Contacts of the helix formed by residues 596 - 605 (chain F) in PDB entry 6T8O
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 GLU 596 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644E ALA* 5.7 2.1 - - - +
472F LYS* 3.4 10.4 + - - -
499F PRO* 3.5 25.9 - - + +
500F LYS* 5.6 10.6 + - + -
594F VAL* 4.1 2.7 - - - +
595F ASP* 1.3 84.9 - - + +
597F PHE* 1.3 60.9 + - - +
598F ALA* 3.1 16.5 - - + +
599F ASP* 3.3 33.9 + - - +
600F MET* 3.1 22.3 + - - +
629F ALA 3.4 1.6 - - - -
630F THR* 3.9 2.2 - - - -
631F GLN* 2.7 44.5 + - - +
632F ARG* 4.1 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 597 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463F LEU* 4.0 20.6 - - + -
594F VAL* 3.7 16.4 - - + +
596F GLU* 1.3 71.1 - - - +
598F ALA* 1.3 59.9 + - - +
600F MET* 3.7 15.7 - - + -
601F MET* 2.9 40.6 + - + +
608F VAL* 5.6 2.8 - - + +
612F ILE* 6.0 7.4 - - + -
628F LEU* 3.7 34.5 - - + -
629F ALA* 3.2 32.9 + - - -
630F THR* 3.7 12.6 - - + -
637F VAL* 3.6 37.7 - - + -
638F ILE* 4.0 11.2 - - + -
642F ILE* 4.9 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 598 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644E ALA* 5.7 0.4 - - + -
596F GLU* 3.3 22.7 - - + +
597F PHE* 1.3 80.8 - - - +
599F ASP* 1.3 59.0 + - - +
601F MET* 3.4 3.1 + - - +
602F MET* 2.9 27.7 + - - +
630F THR* 3.4 14.0 + - - +
632F ARG* 3.6 31.3 + - + +
637F VAL* 3.7 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 599 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617E GLN* 3.9 26.9 + - - +
644E ALA* 4.1 10.3 - - - +
645E ASN* 3.0 33.3 + - - +
500F LYS* 4.6 4.9 - - - +
521F MET* 3.7 2.6 - - + +
596F GLU* 3.3 27.7 + - + +
598F ALA* 1.3 78.2 - - - +
600F MET* 1.3 60.6 + - - +
602F MET* 3.4 29.2 - - + +
603F ILE* 3.0 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 600 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497F ILE* 3.6 33.4 - - + +
499F PRO* 5.6 4.7 - - + -
521F MET* 3.7 23.6 - - + +
524F ALA* 4.0 13.0 - - + -
528F LEU* 4.2 14.6 - - - -
594F VAL* 3.8 28.3 - - + -
596F GLU 3.1 13.2 + - - +
597F PHE* 3.7 10.1 - - - +
599F ASP* 1.3 78.0 - - - +
601F MET* 1.3 61.4 + - - +
603F ILE* 3.4 0.5 + - - +
604F VAL* 3.0 28.1 + - + +
608F VAL* 3.7 30.7 - - + -
612F ILE* 5.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 601 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597F PHE* 2.9 31.0 + - + +
598F ALA* 3.8 3.8 - - - +
600F MET* 1.3 72.0 - - - +
602F MET* 1.3 60.2 + - - +
605F GLY* 2.9 45.9 + - - +
606F LYS* 5.5 0.4 - - - -
608F VAL* 4.7 9.6 - - + +
609F GLU* 3.7 44.6 - - + +
636F ASP 3.3 26.2 - - - +
637F VAL* 3.7 21.1 - - + +
639F THR* 4.7 0.7 - - + -
642F ILE* 5.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 602 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610E GLU* 5.6 5.0 - - - +
613E ALA* 3.6 37.9 - - + +
617E GLN* 4.6 2.0 - - - +
641E LEU* 3.7 43.9 - - + +
644E ALA* 5.2 0.9 - - - -
645E ASN* 4.1 6.5 - - - +
598F ALA 2.9 18.0 + - - +
599F ASP* 3.4 38.4 - - + +
600F MET 3.2 0.2 - - - -
601F MET* 1.3 77.7 - - - +
603F ILE* 1.3 79.4 + - + +
604F VAL 4.7 0.3 - - - -
605F GLY* 4.7 1.0 + - - -
632F ARG* 4.6 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 603 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610E GLU* 6.1 1.2 - - - -
613E ALA* 6.0 0.4 - - + -
614E ARG* 3.9 42.9 + - + +
617E GLN* 3.3 26.5 - - - +
618E LYS* 5.8 2.7 - - - -
520F ASP* 5.9 0.9 - - - +
521F MET* 3.7 42.2 - - + -
522F LYS* 5.4 8.6 + - - +
599F ASP 3.0 12.8 + - - +
602F MET* 1.3 90.4 - - + +
604F VAL* 1.3 66.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 604 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521F MET* 3.7 35.2 - - + +
522F LYS* 5.8 5.8 - - + +
525F ALA* 5.0 8.3 - - + -
600F MET* 3.0 18.6 + - + +
601F MET 3.8 0.2 - - - -
602F MET 4.7 0.7 - - - -
603F ILE* 1.3 81.1 - - + +
605F GLY* 1.3 60.7 + - - +
607F LYS* 4.1 32.5 + - + +
608F VAL* 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 605 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601F MET* 2.9 36.1 + - - +
602F MET 5.4 0.4 - - - -
604F VAL* 1.3 76.9 - - - +
606F LYS* 1.3 64.6 + - - -
607F LYS* 3.2 6.0 + - - -
608F VAL* 3.6 12.2 + - - +
609F GLU 4.0 0.7 + - - -
----------------------------------------------------------
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