Contacts of the helix formed by residues 660 - 669 (chain C) in PDB entry 4YJL
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 660 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657C ARG 3.0 16.5 + - - +
658C GLU 3.4 2.9 - - - +
659C ASN* 1.3 80.4 - - - +
661C CYS* 1.3 64.4 + - - +
663C GLN* 3.4 40.4 + - + +
664C THR* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 661 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617C VAL* 3.9 14.6 - - + -
620C LEU* 4.1 6.5 - - - -
639C LEU* 3.7 25.1 - - - -
656C LEU* 3.0 47.4 + - + +
657C ARG* 4.8 0.8 - - - +
659C ASN 3.3 0.6 - - - -
660C ASN* 1.3 76.6 - - - +
662C LEU* 1.3 60.8 + - + +
663C GLN* 4.0 0.4 + - - -
664C THR* 3.2 6.2 + - - -
665C LEU* 2.9 52.3 + - - +
687C LEU* 4.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 662 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656C LEU* 5.7 0.8 - - + -
657C ARG* 5.3 8.2 - - + +
660C ASN 3.4 0.4 - - - -
661C CYS* 1.3 79.2 - - + +
663C GLN* 1.3 65.5 + - - +
665C LEU* 3.3 6.8 + - - +
666C LEU* 3.0 28.6 + - - +
684C LEU* 4.2 8.6 - - + +
687C LEU* 3.8 38.4 - - + -
694C ASP* 3.6 44.2 - - + +
697C ALA* 4.2 13.0 - - + -
698C LEU* 4.0 21.5 - - + -
701C MET* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 663 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657C ARG* 5.2 2.3 - - - +
660C ASN* 3.4 57.7 + - - +
661C CYS 4.0 0.2 + - - -
662C LEU* 1.3 82.8 + - - +
664C THR* 1.3 60.9 + - - +
666C LEU* 3.4 7.4 + - - +
667C GLN* 3.1 26.0 + - - +
701C MET* 3.6 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 664 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617C VAL* 5.5 1.4 - - - +
620C LEU* 3.6 33.2 - - + -
621C THR* 3.8 23.9 - - + +
659C ASN 4.9 1.9 + - - -
660C ASN* 3.2 16.6 + - - +
661C CYS* 3.2 9.5 + - - -
663C GLN* 1.3 76.3 - - - +
665C LEU* 1.3 60.4 + - - +
667C GLN* 3.0 12.6 + - + +
668C HIS* 2.9 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 665 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C LEU* 4.2 18.6 - - + -
636C GLY* 6.4 0.7 - - - -
639C LEU* 4.6 3.6 - - + -
661C CYS* 2.9 33.8 + - - +
662C LEU* 3.3 7.2 + - - +
664C THR* 1.3 74.8 - - - +
666C LEU* 1.3 61.3 + - - +
668C HIS* 3.2 25.5 + - - +
669C LEU* 3.3 12.5 + - - +
679C ASN 5.6 0.2 - - - -
680C ALA* 3.7 17.9 - - + +
683C THR* 3.6 42.8 - - + +
684C LEU* 3.9 26.2 - - + -
687C LEU* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 666 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662C LEU 3.0 15.3 + - - +
663C GLN* 3.6 8.7 - - - +
665C LEU* 1.3 77.1 - - - +
667C GLN* 1.3 62.6 + - + +
669C LEU* 3.2 23.7 + - + +
670C LYS 4.0 0.2 + - - -
684C LEU* 3.9 21.3 - - + -
698C LEU* 4.0 11.7 - - + -
701C MET* 3.5 46.0 - - + +
703C ALA* 3.6 33.7 - - + -
706C MET* 3.1 32.5 - - - +
707C LEU* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 667 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C GLN 3.1 17.5 + - - +
664C THR* 3.0 13.8 + - + +
666C LEU* 1.3 76.6 - - - +
668C HIS* 1.3 61.1 + - + +
670C LYS* 3.0 64.6 + - - +
671C SER* 3.9 2.3 + - - -
706C MET* 5.3 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 668 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C LEU* 3.0 50.9 + - + +
632C ILE* 3.5 26.4 - - + +
636C GLY* 5.5 2.1 - - - -
664C THR* 2.9 23.7 + - + +
665C LEU* 3.3 21.0 - - - +
666C LEU 3.2 0.2 - - - -
667C GLN* 1.3 75.4 - - + +
669C LEU* 1.3 55.8 + - - +
670C LYS 3.0 5.4 - - - -
671C SER* 3.0 28.1 + - - -
676C ILE* 3.6 23.7 + - + +
677C VAL* 3.5 7.5 - - - +
679C ASN* 6.3 0.4 - - - +
680C ALA* 3.7 14.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 669 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665C LEU 3.6 9.2 - - - +
666C LEU* 3.2 25.5 + - + +
668C HIS* 1.3 76.8 - - - +
670C LYS* 1.3 58.8 + - - +
671C SER 3.3 1.9 + - - +
677C VAL* 3.9 18.6 - - - +
680C ALA* 4.0 11.9 - - + -
681C CYS* 3.8 29.4 - - - -
684C LEU* 3.9 22.2 - - + -
706C MET* 4.1 23.8 - - + +
707C LEU* 4.0 21.3 - - + -
710C LEU* 3.8 23.5 - - + +
----------------------------------------------------------
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