Contacts of the strand formed by residues 548 - 553 (chain A) in PDB entry 3WSZ
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 548 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A TRP* 3.1 6.1 - - - +
543A GLY 3.0 40.5 + - - +
544A ASP* 4.5 4.7 - - + -
546A GLY 3.2 0.8 - - - -
547A GLY* 1.3 80.8 - - - +
549A ILE* 1.3 71.3 + - - +
550A THR* 4.2 0.9 - - + -
563A TYR* 4.5 11.2 - - + -
564A SER 3.6 12.3 - - - +
565A THR* 4.3 4.0 - - + -
595A THR* 4.8 5.4 - - + -
597A PHE* 3.6 22.9 - - + -
617A ALA* 3.8 28.9 - - + +
620A ALA* 4.0 10.3 - - + -
621A LEU* 3.5 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A LEU* 4.0 21.8 - - + -
505A ILE* 3.7 33.7 - - + -
522A ILE* 4.2 13.7 - - + -
540A TYR* 5.3 2.2 - - + -
541A THR 3.8 6.7 - - - +
542A TRP* 3.9 12.6 - - + -
546A GLY 4.6 4.9 - - - +
548A ILE* 1.3 79.4 - - - +
550A THR* 1.3 67.8 + - - +
563A TYR* 3.1 4.6 - - - +
564A SER* 2.8 44.2 + - - +
567A GLU* 4.5 19.1 - - - -
568A GLY 4.7 0.4 - - - +
571A TRP* 3.5 25.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A TYR* 3.4 5.2 - - - +
541A THR* 3.3 38.2 + - - +
542A TRP* 4.8 0.2 - - - +
548A ILE* 4.2 2.9 + - + -
549A ILE* 1.3 80.3 - - - +
551A ALA* 1.3 61.5 + - - +
561A LEU* 3.8 23.6 - - + -
562A LYS 3.4 4.3 - - - -
563A TYR* 4.3 11.2 - - + -
586A LEU* 3.2 19.7 - - - +
597A PHE* 3.4 39.5 - - + -
617A ALA* 5.7 1.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
534A LEU* 3.5 33.0 - - + -
538A HIS* 4.1 4.5 - - + -
539A TYR 3.2 13.0 - - - +
540A TYR* 4.4 5.8 - - + -
549A ILE 4.2 0.2 + - - -
550A THR* 1.3 76.1 - - - +
552A ILE* 1.3 68.3 + - - +
561A LEU* 3.7 0.5 - - - +
562A LYS* 2.6 41.8 + - + +
571A TRP* 4.2 9.4 - - + -
586A LEU* 4.0 1.1 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
538A HIS* 3.2 6.7 - - - -
539A TYR* 2.8 46.0 + - + -
551A ALA* 1.3 81.2 - - - +
553A ALA* 1.3 68.9 + - - +
558A THR* 3.7 19.3 - - - +
560A GLU 4.0 9.9 - - - +
561A LEU* 3.6 15.9 - - + -
562A LYS* 5.8 0.9 - - - +
576A PHE* 4.2 6.3 - - + -
583A VAL* 4.0 22.4 - - + -
586A LEU* 4.0 12.8 - - + -
599A ILE* 3.7 44.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A PRO 4.0 1.6 - - - +
538A HIS* 3.6 22.8 - - + +
539A TYR* 4.5 3.9 - - - -
552A ILE* 1.3 85.0 - - - +
554A GLN* 1.3 66.7 + - - +
555A GLY 4.0 0.3 + - - -
556A MET 4.2 8.9 - - - +
558A THR* 4.0 23.5 + - + -
560A GLU 4.8 1.8 + - - -
562A LYS* 4.5 12.1 - - - +
583A VAL* 5.2 2.9 - - - +
----------------------------------------------------------
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