Contacts of the helix formed by residues 2462 - 2470 (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 SER2462 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2163C MET* 3.5 27.1 + - - +
2461C GLN* 1.3 79.5 - - - +
2463C LEU* 1.3 57.5 + - - +
2464C ASN* 3.0 19.9 + - - +
2465C GLU* 3.0 37.0 + - - +
2466C TYR* 3.0 14.7 + - - -
2499C ASP* 3.4 23.0 + - - +
2501C MET 4.1 2.5 - - - -
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Residues in contact with LEU2463 (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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2461C GLN 3.8 1.6 + - - -
2462C SER* 1.3 72.4 + - - +
2464C ASN* 1.3 64.7 + - - +
2466C TYR* 3.5 3.9 + - - +
2467C ARG* 2.9 43.2 + - + +
2475C TYR* 4.2 16.8 - - + -
2481C LEU* 4.9 2.2 - - + -
2498C ILE* 5.7 1.1 - - + +
2501C MET* 2.9 33.0 + - + +
2502C GLU 3.7 1.3 - - - -
2503C LEU* 3.3 47.0 - - + +
2506C ALA* 3.1 33.2 - - + -
2521C THR* 4.3 15.0 - - + +
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Residues in contact with ASN2464 (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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2462C SER* 3.0 9.7 + - - +
2463C LEU* 1.3 81.1 - - - +
2465C GLU* 1.3 60.5 + - - +
2467C ARG* 3.2 8.6 - - - +
2468C LYS* 2.7 40.3 + - + +
2474C PRO* 2.9 16.8 - - + +
2475C TYR* 2.7 44.8 + - - +
2498C ILE* 3.7 4.0 - - - +
2499C ASP* 3.0 44.3 + - + +
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Residues in contact with GLU2465 (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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2038C SER 5.0 0.2 - - - +
2039C ASN* 3.2 30.6 - - - +
2152C LEU* 3.8 6.6 - - + +
2163C MET 5.7 0.9 - - - +
2166C LYS* 6.1 0.7 - - - -
2461C GLN* 3.2 26.7 - - + +
2462C SER* 3.0 36.2 + - - +
2464C ASN* 1.3 74.2 - - - +
2466C TYR* 1.3 52.2 + - - +
2467C ARG 2.9 3.9 + - - -
2468C LYS* 2.7 44.9 + - - +
2469C ARG* 2.7 35.3 + - - +
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Residues in contact with TYR2466 (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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2150C ARG* 3.3 13.7 + - - -
2151C ALA* 4.7 4.9 - - + -
2152C LEU* 3.3 29.7 + - + +
2380C GLU* 2.7 44.5 + - + -
2460C TYR* 3.2 23.2 - + - -
2461C GLN* 3.1 40.1 + - + +
2462C SER 3.0 23.4 + - - +
2463C LEU 4.0 4.3 - - - +
2465C GLU* 1.3 79.2 - - - +
2467C ARG* 1.3 61.7 + - - +
2469C ARG* 3.8 3.1 - - - -
2470C PHE* 3.4 25.5 + + - -
2503C LEU* 4.0 27.8 - - + -
2525C LEU* 3.9 14.7 - - + +
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Residues in contact with ARG2467 (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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2463C LEU* 2.9 25.7 + - + +
2464C ASN* 3.2 13.9 - - - +
2466C TYR* 1.3 76.4 - - - +
2468C LYS* 1.3 67.4 + - - +
2470C PHE 3.0 8.8 + - - -
2472C LEU* 2.9 46.3 + - + +
2473C LYS* 2.6 32.1 + - - +
2474C PRO* 3.6 3.4 - - + +
2475C TYR* 3.6 48.7 - - - +
2520C GLU* 2.4 44.2 + - - -
2521C THR* 2.4 37.7 + - + +
2525C LEU* 5.6 0.2 - - - -
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Residues in contact with LYS2468 (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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2039C ASN 4.5 3.2 + - - -
2042C GLN* 3.3 40.6 + - - +
2464C ASN* 2.7 19.6 + - - +
2465C GLU* 2.7 38.4 + - - +
2467C ARG* 1.3 71.4 - - - +
2469C ARG* 1.3 55.6 + - - +
2471C SER* 2.7 28.9 + - - -
2472C LEU 3.5 9.6 + - - +
2474C PRO* 4.3 24.7 - - + -
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Residues in contact with ARG2469 (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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2044C ARG* 3.2 53.5 - - - +
2123C LEU* 2.6 37.7 + - - +
2124C ILE* 4.2 6.1 - - - +
2125C ASP* 4.4 4.6 + - - +
2151C ALA* 2.6 35.5 + - - +
2152C LEU* 3.6 28.1 - - + +
2465C GLU 2.7 19.8 + - - +
2466C TYR* 3.5 13.2 - - - +
2468C LYS* 1.3 72.2 - - - +
2470C PHE* 1.3 85.3 + - + +
2471C SER* 2.9 6.9 + - - -
2529C PHE* 6.2 0.2 - - - -
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Residues in contact with PHE2470 (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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2123C LEU* 3.5 29.2 - - + +
2124C ILE* 5.0 2.2 - - + -
2151C ALA* 4.3 10.8 - - + -
2466C TYR* 3.4 11.2 - + - -
2467C ARG 3.0 7.5 + - - +
2469C ARG* 1.3 102.6 - - + +
2471C SER* 1.3 75.5 + - - +
2472C LEU* 3.2 16.2 + - + +
2524C GLU* 3.1 24.0 - - - +
2525C LEU* 3.1 41.7 - - + -
2528C PRO* 3.8 18.6 - - + -
2529C PHE* 3.8 30.1 - + - -
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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