Contacts of the helix formed by residues 2477 - 2483 (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 SER2477 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2475C TYR* 3.3 2.8 + - - +
2476C THR* 1.3 86.8 + - - +
2478C PHE* 1.3 61.6 - - - +
2479C GLU* 3.2 12.3 + - - +
2480C GLU* 2.8 38.4 + - - +
2481C LEU* 3.2 4.7 + - - +
2492C LYS* 6.3 1.6 - - - -
2498C ILE* 3.7 12.1 - - - +
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Residues in contact with PHE2478 (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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2477C SER* 1.3 73.4 - - - +
2479C GLU* 1.3 55.4 - - - +
2481C LEU* 3.1 9.7 + - + +
2482C THR* 2.4 34.5 + - - -
2488C ALA* 3.7 20.0 - - + +
2491C LEU* 3.4 28.0 - - + +
2492C LYS* 3.7 34.1 - - + -
2495C TYR* 3.5 37.0 - + + -
2496C SER 3.3 25.1 - - - -
2498C ILE* 3.4 41.5 - - + +
2501C MET* 4.5 10.5 - - + -
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Residues in contact with GLU2479 (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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2477C SER* 3.0 11.1 + - - +
2478C PHE* 1.3 80.5 - - - +
2480C GLU* 1.3 52.3 + - - +
2482C THR* 3.9 0.2 - - - -
2483C GLY* 2.5 44.3 + - - +
2484C GLU 3.7 12.3 - - - +
2485C LYS* 3.0 53.6 + - + +
2488C ALA* 3.5 12.2 - - + +
2489C ALA* 5.3 1.7 + - - +
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Residues in contact with GLU2480 (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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2474C PRO 4.9 1.5 - - - +
2475C TYR* 3.5 27.8 - - + -
2476C THR* 2.8 46.9 + - - +
2477C SER* 2.8 20.5 + - - +
2479C GLU* 1.3 77.0 - - - +
2481C LEU* 1.3 65.2 + - - +
2482C THR 3.2 0.9 + - - -
2483C GLY* 3.8 4.4 + - - -
2511C LYS* 4.2 10.6 - - - +
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Residues in contact with LEU2481 (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* 4.9 1.1 - - + -
2475C TYR* 3.4 34.7 - - + -
2477C SER 3.2 4.8 + - - +
2478C PHE* 3.1 13.8 + - + +
2480C GLU* 1.3 80.1 - - - +
2482C THR* 1.3 53.9 + - + +
2491C LEU* 5.2 11.0 - - + -
2498C ILE* 4.8 7.0 - - + -
2501C MET* 4.0 19.1 - - + -
2506C ALA* 3.3 49.8 - - + +
2509C VAL* 5.1 1.8 - - + -
2510C GLU* 3.2 20.7 - - + +
2511C LYS* 2.5 33.4 + - - +
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Residues in contact with THR2482 (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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2478C PHE 2.4 24.6 + - - -
2481C LEU* 1.3 78.8 - - + +
2483C GLY* 1.3 56.8 + - - +
2484C GLU* 2.9 24.0 + - - +
2487C MET* 3.6 20.1 - - + +
2488C ALA* 3.4 15.9 - - - +
2491C LEU* 5.2 1.0 - - + +
2509C VAL* 3.2 45.3 - - + +
2511C LYS* 3.0 25.2 - - - +
2512C PRO* 5.4 0.2 - - - +
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Residues in contact with GLY2483 (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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2479C GLU* 2.5 31.9 + - - +
2480C GLU* 3.8 3.7 + - - -
2482C THR* 1.3 71.0 - - - +
2484C GLU* 1.3 62.5 + - - +
2485C LYS* 3.7 3.5 + - - +
2511C LYS* 4.1 13.7 - - - -
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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