Contacts of the helix formed by residues 2485 - 2496 (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 LYS2485 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2479C GLU* 3.0 39.4 + - + +
2483C GLY 4.5 3.4 - - - +
2484C GLU* 1.3 76.7 - - - +
2486C GLU* 1.3 71.8 + - - +
2488C ALA* 4.0 0.7 - - - -
2489C ALA* 3.0 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2486 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2438C ARG* 3.4 33.1 + - - +
2484C GLU* 3.0 12.7 + - + +
2485C LYS* 1.3 83.8 - - - +
2487C MET* 1.3 66.6 + - + +
2489C ALA* 2.9 3.8 + - - +
2490C GLU* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2487 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2181C VAL* 3.4 17.3 - - + -
2436C GLY 3.6 20.6 - - - +
2437C GLY* 4.1 10.1 - - - -
2438C ARG* 3.2 51.1 - - - +
2482C THR* 3.6 16.6 - - + +
2484C GLU* 2.6 44.2 + - + +
2486C GLU* 1.3 71.6 + - - +
2488C ALA* 1.3 53.3 + - - +
2490C GLU* 2.7 13.7 + - - +
2491C LEU* 2.6 38.7 + - - +
2509C VAL* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2488 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2478C PHE* 3.8 11.9 - - + +
2479C GLU* 3.5 25.6 - - + +
2482C THR* 3.4 23.0 + - - +
2484C GLU* 2.8 24.5 + - - +
2485C LYS* 3.6 5.4 - - - +
2487C MET* 1.3 70.5 - - - +
2489C ALA* 1.3 54.6 + - - +
2491C LEU* 2.8 9.4 + - - +
2492C LYS* 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2479C GLU* 5.3 2.2 + - - +
2485C LYS* 3.0 15.7 + - + +
2486C GLU* 2.9 3.9 + - - +
2488C ALA* 1.3 79.2 - - - +
2490C GLU* 1.3 63.4 + - - +
2492C LYS* 3.3 9.6 + - - +
2493C ALA* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2180C LYS* 2.9 67.2 + - + +
2181C VAL* 4.2 3.6 - - + -
2438C ARG* 4.5 3.1 + - - +
2486C GLU* 2.9 18.9 + - - +
2487C MET* 2.7 20.1 + - - +
2489C ALA* 1.3 71.9 - - - +
2491C LEU* 1.3 55.6 + - - +
2493C ALA* 3.0 23.8 - - - +
2494C LEU* 3.6 8.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2491 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2177C VAL* 4.1 7.2 - - + -
2181C VAL* 4.0 26.9 - - + -
2478C PHE* 3.4 20.6 - - + -
2481C LEU* 5.2 5.8 - - + -
2482C THR* 5.2 1.1 - - + +
2487C MET 2.6 22.7 + - - +
2488C ALA* 2.8 9.3 + - - +
2490C GLU* 1.3 70.2 - - - +
2492C LYS* 1.3 53.4 + - - +
2493C ALA 2.7 5.1 + - - -
2494C LEU* 2.5 32.3 + - + +
2495C TYR* 2.8 40.9 + - + -
2501C MET* 4.2 15.7 - - + -
2509C VAL* 3.9 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2492 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2477C SER* 6.3 1.2 - - - -
2478C PHE* 3.7 27.5 - - + -
2488C ALA 2.7 17.9 + - - +
2489C ALA* 3.6 11.0 - - - +
2491C LEU* 1.3 72.0 - - - +
2493C ALA* 1.3 62.6 + - - +
2496C SER* 3.1 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2493 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2489C ALA 3.1 11.3 + - - +
2490C GLU* 3.0 23.1 - - - +
2491C LEU 2.7 0.4 + - - -
2492C LYS* 1.3 82.4 - - - +
2494C LEU* 1.3 61.8 + - + +
2496C SER* 4.3 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2494 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2172C PRO* 3.7 36.0 - - + +
2173C ASP 5.1 0.7 - - - +
2176C GLU* 4.2 24.7 - - + +
2177C VAL* 4.0 34.8 - - + +
2180C LYS* 4.2 19.5 - - + -
2490C GLU* 4.0 15.0 - - + +
2491C LEU* 2.5 19.4 + - + +
2493C ALA* 1.3 79.3 - - + +
2495C TYR* 1.3 68.0 + - + +
2496C SER* 4.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR2495 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2167C GLY* 5.8 1.4 - - - -
2168C ASN* 5.3 3.1 + - - -
2171C LEU* 3.9 4.3 - - + -
2172C PRO* 3.3 29.8 - - + -
2177C VAL* 4.0 14.7 - - + +
2452C ILE* 5.3 0.3 - - - +
2456C ARG* 3.6 10.0 + - - -
2478C PHE* 3.5 19.1 - - + -
2491C LEU* 2.8 28.4 + - + -
2494C LEU* 1.3 79.2 - - + +
2496C SER* 1.3 65.8 + - - +
2497C ASP* 2.7 22.0 + - - +
2500C VAL* 2.8 39.1 - - + +
2501C MET* 3.4 23.3 - - - -
2502C GLU* 3.3 39.3 + - + +
2505C PRO* 3.9 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2496 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2168C ASN* 4.5 13.7 + - - -
2478C PHE* 3.3 7.8 - - - -
2492C LYS* 3.1 49.6 + - - +
2493C ALA 4.3 5.7 + - - -
2494C LEU 4.3 4.3 + - - -
2495C TYR* 1.3 81.5 + - - +
2497C ASP* 1.3 59.0 + - - -
2498C ILE 3.4 0.5 + - - -
----------------------------------------------------------
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