Contacts of the helix formed by residues 2444 - 2458 (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 VAL2444 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2388C HIS* 3.5 42.2 - - + +
2391C LEU* 3.3 34.5 - - + -
2404C PHE* 4.0 9.0 - - + -
2440C VAL* 3.6 11.9 - - + -
2441C PRO* 3.4 15.4 + - + +
2442C ILE 3.1 0.4 - - - -
2443C ALA* 1.3 75.8 - - - +
2445C GLN* 1.3 68.1 + - - +
2446C ALA 3.4 1.3 - - - -
2447C VAL* 3.0 23.5 + - + -
2448C ALA* 3.2 2.5 + - - +
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Residues in contact with GLN2445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2175C LYS* 5.9 2.4 - - - +
2178C LEU* 4.1 22.8 - - + +
2179C GLU* 5.3 4.7 - - - +
2183C LEU* 3.3 34.8 - - + +
2440C VAL* 5.3 0.7 - - - -
2441C PRO 3.4 5.7 + - - -
2442C ILE* 2.8 29.7 + - + +
2443C ALA 3.0 2.3 - - - +
2444C VAL* 1.3 78.3 - - - +
2446C ALA* 1.3 67.8 + - - +
2447C VAL 3.1 0.2 + - - -
2448C ALA* 3.3 4.3 + - - +
2449C LYS* 3.2 17.7 + - - +
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Residues in contact with ALA2446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2443C ALA 4.4 4.6 + - - +
2444C VAL 3.2 1.3 + - - -
2445C GLN* 1.3 79.6 - - - +
2447C VAL* 1.3 69.2 + - + +
2449C LYS* 3.2 8.9 + - - +
2450C ALA* 3.0 17.9 + - - +
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Residues in contact with VAL2447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2386C HIS* 5.8 0.2 - - + -
2388C HIS* 2.9 38.4 - - + +
2444C VAL* 3.0 19.6 + - + +
2446C ALA* 1.3 78.9 - - + +
2448C ALA* 1.3 54.3 + - - +
2450C ALA* 2.6 34.4 + - + +
2451C SER* 2.9 13.2 + - - +
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Residues in contact with ALA2448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2178C LEU* 4.5 10.3 - - + -
2182C LEU* 5.1 4.7 - - + -
2388C HIS* 3.7 20.2 - - + +
2440C VAL* 3.8 25.6 - - + -
2444C VAL 3.2 3.0 + - - +
2445C GLN 3.8 6.1 - - - +
2447C VAL* 1.3 80.2 - - - +
2449C LYS* 1.3 60.3 + - - +
2451C SER* 3.2 22.9 - - - -
2452C ILE* 2.8 18.9 - - - +
2504C TYR* 3.6 7.3 - - + +
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Residues in contact with LYS2449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2173C ASP* 5.5 1.5 + - - -
2174C SER* 2.8 32.5 + - - +
2175C LYS* 3.9 18.4 - - - +
2178C LEU* 4.1 20.6 - - + +
2445C GLN 3.2 10.8 + - - +
2446C ALA* 3.3 12.6 - - - +
2447C VAL 2.7 4.6 + - - -
2448C ALA* 1.3 71.2 - - - +
2450C ALA* 1.3 55.6 + - - +
2452C ILE* 2.6 35.1 + - - +
2453C ASP* 2.8 32.2 + - - +
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Residues in contact with ALA2450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2446C ALA 3.0 7.4 + - - +
2447C VAL* 2.6 17.2 + - - +
2449C LYS* 1.3 73.1 - - - +
2451C SER* 1.3 55.1 + - - +
2452C ILE 2.5 14.4 + - - -
2453C ASP* 2.6 27.3 + - - +
2454C GLN* 2.7 31.5 + - + +
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Residues in contact with SER2451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2383C THR* 4.2 6.1 - - - +
2386C HIS* 3.4 29.2 - - - -
2388C HIS* 3.5 8.0 - - - -
2447C VAL* 2.9 16.8 + - - +
2448C ALA* 3.2 18.8 - - - -
2450C ALA* 1.3 74.6 - - - +
2452C ILE* 1.3 47.9 + - - +
2454C GLN* 3.9 10.6 - - - +
2455C SER* 2.6 30.3 + - - -
2504C TYR* 3.2 24.7 - - - -
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Residues in contact with ILE2452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2174C SER* 4.3 20.2 - - - +
2177C VAL* 5.8 4.9 - - + -
2178C LEU* 4.7 4.9 - - + +
2182C LEU* 4.1 21.5 - - + -
2448C ALA 2.8 25.6 - - - +
2449C LYS* 2.6 21.6 + - + +
2450C ALA 2.5 4.2 + - - -
2451C SER* 1.3 69.4 - - - +
2453C ASP* 1.3 70.2 + - - +
2454C GLN 3.1 1.4 + - - -
2455C SER* 3.1 14.6 + - - -
2456C ARG* 3.2 27.7 + - - +
2495C TYR* 5.3 0.4 - - - +
2502C GLU* 3.1 27.3 - - - +
2504C TYR* 3.7 18.2 - - + -
2505C PRO* 4.5 10.3 - - + -
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Residues in contact with ASP2453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2174C SER* 2.9 26.3 + - - -
2449C LYS* 2.8 30.3 + - - +
2450C ALA* 2.6 31.2 + - - +
2452C ILE* 1.3 70.5 - - - +
2454C GLN* 1.3 59.9 - - + +
2456C ARG* 2.8 33.8 - - - +
2457C GLU* 3.0 13.6 + - + +
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Residues in contact with GLN2454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2212C THR* 6.3 0.8 - - - +
2214C HIS* 4.9 16.2 + - - -
2218C PRO* 3.8 23.5 - - + +
2382C ASN* 5.9 0.4 + - - -
2386C HIS* 4.8 10.9 + - - -
2450C ALA* 2.7 38.0 + - + +
2451C SER* 3.9 13.7 - - - +
2453C ASP* 1.3 66.5 - - + +
2455C SER* 1.3 56.2 + - - +
2456C ARG 2.5 5.6 + - - -
2457C GLU* 2.4 52.3 + - - +
2458C MET* 2.9 16.6 + - + +
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Residues in contact with SER2455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2383C THR* 4.5 5.8 - - - +
2451C SER 2.6 22.0 + - - -
2452C ILE* 3.1 9.0 + - - -
2454C GLN* 1.3 75.9 - - - +
2456C ARG* 1.3 57.1 + - - +
2458C MET* 3.3 3.1 - - - -
2459C LYS 3.3 2.6 + - - -
2460C TYR* 2.7 72.6 + - - +
2502C GLU* 5.4 3.3 + - - -
2504C TYR* 4.5 10.2 - - - +
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Residues in contact with ARG2456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2162C PRO* 6.4 0.9 - - + -
2163C MET* 6.0 6.5 - - + -
2171C LEU* 3.2 29.5 + - + +
2172C PRO* 2.8 31.6 + - - +
2173C ASP* 4.8 0.8 - - - +
2174C SER* 4.6 7.7 - - - +
2177C VAL* 4.7 3.6 - - - +
2452C ILE* 3.2 30.0 + - - +
2453C ASP* 2.8 17.2 + - - +
2454C GLN 2.5 4.8 + - - -
2455C SER* 1.3 73.1 - - - +
2457C GLU* 1.3 55.7 + - - +
2459C LYS* 2.7 33.7 + - - +
2460C TYR* 4.8 1.3 - - - +
2495C TYR* 3.6 11.3 + - - -
2502C GLU* 2.4 50.9 + - - +
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Residues in contact with GLU2457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2218C PRO* 3.7 20.2 - - + +
2453C ASP* 3.0 14.7 + - + +
2454C GLN* 2.4 53.9 + - - +
2456C ARG* 1.3 69.2 - - - +
2458C MET* 1.3 53.2 + - + +
2459C LYS* 2.6 33.2 + - - +
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Residues in contact with MET2458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2132C VAL* 4.4 16.8 - - + -
2148C TYR* 5.3 0.4 - - + -
2150C ARG* 2.7 33.1 + - - +
2154C PRO* 4.1 3.0 - - - +
2218C PRO* 2.9 58.6 - - + +
2219C GLY* 2.9 12.3 - - - +
2379C SER* 3.1 26.5 - - - +
2382C ASN* 6.1 1.3 - - - +
2383C THR* 5.6 0.7 - - - -
2454C GLN* 2.9 12.8 + - + +
2455C SER* 3.8 5.8 - - - +
2457C GLU* 1.3 72.4 - - - +
2459C LYS* 1.3 69.3 + - - +
2460C TYR* 2.6 25.9 + - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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