Contacts of the helix formed by residues 411 - 417 (chain C) in PDB entry 6V99
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 THR 411 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLU* 3.7 31.0 + - + +
32C ARG* 6.2 2.0 - - - +
378C ASP* 4.0 20.1 - - - +
381C VAL* 3.7 6.5 - - - -
409C LEU* 4.5 6.8 - - - +
410C ILE* 1.3 75.1 - - - +
412C GLN* 1.3 69.1 + - + +
413C SER* 3.8 18.6 - - - +
414C MET* 3.1 24.6 + - - +
415C ILE* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 412 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C ASP* 5.0 0.8 + - - +
379C HIS 5.8 1.3 - - - +
380C GLY 4.1 4.0 - - - +
381C VAL* 3.4 18.2 - - + +
382C VAL* 2.9 38.9 + - - +
411C THR* 1.3 77.7 - - + +
413C SER* 1.3 52.2 + - - +
415C ILE* 3.0 20.6 + - - +
416C ASP* 2.7 71.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 413 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ARG* 4.5 14.2 + - - -
411C THR* 3.2 14.2 - - - +
412C GLN* 1.3 78.6 - - - +
414C MET* 1.3 63.0 + - - +
416C ASP* 3.4 10.7 + - - +
417C LYS* 3.3 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 414 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLU* 4.9 10.1 - - - +
399C ARG 3.8 17.3 - - - +
400C PHE* 3.1 31.6 - - + -
401C ARG* 3.9 15.9 - - - -
409C LEU 2.9 28.0 - - - +
410C ILE* 3.3 13.2 - - - -
411C THR* 3.1 26.0 + - - +
413C SER* 1.3 76.2 - - - +
415C ILE* 1.3 66.0 + - - +
417C LYS* 3.2 20.7 + - + +
418C LEU* 3.5 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 415 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C VAL* 4.1 14.4 - - + -
382C VAL 3.7 18.8 - - - +
383C ILE* 4.2 4.7 - - + -
384C PRO* 3.8 19.7 - - + -
387C LEU* 4.0 16.6 - - + -
400C PHE* 3.8 15.0 - - + -
410C ILE* 3.8 23.1 - - + -
411C THR 3.1 13.3 + - - +
412C GLN* 3.0 18.7 + - - +
414C MET* 1.3 74.4 - - - +
416C ASP* 1.3 65.8 + - - +
418C LEU* 2.9 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 416 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C GLN* 2.7 54.0 + - - +
413C SER* 3.7 10.3 - - - +
414C MET 3.3 0.4 - - - -
415C ILE* 1.3 73.1 - - - +
417C LYS* 1.3 60.1 + - + +
418C LEU 3.2 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 417 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C SER* 3.3 23.3 + - - +
414C MET* 3.2 13.8 + - + +
415C ILE 3.0 1.6 + - - -
416C ASP* 1.3 77.1 - - + +
418C LEU* 1.3 62.4 + - + +
419C ASP 4.0 0.3 + - - -
420C LEU 5.7 0.9 - - - -
----------------------------------------------------------
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