Contacts of the strand formed by residues 572 - 579 (chain C) in PDB entry 4BUR
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 VAL 572 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C LEU* 3.5 4.7 - - - -
569C ARG 2.9 37.6 + - - +
570C ASP* 3.3 6.0 - - + +
571C LYS* 1.3 80.1 - - - +
573C VAL* 1.3 73.9 + - - +
574C VAL* 3.3 14.7 + - + +
595C GLY* 3.9 25.8 - - - +
596C GLU 3.6 17.9 - - - +
597C GLN* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 573 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C LEU* 5.1 0.9 - - - +
566C PHE* 3.9 15.7 - - + -
567C TYR 3.6 4.3 - - - -
568C LEU* 4.1 6.5 - - + -
571C LYS 3.9 0.6 + - - -
572C VAL* 1.3 77.2 - - - +
574C VAL* 1.3 62.7 + - - +
575C GLY 3.5 20.0 - - - +
576C ILE* 3.7 18.4 - - + -
591C ILE* 4.0 20.6 - - + +
592C ILE* 3.9 18.7 - - + +
595C GLY* 5.2 0.5 - - - -
596C GLU 4.2 3.4 + - - -
598C HIS* 3.7 17.9 - - + -
601C LEU* 3.7 31.0 - - + -
604C VAL* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 574 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C LEU* 3.7 25.8 - - + +
496C GLY* 3.5 4.3 - - - -
497C LEU* 2.6 56.9 + - + +
502C LEU* 4.6 7.6 - - + -
567C TYR 3.0 17.2 + - - +
569C ARG* 4.0 32.3 - - + +
572C VAL* 3.3 25.6 - - + +
573C VAL* 1.3 79.3 - - - +
575C GLY* 1.3 52.4 + - - +
592C ILE* 3.6 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 575 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C ILE 3.4 11.7 - - - -
497C LEU 3.6 17.5 - - - -
498C VAL* 4.2 0.2 - - - -
566C PHE* 3.6 0.5 - - - -
567C TYR* 2.9 32.9 + - - -
573C VAL* 3.5 4.5 - - - +
574C VAL* 1.3 81.5 - - - +
576C ILE* 1.3 68.3 + - - +
592C ILE* 3.6 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 576 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C GLU 4.1 0.2 - - - +
494C ALA* 3.2 6.6 - - - +
495C ILE* 3.0 39.5 + - + +
498C VAL* 3.8 2.2 - - - +
564C VAL* 3.6 28.3 - - + -
565C ILE 3.4 6.3 - - - +
566C PHE* 4.2 6.5 - - + -
573C VAL* 3.7 19.3 - - + -
575C GLY* 1.3 79.9 - - - +
577C VAL* 1.3 70.2 + - - +
578C LEU* 3.9 13.9 - - + +
588C ALA* 3.7 36.3 - - + +
591C ILE* 4.3 10.1 - - + -
592C ILE* 4.1 8.3 - - + -
608C PHE* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 577 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C ILE* 5.4 1.3 - - + -
344C LEU* 4.8 7.9 - - + -
492C TYR* 3.9 25.8 - - + -
493C GLU 3.5 3.1 - - - -
494C ALA* 4.0 12.6 - - + -
498C VAL* 4.1 9.6 - - + -
564C VAL* 3.5 7.8 - - - +
565C ILE* 3.0 52.9 + - + +
567C TYR* 3.5 31.2 - - + +
576C ILE* 1.3 76.5 - - - +
578C LEU* 1.3 63.2 + - - +
579C TRP* 3.8 15.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 578 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C TYR* 3.0 27.1 - - - +
493C GLU* 2.7 32.9 + - + +
494C ALA* 5.8 0.2 - - - -
495C ILE* 6.0 0.7 - - + -
563C GLY 4.1 1.1 - - - -
564C VAL* 3.9 13.0 - - + -
576C ILE* 3.9 9.9 - - + -
577C VAL* 1.3 70.9 - - - +
579C TRP* 1.3 60.7 + - - +
580C ASN 3.6 0.5 + - - -
581C ILE* 3.5 22.9 + - + +
584C ARG* 4.0 11.0 - - + +
585C MET* 3.8 43.1 - - + +
588C ALA* 4.7 3.4 - - + -
608C PHE* 3.6 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 579 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 3.7 26.7 - - + -
348C LEU* 3.5 34.8 - - + +
351C TRP* 3.7 15.2 - + - -
352C THR* 3.6 22.2 - - + -
486C LEU* 6.1 0.2 - - + -
490C VAL* 3.7 24.9 - - + -
491C GLY 5.3 0.4 - - - -
492C TYR* 3.6 37.5 - + + -
508C PHE* 4.4 2.9 - + - -
560C TYR 2.9 29.1 + - - -
561C GLY 3.9 12.1 - - - -
562C LYS 4.1 1.6 - - - -
563C GLY* 2.7 43.8 + - - +
565C ILE* 4.1 9.2 - - + -
577C VAL* 3.8 8.7 + - + -
578C LEU* 1.3 68.8 - - - +
580C ASN* 1.3 76.9 + - - +
581C ILE* 3.3 4.5 - - - +
----------------------------------------------------------
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