Contacts of the helix formed by residues 405 - 416 (chain C) in PDB entry 5E9W
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 405 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C GLU 5.3 0.9 - - - +
402C LYS* 3.2 14.6 + - - +
403C ILE 3.1 2.1 - - - +
404C LYS* 1.3 79.7 - - - +
406C ASN* 1.3 57.8 + - - +
407C GLU* 2.8 29.0 + - - +
408C ASN* 2.9 40.5 + - - +
409C LYS* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 406 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C LYS 4.0 3.0 + - - -
405C ASN* 1.3 74.5 + - - +
407C GLU* 1.3 68.6 + - - +
409C LYS* 3.3 25.0 + - - +
410C MET* 3.0 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 407 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C ASN* 2.8 34.7 + - - +
406C ASN* 1.3 86.6 + - - +
408C ASN* 1.3 65.7 + - - +
410C MET* 3.5 6.4 + - - +
411C LEU* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 408 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TRP* 2.9 37.7 + - + +
182C VAL* 3.6 34.7 - - + +
402C LYS* 3.1 33.5 + - - +
405C ASN* 2.9 27.4 + - - +
407C GLU* 1.3 77.8 - - - +
409C LYS* 1.3 57.6 + - - +
411C LEU* 3.3 8.5 - - - +
412C LEU 3.0 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 409 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ILE* 4.0 39.9 + - + +
404C LYS* 5.8 0.4 - - - +
405C ASN 2.9 14.2 + - - +
406C ASN* 3.8 28.3 - - - +
407C GLU 3.2 0.4 - - - -
408C ASN* 1.3 77.1 - - - +
410C MET* 1.3 64.6 + - + +
412C LEU* 3.2 8.8 + - - +
413C LYS* 3.0 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 410 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C ASN* 3.0 36.3 + - - +
407C GLU* 4.5 5.2 - - - +
409C LYS* 1.3 78.6 - - + +
411C LEU* 1.3 61.1 + - - +
413C LYS* 3.7 9.2 - - + +
414C ARG* 2.8 69.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TRP* 3.7 21.3 - - + +
181C SER* 4.4 15.5 - - - -
182C VAL* 4.2 14.8 - - + -
407C GLU 3.1 15.4 + - - +
408C ASN* 3.3 13.0 - - - +
410C MET* 1.3 73.8 - - - +
412C LEU* 1.3 66.0 + - - +
414C ARG* 3.2 6.5 + - + +
415C MET* 3.0 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 412 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ASN* 4.4 13.2 - - - +
175C PHE* 4.5 6.7 - - + -
178C TRP* 3.3 52.7 - - + +
399C TYR* 4.6 4.0 - - + -
403C ILE* 3.8 24.0 - - + -
408C ASN 3.0 7.5 + - - +
409C LYS 3.2 7.6 + - - +
411C LEU* 1.3 74.3 - - - +
413C LYS* 1.3 83.4 + - + +
415C MET* 3.4 5.0 + - - +
416C GLN 3.0 33.5 + - - +
455C THR* 3.6 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 413 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ILE* 4.9 2.5 - - - +
409C LYS* 3.0 37.8 + - + +
410C MET* 3.8 10.3 - - + +
411C LEU 3.1 0.2 - - - -
412C LEU* 1.3 104.9 - - + +
414C ARG* 1.3 68.2 + - - +
416C GLN* 3.3 27.3 + - - +
455C THR* 3.6 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 414 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C MET* 2.8 63.2 + - - +
411C LEU* 3.8 7.9 - - + +
413C LYS* 1.3 81.8 - - - +
415C MET* 1.3 64.2 + - + +
416C GLN* 3.5 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 415 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C PHE* 4.7 6.2 - - - -
174C ASN* 2.9 35.2 - - - +
177C ASN* 3.7 33.4 - - + +
178C TRP* 3.7 28.0 - - + +
181C SER* 4.5 7.9 - - - +
214C LYS* 5.8 0.4 - - - -
411C LEU* 3.0 40.9 + - + +
412C LEU* 3.6 5.2 - - - +
414C ARG* 1.3 77.1 - - + +
416C GLN* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 416 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C PHE* 4.9 12.8 - - + -
171C TYR* 4.5 25.3 + - + -
174C ASN* 2.6 32.5 + - - -
412C LEU* 3.0 21.2 + - - +
413C LYS* 3.3 19.9 + - - +
414C ARG 3.2 6.6 - - - +
415C MET* 1.3 80.0 - - - +
455C THR* 5.6 3.6 - - - +
----------------------------------------------------------
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