Contacts of the helix formed by residues 591 - 602 (chain B) in PDB entry 5B2R
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 LEU 591 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B LEU 5.3 0.2 - - - +
516B GLU* 3.7 26.5 - - + +
517B TYR* 3.9 30.1 - - + +
520B VAL* 3.6 25.6 - - + -
549B VAL* 4.3 5.4 - - + -
553B PHE* 3.8 36.9 + - + +
554B LYS* 3.9 23.6 - - + -
557B ARG 4.3 3.8 + - - -
590B SER* 1.3 72.1 - - - +
592B GLY* 1.3 63.6 + - - +
593B THR 3.4 2.7 - - - -
594B TYR* 3.3 15.7 + - + -
595B HIS* 3.1 26.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 592 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B HIS* 6.4 0.7 - - - -
516B GLU* 3.1 10.7 + - - -
557B ARG* 3.4 18.2 + - - -
590B SER* 3.3 12.2 + - - -
591B LEU* 1.3 75.0 - - - +
593B THR* 1.3 57.8 + - - +
595B HIS* 3.2 2.5 + - - -
596B ASP* 2.9 35.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 593 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B HIS* 2.6 43.4 + - - +
513B LEU* 3.6 17.3 - - + -
516B GLU* 2.9 13.9 + - - -
592B GLY* 1.3 71.9 - - - +
594B TYR* 1.3 60.9 + - - +
596B ASP* 3.1 0.8 + - - +
597B LEU* 2.8 45.1 + - + +
620B VAL* 4.0 12.1 - - + -
656B TYR* 3.8 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 594 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B LEU* 3.4 20.8 - - + +
516B GLU* 4.5 0.4 + - - -
517B TYR* 3.6 19.3 - + + -
554B LYS* 3.5 43.8 - - + +
591B LEU* 3.3 21.6 + - + +
593B THR* 1.3 78.5 - - - +
595B HIS* 1.3 73.1 + + - +
597B LEU* 5.0 0.4 - - - -
598B LEU* 2.9 43.3 + - + +
604B LYS* 3.4 19.2 + - + +
607B LEU* 3.4 35.4 - - + +
608B ASP* 2.6 37.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B PHE 2.8 25.8 + - - -
554B LYS* 3.3 30.3 - - - -
555B THR 3.5 5.2 - - - -
556B ASN 3.1 26.3 + - - -
557B ARG* 3.6 40.7 + - + +
591B LEU* 3.1 23.9 + - - -
592B GLY 3.8 2.7 - - - +
593B THR 3.2 0.4 - - - -
594B TYR* 1.3 80.3 - + - +
596B ASP* 1.3 66.8 + - - +
598B LEU* 3.7 13.5 - - + +
599B LYS* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 596 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ARG* 2.7 34.9 + - - +
592B GLY 2.9 18.6 + - - +
593B THR* 3.1 5.3 + - - +
595B HIS* 1.3 77.2 - - - +
597B LEU* 1.3 63.8 + - + +
599B LYS* 3.4 5.3 + - - +
600B ILE* 3.2 25.8 + - - +
654B ARG* 3.7 25.2 + - - +
656B TYR* 2.6 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 597 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B LEU* 4.2 14.1 - - + -
593B THR* 2.8 38.4 + - + +
594B TYR 4.0 2.5 - - - +
596B ASP* 1.3 73.6 - - + +
598B LEU* 1.3 58.9 + - - +
600B ILE* 4.3 9.4 - - + +
601B ILE* 2.7 44.4 + - + +
607B LEU* 4.2 11.0 - - + -
616B LEU* 4.2 24.0 - - + +
619B ILE* 5.4 3.1 - - + -
620B VAL* 4.4 10.3 - - + -
623B LEU* 4.9 7.2 - - + -
651B LEU* 3.9 27.6 - - + -
654B ARG* 4.6 11.4 - - + -
656B TYR* 4.7 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 598 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B LYS 4.7 7.9 - - - +
594B TYR* 2.9 35.4 + - + +
595B HIS* 3.7 16.4 - - + +
597B LEU* 1.3 77.3 - - - +
599B LYS* 1.3 58.2 + - - +
601B ILE* 4.7 0.4 - - - -
602B LYS* 2.8 33.6 + - - +
603B ASP 4.2 5.4 - - - +
604B LYS* 3.7 44.9 - - + +
607B LEU* 3.7 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 599 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ASP* 3.7 36.8 + - - +
277B ASN* 6.3 0.4 - - - +
280B ALA* 6.0 4.3 - - - -
557B ARG* 5.3 4.5 - - - +
595B HIS 3.1 13.1 + - - +
596B ASP* 3.6 10.8 - - - +
597B LEU 3.3 0.2 - - - -
598B LEU* 1.3 76.9 - - - +
600B ILE* 1.3 61.2 + - + +
602B LYS* 2.9 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 600 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B ASP 3.2 14.3 + - - +
597B LEU* 3.1 11.7 + - + +
599B LYS* 1.3 83.8 - - + +
601B ILE* 1.3 67.3 + - + +
602B LYS* 4.0 8.6 + - - +
647B VAL* 3.7 22.1 - - + +
650B GLN* 3.9 25.2 - - + +
651B LEU* 3.8 37.9 - - + +
654B ARG* 3.6 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 601 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B LEU* 2.7 31.8 + - + +
598B LEU* 4.7 1.8 - - - -
600B ILE* 1.3 80.6 - - + +
602B LYS* 1.3 68.7 + - - +
603B ASP* 3.2 34.7 + - + +
606B PHE* 3.7 28.3 - - + -
607B LEU* 4.0 14.6 - - + -
616B LEU* 5.4 2.9 - - + -
643B PHE* 3.9 27.6 - - + -
647B VAL* 3.8 23.7 - - + +
651B LEU* 4.6 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B LEU* 2.8 22.1 + - - +
599B LYS* 2.9 41.8 + - + +
600B ILE* 4.0 8.3 + - - +
601B ILE* 1.3 80.6 - - - +
603B ASP* 1.3 58.1 + - - +
604B LYS 4.1 0.9 - - - -
647B VAL* 5.7 4.5 - - + -
650B GLN* 6.3 0.8 - - - +
----------------------------------------------------------
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