Contacts of the helix formed by residues 2537 - 2541 (chain C) in PDB entry 1DDX
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 ASN2537 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2228C VAL* 3.2 27.0 + - + +
2337C ILE* 4.2 4.2 - - - +
2341C ILE* 4.2 7.6 - - + -
2373C TYR* 3.9 3.7 - - - -
2533C GLY 4.1 12.0 + - - +
2534C LEU 3.7 16.5 + - - +
2535C MET 2.5 14.1 + - - +
2536C GLY* 1.3 75.8 - - - +
2538C PRO* 1.3 83.9 - - - +
2539C ILE* 2.7 49.2 + - - +
2540C CYS* 2.9 13.0 + - - +
3139D TRP* 3.7 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO2538 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2373C TYR 5.2 3.1 - - - +
2536C GLY 3.5 4.9 - - - +
2537C ASN* 1.3 86.2 - - - +
2539C ILE* 1.3 54.7 + - + +
2540C CYS 2.5 13.3 + - - -
2541C SER* 2.4 34.0 + - - +
2544C TYR* 4.3 13.2 - - + -
3127D PRO* 4.5 8.7 - - + -
3139D TRP* 3.3 36.1 - - + -
3142D PHE* 3.5 42.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2539 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2334C LEU* 4.9 15.5 - - + +
2337C ILE* 3.9 20.0 - - + -
2338C GLY* 4.2 18.8 - - - +
2341C ILE* 5.5 1.6 - - + -
2361C PHE* 5.1 2.9 - - + -
2537C ASN* 2.7 29.6 + - - +
2538C PRO* 1.3 75.1 - - + +
2540C CYS* 1.3 68.5 + - - +
2541C SER 3.3 1.8 - - - -
2544C TYR* 3.8 27.5 - - + +
2545C TRP* 3.3 41.4 + - + -
2550C PHE* 3.8 20.6 - - + -
3139D TRP* 4.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS2540 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2341C ILE* 4.4 2.7 - - - -
2361C PHE* 3.7 35.4 - - - -
2363C PRO* 3.1 29.7 - - + +
2367C PHE* 3.6 1.8 - - - -
2373C TYR* 2.8 23.6 + - + -
2534C LEU 3.7 14.1 - - - -
2535C MET* 3.0 32.8 - - + +
2537C ASN* 2.9 5.8 + - - +
2538C PRO 2.5 8.1 + - - -
2539C ILE* 1.3 84.0 - - - +
2541C SER* 1.3 56.0 + - - -
2545C TRP* 4.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2541 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2367C PHE* 3.9 1.6 - - - -
2373C TYR* 3.4 20.5 - - - -
2538C PRO 2.4 28.1 + - - -
2540C CYS* 1.3 73.7 - - - +
2542C PRO* 1.3 73.5 - - - +
2543C GLN* 3.2 14.8 + - - -
2544C TYR* 3.1 23.7 + - - +
2545C TRP* 3.1 19.8 + - - +
3127D PRO* 3.5 14.1 - - - +
----------------------------------------------------------
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