Contacts of the helix formed by residues 595 - 606 (chain i) in PDB entry 5M32
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 ASN 595 (chain i).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590i TYR* 3.7 15.6 - - + +
594i GLY* 1.3 67.1 - - - -
596i ASN* 1.3 57.8 + - - +
597i LYS* 2.9 9.9 - - + +
598i ALA* 2.9 33.9 + - + +
599i ILE* 3.1 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 596 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53e PHE* 5.9 5.4 - - - +
56e VAL* 4.9 14.9 - - + +
594i GLY 2.8 11.7 + - - +
595i ASN* 1.3 67.5 - - - +
597i LYS* 1.3 60.4 + - - +
598i ALA 3.3 0.2 - - - -
599i ILE* 3.6 14.2 - - + +
600i ARG* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 597 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595i ASN* 2.9 6.3 - - + +
596i ASN* 1.3 78.7 - - - +
598i ALA* 1.3 63.8 + - - +
600i ARG* 3.2 5.3 + - - +
601i ARG* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 598 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564i ASP* 5.8 7.6 - - + -
590i TYR* 5.7 5.2 - - + -
595i ASN* 2.9 20.4 + - + +
597i LYS* 1.3 79.3 - - - +
599i ILE* 1.3 62.9 + - - +
601i ARG* 3.2 7.9 + - - +
602i LEU* 2.9 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 599 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56e VAL* 6.0 2.9 - - + -
595i ASN 3.1 7.5 + - - +
596i ASN* 3.6 19.3 - - + +
598i ALA* 1.3 76.7 - - - +
600i ARG* 1.3 51.7 + - - +
602i LEU* 3.2 8.4 + - - +
603i LEU* 2.7 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 600 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56e VAL* 4.5 26.6 - - + +
59e GLU* 5.1 9.8 - - + +
596i ASN 2.9 18.2 + - - +
597i LYS* 3.5 5.8 - - - +
599i ILE* 1.3 76.1 - - - +
601i ARG* 1.3 63.5 + - - +
603i LEU* 2.9 18.6 + - - +
604i HIS* 3.0 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 601 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597i LYS 2.9 13.4 + - - +
598i ALA* 3.5 11.2 - - - +
600i ARG* 1.3 75.5 - - - +
602i LEU* 1.3 65.5 + - - +
604i HIS* 3.1 8.4 + - - +
605i VAL* 3.0 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 602 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586i VAL* 5.4 12.6 - - + -
598i ALA 2.9 13.0 + - - +
599i ILE* 3.3 11.4 - - - +
601i ARG* 1.3 75.1 - - - +
603i LEU* 1.3 54.0 + - - +
605i VAL* 3.0 10.9 + - - +
606i ALA* 2.5 37.7 + - - +
618i ALA* 5.3 2.1 - - + +
621i SER* 6.1 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 603 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56e VAL 5.8 2.0 - - - +
60e TYR* 5.1 17.7 - - + +
599i ILE 2.7 18.0 + - - +
600i ARG* 2.9 16.1 + - - +
602i LEU* 1.3 74.2 - - - +
604i HIS* 1.3 59.7 + - - +
606i ALA* 3.1 22.2 + - - +
607i VAL* 3.4 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 604 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59e GLU* 5.3 4.9 - - + +
60e TYR* 6.2 1.8 - - - +
63e ASP* 4.7 21.5 - - + +
600i ARG 3.0 11.6 + - - +
601i ARG* 3.1 7.8 + - - +
603i LEU* 1.3 73.9 - - - +
605i VAL* 1.3 64.3 + - - +
607i VAL* 3.4 5.6 + - - +
608i SER* 3.2 21.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 605 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571i CYS* 6.1 2.5 - - + +
601i ARG 3.0 11.1 + - - +
602i LEU* 3.0 12.2 + - - +
604i HIS* 1.3 75.5 - - - +
606i ALA* 1.3 56.5 + - - +
607i VAL 3.1 1.8 - - - -
608i SER* 3.0 23.6 + - - -
609i ASP* 3.2 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 606 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602i LEU 2.5 18.3 + - - +
603i LEU* 3.1 19.2 + - - +
605i VAL* 1.3 71.5 - - - +
607i VAL* 1.3 56.0 + - - +
608i SER 3.7 0.2 - - - -
609i ASP* 4.7 3.1 - - - +
615i ARG* 4.4 17.1 - - - +
618i ALA* 3.4 31.5 - - + +
----------------------------------------------------------
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