Contacts of the helix formed by residues 599 - 610 (chain O) in PDB entry 6CNC
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 599 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595O LEU 4.1 1.4 + - - +
596O LYS* 3.6 4.0 + - - -
598O GLU* 1.3 78.9 - - - +
600O SER* 1.3 54.4 + - - +
601O THR 3.1 2.9 - - - -
602O LEU* 2.5 30.8 + - + +
603O LEU* 2.2 60.0 + - + +
626O GLN* 2.3 42.4 + - - +
627O LEU* 5.3 4.4 - - - +
630O VAL* 3.2 39.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 600 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596O LYS 2.9 16.7 + - - -
597O GLN* 3.2 30.0 + - - +
598O GLU 3.3 0.2 - - - -
599O ASN* 1.3 76.4 - - - +
601O THR* 1.3 59.2 + - - +
603O LEU* 3.9 9.8 + - - +
604O LYS* 4.0 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 601 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597O GLN 4.9 0.6 + - - +
598O GLU 5.1 5.4 - - - +
599O ASN 4.8 1.8 - - - -
600O SER* 1.3 77.5 - - - +
602O LEU* 1.3 67.0 + - + +
603O LEU 3.4 0.2 - - - -
604O LYS* 4.3 2.5 + - - +
605O LYS* 3.6 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 602 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598O GLU 5.2 0.4 - - - +
599O ASN* 2.5 47.8 + - + +
601O THR* 1.3 79.5 - - + +
603O LEU* 1.3 57.9 + - - +
605O LYS* 3.3 26.4 + - + +
606O ALA* 2.9 29.8 + - + +
620O LEU* 5.4 2.2 - - + -
623O GLU* 3.6 42.8 - - + +
626O GLN* 3.3 20.6 - - + +
627O LEU* 5.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 603 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596O LYS* 3.5 60.3 - - + +
599O ASN* 2.2 49.9 + - + +
600O SER* 4.2 6.3 - - - +
601O THR 3.4 0.2 - - - -
602O LEU* 1.3 67.2 - - - +
604O LYS* 1.3 60.9 + - + +
606O ALA* 2.9 9.4 + - + +
607O ASN* 2.9 38.5 + - - +
630O VAL* 5.7 5.6 - - + -
66Q LYS* 5.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 604 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600O SER 4.0 15.0 + - - +
601O THR* 4.8 3.1 - - - +
602O LEU 3.5 0.2 - - - -
603O LEU* 1.3 79.1 - - + +
605O LYS* 1.3 61.7 + - - +
607O ASN* 3.9 11.6 - - - +
608O ARG* 3.2 62.3 + - - +
66Q LYS* 6.3 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 605 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601O THR 3.6 16.8 + - - +
602O LEU* 3.3 26.9 + - + +
603O LEU 3.1 0.2 - - - -
604O LYS* 1.3 79.3 - - - +
606O ALA* 1.3 57.4 + - - +
608O ARG* 3.9 0.4 - - - -
609O ASP* 3.0 42.2 + - + +
620O LEU* 4.0 26.1 - - - +
623O GLU* 5.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 606 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602O LEU* 2.9 19.6 + - + +
603O LEU* 2.9 6.7 + - + +
605O LYS* 1.3 76.2 - - - +
607O ASN* 1.3 64.5 + - - +
609O ASP* 4.0 8.5 + - - +
610O ASP* 4.1 19.2 + - - +
623O GLU* 4.3 17.9 - - - +
627O LEU* 5.0 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 607 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603O LEU* 2.9 27.4 + - - +
604O LYS* 3.9 11.9 - - - +
606O ALA* 1.3 82.6 - - - +
608O ARG* 1.3 66.5 + - + +
609O ASP 3.7 0.3 + - - -
610O ASP* 4.1 10.9 + - - +
63Q LYS* 3.3 34.3 + - - +
67Q ASP* 5.9 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 608 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604O LYS* 3.2 55.7 + - - +
605O LYS* 3.9 0.9 - - - -
607O ASN* 1.3 81.7 - - + +
609O ASP* 1.3 62.7 + - - +
610O ASP 4.8 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 609 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605O LYS* 3.0 29.6 + - + +
606O ALA* 4.3 6.1 - - - +
607O ASN 3.4 0.4 - - - -
608O ARG* 1.3 78.1 - - - +
610O ASP* 1.3 71.3 + - - +
619O LEU* 3.2 34.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 610 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606O ALA 4.1 16.0 + - - +
607O ASN 4.1 7.8 + - - +
608O ARG 3.6 2.8 - - - -
609O ASP* 1.3 90.1 - - - +
619O LEU* 6.1 0.2 - - - +
----------------------------------------------------------
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