Contacts of the helix formed by residues 596 - 608 (chain F) in PDB entry 6X34
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 596 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561F LEU* 4.7 8.4 - - + +
589F LEU* 5.2 2.2 + - - +
590F LEU* 5.5 3.3 - - - +
593F HIS* 3.4 21.4 + - - +
594F GLY 2.8 27.9 + - - -
595F ARG* 1.3 77.9 - - - +
597F HIS* 1.3 64.4 + - - +
598F LYS* 3.3 5.5 + - + +
599F VAL* 3.5 30.5 + - + +
600F LEU* 3.3 19.4 - - - +
1662F PHE* 4.5 4.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 597 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596F ASN* 1.3 71.7 - - - +
598F LYS* 1.3 72.8 + - - +
599F VAL 3.4 0.6 + - - -
600F LEU* 4.1 8.0 + - - -
601F ASP* 4.1 5.5 + - - +
1661F GLN* 3.5 26.2 - - + +
1662F PHE* 5.0 6.6 - - + +
1665F HIS* 2.8 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 598 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558F SER* 6.0 2.2 - - - +
561F LEU* 3.7 23.3 - - + -
562F GLU* 6.5 0.4 - - - -
565F TYR* 4.8 4.4 - - + +
596F ASN* 3.2 2.8 - - + +
597F HIS* 1.3 106.1 - - - +
599F VAL* 1.3 63.0 + - - +
600F LEU 3.4 0.4 - - - -
601F ASP* 3.6 10.2 + - + +
602F VAL* 3.3 24.1 + - - +
1661F GLN* 4.1 10.6 + - - +
1665F HIS* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 599 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561F LEU* 3.7 34.1 - - + -
586F ILE* 4.2 15.0 - - + +
589F LEU* 4.6 11.9 - - + -
590F LEU* 3.8 32.8 - - + -
596F ASN* 3.5 28.2 + - + +
597F HIS 3.4 0.6 - - - -
598F LYS* 1.3 76.5 - - - +
600F LEU* 1.3 60.3 + - - +
602F VAL* 3.0 6.1 + - + +
603F LEU* 2.9 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 600 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590F LEU* 5.0 10.3 - - + -
596F ASN 3.3 20.6 - - - +
597F HIS* 4.5 2.7 - - - +
598F LYS 3.4 0.4 - - - -
599F VAL* 1.3 79.3 - - + +
601F ASP* 1.3 57.0 + - - +
603F LEU* 3.6 9.5 - - - +
604F CYS* 2.9 29.3 + - - +
632F LEU* 4.8 9.4 - - + -
1662F PHE* 3.7 23.6 - - + -
1665F HIS* 3.5 25.8 - - + +
1666F THR* 3.5 41.7 - - - +
1669F LEU* 4.3 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 601 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565F TYR* 3.6 26.8 - - + +
597F HIS 4.1 6.7 + - - +
598F LYS* 3.6 15.7 + - + +
599F VAL 3.2 0.6 - - - -
600F LEU* 1.3 79.1 - - - +
602F VAL* 1.3 56.9 + - - +
604F CYS* 3.3 7.6 + - - +
605F SER* 2.9 30.1 + - - -
1665F HIS* 5.3 4.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 602 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561F LEU* 4.0 18.4 - - + -
564F LEU* 4.3 18.2 - - + +
565F TYR* 3.6 30.7 - - + +
568F LEU* 4.0 22.7 - - + -
586F ILE* 5.0 9.2 - - + -
598F LYS 3.3 16.6 + - - +
599F VAL* 3.0 9.5 + - + +
601F ASP* 1.3 76.7 - - - +
603F LEU* 1.3 61.9 + - + +
605F SER* 3.0 9.3 + - - -
606F LEU* 2.9 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 603 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583F ILE* 5.0 12.8 - - + -
586F ILE* 3.6 31.2 - - + -
587F ILE* 5.2 7.9 - - + -
590F LEU* 5.3 4.5 - - + -
599F VAL* 2.9 32.8 + - + +
600F LEU* 3.6 9.9 - - + +
602F VAL* 1.3 80.9 - - + +
604F CYS* 1.3 57.1 + - - +
606F LEU* 3.3 13.7 + - + +
607F CYS* 2.9 29.1 + - - +
621F ILE* 4.9 17.5 - - + -
625F LEU* 5.4 7.2 - - + -
1669F LEU* 3.8 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 604 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600F LEU 2.9 17.2 + - - +
601F ASP* 3.3 7.6 + - - +
603F LEU* 1.3 76.0 - - - +
605F SER* 1.3 63.3 + - - +
607F CYS* 3.3 17.3 + - - +
608F VAL* 3.7 14.8 + - - +
1668F ARG* 4.8 19.7 - - + -
1669F LEU* 4.0 15.8 - - + +
1672F ALA* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 605 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565F TYR* 4.9 11.3 + - - -
568F LEU* 3.7 36.5 - - - +
569F ILE* 4.9 14.1 - - - -
575F LEU* 4.0 5.2 - - - +
601F ASP 2.9 14.6 + - - -
602F VAL* 3.0 13.6 + - - -
604F CYS* 1.3 78.3 - - - +
606F LEU* 1.3 60.8 + - - +
608F VAL 3.0 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 606 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568F LEU* 3.7 32.5 - - + -
575F LEU* 3.2 30.1 - - + +
578F ILE* 3.8 42.6 - - + -
582F HIS* 6.1 3.6 - - + -
583F ILE* 5.6 14.4 - - + +
586F ILE* 6.0 5.6 - - + -
602F VAL* 2.9 17.2 + - + +
603F LEU* 3.6 14.6 - - + +
605F SER* 1.3 78.5 + - - +
607F CYS* 1.3 64.7 + - - +
617F ASN* 4.0 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 607 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575F LEU* 4.9 0.2 - - - -
603F LEU 2.9 16.0 + - - +
604F CYS* 3.5 11.2 - - - +
605F SER 3.2 0.6 - - - -
606F LEU* 1.3 79.4 - - - +
608F VAL* 1.3 61.0 + - + +
614F VAL* 3.5 23.2 + - - +
617F ASN* 5.2 3.6 - - - -
618F GLN* 3.4 36.0 + - - +
1669F LEU* 5.4 3.6 - - + -
1672F ALA* 3.4 28.9 - - + -
1673F VAL* 3.6 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 608 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575F LEU* 4.4 1.1 - - - +
604F CYS* 3.7 14.8 + - - +
605F SER* 3.0 20.0 - - - +
607F CYS* 1.3 82.1 - - + +
609F CYS* 1.3 76.9 + - - +
611F GLY* 4.9 1.1 - - - +
612F VAL 3.3 13.0 - - - +
613F ALA* 4.5 4.9 - - + +
618F GLN* 5.3 2.5 - - - +
1672F ALA* 5.4 9.6 - - + +
1676F LEU* 4.1 31.0 - - + -
----------------------------------------------------------
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