Contacts of the helix formed by residues 585 - 595 (chain B) in PDB entry 5YPO
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 SER 585 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B THR* 4.6 0.9 - - - -
583B VAL* 3.5 10.6 - - - +
584B SER* 1.3 80.2 + - - +
586B ARG* 1.3 64.1 + - - +
587B GLU* 3.3 10.9 + - - +
588B LYS* 3.0 37.1 + - - +
589B MET* 3.2 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B THR* 3.8 23.5 + - + +
584B SER 3.8 4.0 + - - -
585B SER* 1.3 72.7 - - - +
587B GLU* 1.3 58.0 + - - +
589B MET* 3.2 1.9 + - - +
590B GLU* 2.8 53.4 + - - +
603B GLN* 2.7 25.0 + - - +
606B SER 2.5 32.3 + - - -
607B HIS* 3.9 8.5 + - - +
608B LEU* 3.4 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B SER* 3.2 8.1 + - - +
586B ARG* 1.3 77.9 - - - +
588B LYS* 1.3 62.3 - - - +
590B GLU* 3.2 13.1 + - - +
591B LYS* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 588 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B VAL* 4.4 12.6 - - + -
585B SER* 3.0 29.7 + - - +
587B GLU* 1.3 76.6 - - - +
589B MET* 1.3 63.7 + - - +
591B LYS* 3.2 5.7 + - + +
592B ASP* 3.0 57.0 + - - +
597B LYS* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 589 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B HIS* 4.0 19.7 - - + +
567B THR* 3.7 37.0 - - + -
583B VAL* 4.2 14.1 - - + -
585B SER 3.2 4.5 + - - +
586B ARG 3.2 2.2 + - - +
588B LYS* 1.3 81.7 - - - +
590B GLU* 1.3 56.9 + - - +
592B ASP* 3.2 6.8 + - - +
593B ILE* 2.8 43.9 + - + +
598B PHE* 3.9 24.0 - - + -
608B LEU* 4.0 9.6 - - + -
609B TYR* 3.7 39.9 - - - +
610B GLY* 3.7 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 590 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ARG* 2.8 51.3 + - - +
587B GLU* 3.2 11.4 + - - +
589B MET* 1.3 76.9 - - - +
591B LYS* 1.4 61.0 + - - +
593B ILE* 3.4 8.1 + - + +
594B GLN* 3.1 23.4 + - - +
608B LEU* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 591 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B GLU 2.9 17.0 + - - +
588B LYS* 3.7 6.3 - - + +
590B GLU* 1.4 74.8 - - - +
592B ASP* 1.3 61.2 - - - +
594B GLN* 3.1 33.6 + - - +
595B ALA* 2.8 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 592 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B LYS* 3.0 58.6 + - - +
589B MET* 3.7 5.5 - - - +
591B LYS* 1.3 80.7 - - - +
593B ILE* 1.3 62.7 + - - +
595B ALA* 3.3 7.1 + - - +
596B HIS 3.3 0.2 + - - -
597B LYS* 2.9 54.1 + - + +
598B PHE* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 593 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B MET* 2.8 42.7 + - + +
590B GLU* 3.7 7.2 - - + +
592B ASP* 1.3 71.6 - - - +
594B GLN* 1.3 60.4 + - + +
596B HIS* 3.0 22.7 + - - -
597B LYS 4.8 0.9 - - - +
598B PHE* 3.6 25.5 + - + +
601B ALA* 3.8 29.2 - - + -
602B GLY 5.5 0.7 - - - +
608B LEU* 4.2 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 594 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B GLU 3.1 16.5 + - - +
591B LYS* 3.1 31.6 + - - +
593B ILE* 1.3 78.3 - - - +
595B ALA* 1.3 56.9 + - - +
596B HIS* 3.2 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B LYS* 2.8 32.4 + - + +
592B ASP* 3.3 6.4 + - - +
594B GLN* 1.3 74.6 - - - +
596B HIS* 1.3 72.4 + - - +
597B LYS* 3.2 28.5 + - + +
----------------------------------------------------------
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