Contacts of the strand formed by residues 543 - 547 (chain B) in PDB entry 4RS6
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 THR 543 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537B LEU* 3.3 5.9 - - - +
538B LEU* 3.0 54.9 + - + +
540B ASP* 3.2 13.6 + - - -
542B LYS* 1.3 80.6 - - - +
544B VAL* 1.3 67.1 + - - +
545B HIS* 4.3 0.4 - - + -
555B VAL* 3.9 24.2 - - + -
556B PHE 4.1 6.5 - - - +
557B PRO* 4.4 1.8 - - + +
595B ILE* 3.1 33.9 - - + +
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Residues in contact with VAL 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B MET* 3.9 23.1 - - + -
536B SER 3.3 8.1 - - - +
537B LEU* 4.4 2.2 - - + -
543B THR* 1.3 79.7 - - - +
545B HIS* 1.3 81.5 + - - +
546B TYR 4.4 0.2 - - - +
554B SER 3.4 1.2 - - - +
555B VAL* 3.4 2.9 - - - +
556B PHE* 2.9 55.8 + - + +
558B ALA* 3.8 32.8 - - + -
569B VAL* 4.3 11.4 - - + -
572B LEU* 4.4 10.5 - - + -
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Residues in contact with HIS 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B MET* 3.1 4.9 - - - +
536B SER* 2.7 47.5 + - - -
538B LEU* 3.6 26.3 - - + +
543B THR* 4.3 0.4 + - + -
544B VAL* 1.3 83.6 - - - +
546B TYR* 1.3 60.1 + - - +
547B TYR* 4.2 21.8 + - + -
553B CYS* 4.2 9.2 - - - -
554B SER 3.3 2.7 - - - -
555B VAL* 3.4 23.1 - - + +
595B ILE 3.0 24.8 + - - -
596B ARG 3.7 8.7 - - - -
597B ARG 3.5 25.3 + - - -
598B PRO* 4.5 1.1 - - + -
599B ARG* 4.4 9.7 + - + +
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Residues in contact with TYR 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ALA* 4.3 20.8 - - + +
534B HIS 3.4 4.9 - - - -
535B MET* 3.9 21.5 - - + -
545B HIS* 1.3 74.9 - - - +
547B TYR* 1.3 61.8 + - - +
548B ALA* 2.9 43.6 - - + +
549B GLU* 5.4 2.1 + - - +
552B GLN 4.4 4.7 - - - -
553B CYS* 3.4 2.3 - - - -
554B SER* 2.8 44.1 + - - +
556B PHE* 4.0 16.4 - - + -
565B PHE* 2.9 48.4 - + - -
568B GLN* 4.6 5.8 + - - -
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Residues in contact with TYR 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B GLY 4.7 0.3 - - - +
534B HIS* 2.8 45.3 + - + +
536B SER* 5.4 2.9 - - - -
545B HIS* 4.2 17.4 + - + -
546B TYR* 1.3 82.2 - - - +
548B ALA* 1.3 65.7 + - - +
551B GLY 4.0 14.1 - - - -
552B GLN 4.0 3.6 - - - -
553B CYS* 3.3 48.5 - - + -
598B PRO* 3.7 27.2 - - + +
599B ARG* 3.9 8.6 + - + -
601B TYR* 3.8 50.2 - + + -
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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) + - + + + + + -
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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