Contacts of the helix formed by residues 697 - 710 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E ASP* 4.0 13.0 + - - -
695E PHE* 4.0 22.5 - - - -
696E VAL* 1.3 81.7 - - - +
698E ASP* 1.3 66.5 + - - +
699E ASP* 3.4 20.5 + - - +
700E GLU* 3.5 13.7 + - - +
701E VAL* 3.3 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 698 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D ARG* 5.9 2.0 + - - -
477E ASN* 5.1 2.9 + - - -
503E GLU* 4.1 18.9 - - - +
506E ILE* 5.3 4.0 - - + +
696E VAL 5.4 0.7 - - - +
697E SER* 1.3 73.6 - - - +
699E ASP* 1.3 63.3 + - - +
701E VAL* 3.2 10.9 + - - +
702E HIS* 2.9 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 699 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E ASP* 5.0 4.7 - - - +
697E SER* 3.2 12.1 + - - +
698E ASP* 1.3 82.6 - - - +
700E GLU* 1.3 57.1 + - - +
702E HIS* 3.5 9.9 + - - +
703E ARG* 2.9 48.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 700 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321E LEU* 3.5 30.1 - - + +
322E ASP* 2.8 44.7 + - - +
422E ARG* 4.9 2.1 + - - -
423E PHE* 4.6 10.7 - - - +
424E SER 5.7 0.5 + - - -
481E LEU* 4.9 1.3 - - + -
695E PHE 4.9 0.4 - - - +
696E VAL* 3.5 26.1 - - + +
697E SER* 3.5 13.3 + - - +
698E ASP 3.4 0.4 - - - -
699E ASP* 1.3 76.9 - - - +
701E VAL* 1.3 58.9 + - - +
703E ARG* 3.2 23.0 + - - +
704E VAL* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 701 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477E ASN* 4.7 13.0 - - + +
481E LEU* 4.1 13.9 - - + -
506E ILE* 3.7 26.0 - - + -
507E TYR* 3.6 33.9 - - + +
696E VAL* 3.8 16.8 - - + -
697E SER 3.3 18.4 - - - +
698E ASP* 3.2 12.4 + - - +
700E GLU* 1.3 74.1 - - - +
702E HIS* 1.3 60.8 + - - +
704E VAL* 3.4 2.3 + - - +
705E VAL* 3.0 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 702 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D ARG* 4.4 14.3 + - - -
506E ILE* 3.5 30.1 - - + +
698E ASP* 2.9 37.1 + - + +
699E ASP* 3.7 11.0 - - - +
701E VAL* 1.3 75.2 - - - +
703E ARG* 1.3 56.8 + - - +
705E VAL* 3.5 5.1 + - - +
706E GLU* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 703 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E LEU* 3.3 48.2 + - + -
321E LEU* 5.6 0.2 - - - +
322E ASP* 3.9 16.9 + - - -
699E ASP* 2.9 35.4 + - - +
700E GLU* 3.5 41.6 - - - +
701E VAL 3.2 0.2 - - - -
702E HIS* 1.3 78.1 - - - +
704E VAL* 1.3 57.1 + - + +
706E GLU* 3.4 6.1 + - - +
707E ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 704 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E PRO* 5.6 2.0 - - + -
320E LEU* 3.9 16.8 - - + -
321E LEU* 4.6 4.5 - - + -
481E LEU* 4.3 10.3 - - + -
484E LEU* 3.9 23.8 - - + -
485E PHE* 3.6 35.7 - - + -
507E TYR* 6.5 0.2 - - + -
700E GLU 2.9 20.6 + - - +
701E VAL* 4.1 4.7 - - + +
703E ARG* 1.3 75.0 - - + +
705E VAL* 1.3 60.5 + - - +
707E ALA* 3.7 1.5 - - + +
708E TRP* 2.9 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 705 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484E LEU* 5.7 0.9 - - + -
506E ILE* 3.4 31.9 - - + +
507E TYR* 3.7 28.0 - - + -
508E GLU 4.6 4.7 - - - +
510E ILE* 4.1 17.2 - - + +
701E VAL 3.0 21.9 + - - +
702E HIS* 3.8 6.3 - - - +
704E VAL* 1.3 77.3 - - + +
706E GLU* 1.3 57.6 + - - +
708E TRP* 3.3 2.3 + - - +
709E LYS* 2.9 47.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 706 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702E HIS 2.9 18.3 + - - +
703E ARG* 3.8 6.5 - - - +
705E VAL* 1.3 76.2 - - - +
707E ALA* 1.3 57.9 + - - +
709E LYS* 3.7 15.4 + - - +
710E LEU* 2.9 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 707 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E PRO* 5.0 12.6 - - + -
320E LEU* 3.8 24.2 - - + -
703E ARG 2.9 18.5 + - - +
704E VAL 3.2 5.1 + - - +
706E GLU* 1.3 76.9 - - - +
708E TRP* 1.3 60.8 + - - +
710E LEU* 3.8 8.3 + - - +
711E ARG* 3.3 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 708 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E LEU* 4.8 5.6 - - + -
316E PRO* 3.5 32.5 - - + +
484E LEU* 3.3 48.4 + - + +
487E SER 3.8 8.5 - - - -
488E THR* 4.5 4.3 - - + -
489E PRO* 4.1 16.2 - - + -
510E ILE* 3.8 22.4 - - + -
511E PRO* 4.1 19.6 - - + +
512E HIS* 3.4 29.8 - + - -
704E VAL* 2.9 37.5 + - + +
705E VAL 3.9 0.2 - - - +
707E ALA* 1.3 77.2 - - - +
709E LYS* 1.3 59.6 + - - +
710E LEU 3.2 0.4 - - - -
711E ARG* 2.9 23.8 + - + -
712E GLY* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 709 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508E GLU 4.3 8.9 + - - +
509E GLY* 3.3 40.5 - - - +
510E ILE 4.2 0.7 - - - +
705E VAL* 2.9 35.7 + - + +
706E GLU* 3.4 17.0 + - - +
708E TRP* 1.3 75.3 - - - +
710E LEU* 1.3 62.1 + - - +
711E ARG 3.3 0.2 - - - -
712E GLY 3.9 12.4 - - - +
714E PRO* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 710 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706E GLU* 2.9 44.3 + - + +
707E ALA* 4.2 7.2 - - - +
708E TRP 3.2 0.2 - - - -
709E LYS* 1.3 79.0 - - - +
711E ARG* 1.3 59.9 + - - +
----------------------------------------------------------
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