8 + - - +
560A ALA* 4.9 3.1 - - - +
568A TYR* 5.4 1.9 - - - -
596A GLN 4.3 1.9 + - - -
----------------------------------------------------------
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