Contacts of the helix formed by residues 697 - 712 (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 SER 697 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F ASP* 3.7 19.5 + - - -
695F PHE* 4.1 25.2 + - - -
696F VAL* 1.3 75.0 - - - +
698F ASP* 1.3 63.2 + - - +
699F ASP* 3.7 13.9 + - - +
700F GLU* 3.3 10.0 + - - +
701F VAL* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 698 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477F ASN* 5.6 3.8 + - - -
503F GLU* 5.7 1.0 - - - +
506F ILE* 4.5 14.9 - - + +
697F SER* 1.3 74.8 - - - +
699F ASP* 1.3 61.9 + - - +
701F VAL* 4.2 8.6 - - - +
702F HIS* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 699 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F ASP* 4.7 10.0 - - - +
697F SER* 3.2 9.9 + - - +
698F ASP* 1.3 79.7 - - - +
700F GLU* 1.3 57.0 + - - +
702F HIS* 4.0 2.8 - - - +
703F ARG* 2.9 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 700 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F LEU 4.9 0.7 - - - -
321F LEU* 3.5 30.4 - - + +
322F ASP* 2.7 58.0 + - - +
422F ARG* 4.8 5.6 + - - -
423F PHE* 4.0 11.7 - - - +
424F SER 5.3 0.2 + - - -
481F LEU* 4.6 1.3 - - - -
695F PHE 4.4 2.7 - - - +
696F VAL* 3.3 30.8 - - + +
697F SER* 3.3 11.3 + - - +
699F ASP* 1.3 75.8 - - - +
701F VAL* 1.3 62.9 + - - +
703F ARG* 3.4 8.6 + - - +
704F VAL* 3.0 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 701 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477F ASN* 4.5 13.2 - - + +
481F LEU* 3.8 25.1 - - + +
506F ILE* 3.7 26.9 - - + -
507F TYR* 3.6 30.7 - - + +
696F VAL* 3.9 12.3 - - + +
697F SER 3.0 21.8 + - - +
698F ASP* 4.0 8.7 - - - +
700F GLU* 1.3 77.5 - - - +
702F HIS* 1.3 57.9 + - - +
704F VAL* 3.4 1.6 + - - +
705F VAL* 2.9 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 702 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548E ARG* 5.3 6.3 + - - -
506F ILE* 4.2 20.9 - - + +
698F ASP 2.9 21.9 + - - +
699F ASP* 4.1 3.1 - - - +
701F VAL* 1.3 74.3 - - - +
703F ARG* 1.3 59.5 + - - +
705F VAL* 3.9 6.1 - - - +
706F GLU* 2.9 61.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 703 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F LEU* 2.8 50.7 + - + +
321F LEU 4.3 3.2 + - - -
322F ASP* 4.1 15.8 + - - -
699F ASP* 2.9 43.4 + - - +
700F GLU* 3.8 11.6 - - - +
701F VAL 3.2 0.2 - - - -
702F HIS* 1.3 81.7 - - + +
704F VAL* 1.3 57.6 + - + +
706F GLU* 3.8 4.0 - - - +
707F ALA* 2.9 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 704 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F PRO* 4.6 4.9 - - + -
320F LEU* 4.9 13.0 - - + +
321F LEU* 4.6 4.7 - - + -
481F LEU* 4.5 14.6 - - + -
484F LEU* 4.9 12.3 - - + -
485F PHE* 3.5 42.4 - - + -
700F GLU* 3.0 18.8 + - - +
701F VAL 4.1 1.8 - - - +
703F ARG* 1.3 74.3 - - + +
705F VAL* 1.3 62.6 + - + +
707F ALA* 3.2 6.2 + - - +
708F TRP* 2.9 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 705 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481F LEU* 6.1 0.4 - - + -
484F LEU* 5.1 6.3 - - + -
506F ILE* 3.6 20.2 - - + +
507F TYR* 3.5 34.8 - - + -
508F GLU 3.7 17.5 - - - +
510F ILE* 3.9 18.7 - - + +
701F VAL* 2.9 23.5 + - + +
702F HIS* 3.9 6.7 - - - +
704F VAL* 1.3 77.7 - - + +
706F GLU* 1.3 61.2 + - + +
708F TRP* 3.3 2.6 + - - -
709F LYS* 2.9 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 706 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702F HIS* 2.9 53.0 + - + +
703F ARG* 4.0 4.3 - - - +
705F VAL* 1.3 77.2 - - + +
707F ALA* 1.3 60.6 + - - +
709F LYS* 3.7 33.7 + - - +
710F LEU* 2.9 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 707 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F PRO* 4.3 22.7 - - + -
320F LEU* 4.5 11.2 - - + -
703F ARG 2.9 19.3 + - - +
704F VAL* 3.2 10.1 + - - +
706F GLU* 1.3 76.4 - - - +
708F TRP* 1.3 58.1 + - - +
710F LEU* 3.3 7.7 + - - +
711F ARG* 2.9 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 708 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F LEU* 3.7 35.0 - - + -
316F PRO* 3.4 25.8 - - + +
484F LEU* 3.2 38.4 + - + +
487F SER 3.9 7.6 - - - -
488F THR* 4.4 4.0 - - + -
489F PRO* 3.8 15.5 - - + -
510F ILE* 3.8 22.0 - - + -
511F PRO* 3.7 21.9 - - + +
512F HIS* 3.4 33.7 - + - -
704F VAL* 2.9 38.4 + - + +
707F ALA* 1.3 73.1 - - - +
709F LYS* 1.3 60.6 + - - +
711F ARG* 3.7 13.8 - - + +
712F GLY* 3.0 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 709 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508F GLU* 3.4 22.2 + - - +
509F GLY* 3.6 35.0 - - - +
510F ILE 3.9 2.0 - - - +
705F VAL* 2.9 22.9 + - + +
706F GLU* 3.8 34.1 + - - +
707F ALA 3.3 0.2 - - - -
708F TRP* 1.3 76.4 - - - +
710F LEU* 1.3 61.9 + - + +
712F GLY 2.9 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 710 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706F GLU* 2.9 30.0 + - + +
707F ALA* 3.8 6.5 - - - +
708F TRP 3.2 0.2 - - - -
709F LYS* 1.3 82.2 - - + +
711F ARG* 1.3 59.2 + - + +
712F GLY 3.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 711 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F LEU* 3.0 45.8 + - - +
316F PRO* 4.2 20.7 - - - +
317F PRO* 5.8 1.4 - - - +
707F ALA* 2.9 22.4 + - - +
708F TRP* 3.4 16.6 + - + +
710F LEU* 1.3 79.4 - - + +
712F GLY* 1.3 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 712 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509F GLY 5.2 0.5 - - - +
511F PRO* 4.3 14.7 - - - +
708F TRP* 3.0 11.4 + - - +
709F LYS* 2.9 23.6 - - - +
710F LEU 3.4 1.4 - - - -
711F ARG* 1.3 78.3 - - - +
713F ALA* 1.3 61.1 + - - -
714F PRO* 4.4 2.4 - - - +
----------------------------------------------------------
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