Contacts of the helix formed by residues 556 - 563 (chain E) in PDB entry 6DWZ
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 LYS 556 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E LYS* 3.9 32.2 - - - +
199E HIS* 5.8 0.2 - - - +
552E PRO 4.3 7.3 + - - +
553E LYS 5.9 1.1 - - - +
554E LEU 2.7 5.3 + - - -
555E SER* 1.3 75.9 - - - +
557E LEU* 1.3 59.6 + - - +
559E LEU* 3.0 31.5 - - + +
560E SER* 3.0 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 557 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435E PHE* 3.9 16.4 - - + -
453E PHE* 5.6 5.6 - - + -
454E CYS* 3.4 46.4 - - + +
457E LYS* 5.7 7.2 - - + -
458E MET* 4.6 13.9 - - + +
553E LYS 5.0 7.7 + - - +
554E LEU* 2.4 32.1 + - + +
556E LYS* 1.3 63.8 - - - +
558E ALA* 1.3 58.0 + - - +
559E LEU 2.9 3.8 - - - -
560E SER* 3.0 20.8 + - - +
561E LEU* 2.9 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 558 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435E PHE* 3.3 31.5 - - + +
544E TRP* 3.2 49.1 - - + +
554E LEU 3.7 2.6 + - - -
556E LYS 3.5 0.2 - - - -
557E LEU* 1.3 76.5 - - - +
559E LEU* 1.3 60.1 + - - +
561E LEU* 3.9 3.8 - - - -
562E LEU* 3.0 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 559 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E LYS* 6.0 0.4 - - - +
199E HIS* 3.8 34.3 + - + +
201E ASN 6.0 0.9 - - - +
541E MET 5.2 4.7 - - - +
544E TRP* 4.2 22.7 - - + +
545E ASN* 4.8 12.3 - - - +
555E SER 3.0 20.0 - - - +
556E LYS* 3.0 44.8 + - + +
557E LEU 2.9 0.8 - - - -
558E ALA* 1.3 78.5 - - - +
560E SER* 1.3 63.8 + - - +
561E LEU 3.1 2.2 + - - -
562E LEU* 4.2 1.2 - - + +
563E SER* 3.4 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 560 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E LYS 5.7 0.4 - - - -
173E ASP* 4.1 1.8 - - - -
174E GLY* 3.8 30.3 - - - +
199E HIS* 4.2 2.7 - - - -
244E LYS* 3.3 19.2 + - - +
428E TRP* 4.6 0.5 - - - -
556E LYS 3.0 12.3 + - - -
557E LEU* 3.0 15.3 + - - +
559E LEU* 1.3 76.2 - - - +
561E LEU* 1.3 71.7 + - - +
563E SER* 3.7 9.8 + - - -
564E ILE* 3.1 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 561 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382E LEU* 3.9 15.8 - - + +
428E TRP* 3.3 66.4 - - + +
431E THR* 3.8 19.3 - - + -
432E ALA* 3.6 23.3 - - + +
435E PHE* 4.1 14.6 - - + -
453E PHE* 4.9 4.3 - - + -
557E LEU* 2.9 21.5 + - + +
558E ALA* 4.3 0.9 - - - -
560E SER* 1.3 84.2 + - - +
562E LEU* 1.3 60.4 + - + +
563E SER 3.1 4.5 - - - -
564E ILE* 3.1 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 562 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E LEU* 5.0 3.1 - - - +
379E SER 4.9 0.3 - - - +
380E PRO* 3.1 35.1 - - + +
382E LEU* 5.6 3.1 - - - -
383E CYS* 4.1 27.1 - - + -
432E ALA* 4.6 4.0 - - + +
435E PHE* 3.7 18.8 - - + +
540E VAL* 3.4 49.4 - - + +
541E MET* 4.3 10.7 - - + +
544E TRP* 4.2 14.1 - - + -
558E ALA* 3.0 27.1 + - + +
559E LEU* 4.6 1.3 - - + +
561E LEU* 1.3 75.5 - - - +
563E SER* 1.3 55.5 + - - +
564E ILE 3.3 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 563 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174E GLY 3.2 22.0 + - - -
176E SER* 2.5 28.7 + - - -
197E HIS* 3.7 10.6 - - - +
198E TYR* 4.1 12.8 - - - -
199E HIS* 3.9 15.7 - - - -
204E LEU* 4.4 15.7 - - - +
559E LEU 3.4 14.2 + - - -
560E SER 3.7 6.6 + - - -
561E LEU 3.1 1.8 - - - -
562E LEU* 1.3 75.1 - - - +
564E ILE* 1.3 55.7 + - - +
565E PRO* 3.9 0.6 - - - +
----------------------------------------------------------
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