Contacts of the strand formed by residues 402 - 406 (chain C) in PDB entry 4DVQ
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 LEU 402 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 5.0 7.6 - - + -
87C ARG 2.9 14.5 + - - +
88C MET* 3.3 26.4 - - + +
89C VAL 2.8 26.9 + - - +
111C MET* 4.4 21.5 - - + -
383C GLU* 3.6 42.6 - - + +
384C ARG 3.7 8.5 - - - +
385C VAL* 4.3 18.8 - - + +
400C GLY 3.9 2.0 + - - -
401C THR* 1.3 69.7 - - - +
403C VAL* 1.3 65.2 + - - +
404C GLN* 4.4 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 403 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C VAL* 3.3 11.0 - - + +
91C VAL* 4.2 16.6 - - + -
100C LEU* 3.7 39.7 - - + +
383C GLU* 3.3 4.2 - - - -
384C ARG 3.0 29.7 + - - +
386C VAL* 4.1 9.9 - - + -
390C LEU* 4.8 0.2 - - + -
392C LEU* 4.1 21.8 - - + -
397C ILE* 4.5 19.5 - - + -
401C THR* 4.0 11.4 - - + +
402C LEU* 1.3 72.6 - - - +
404C GLN* 1.3 63.2 + - - +
405C VAL 4.1 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 404 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C MET* 4.8 0.4 - - - +
88C MET* 3.7 31.8 - - + +
89C VAL 2.8 12.9 + - - +
90C CYS* 3.5 5.0 - - - +
91C VAL* 2.8 30.7 + - - +
239C PHE* 6.0 1.9 - - - -
381C PHE* 3.1 33.5 - - + -
382C LEU 3.4 11.2 - - - +
383C GLU* 3.9 13.4 - - + +
402C LEU* 3.9 11.4 + - + +
403C VAL* 1.3 74.2 - - - +
405C VAL* 1.3 61.0 + - - +
406C PHE* 3.1 34.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 405 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C VAL* 3.6 24.2 - - + +
92C MET* 4.8 2.9 - - - -
97C VAL* 3.7 33.4 - - + -
100C LEU* 3.8 25.1 - - + -
381C PHE* 3.0 7.4 - - - -
382C LEU* 2.8 54.1 + - + +
404C GLN* 1.3 73.6 - - - +
406C PHE* 1.3 62.1 + - - +
407C LEU* 3.5 20.1 + - + +
410C LEU* 4.2 6.7 - - + -
445C PHE* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 406 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 4.6 5.6 - - + -
65C HIS* 5.6 0.7 - - - -
68C MET* 3.4 50.7 - - + -
72C PHE* 4.0 18.4 - + + -
90C CYS* 4.0 10.3 - - + -
91C VAL 3.0 10.3 + - - -
92C MET* 3.9 6.6 - - - +
380C LEU* 3.7 26.9 - - + -
381C PHE* 3.5 30.7 - + + -
404C GLN* 3.1 41.1 - - + -
405C VAL* 1.3 72.8 - - - +
407C LEU* 1.3 60.5 + - - +
408C TYR* 3.4 3.4 - - + +
409C SER* 3.5 5.8 + - - +
410C LEU* 3.1 24.6 + - - +
----------------------------------------------------------
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