Contacts of the helix formed by residues 410 - 418 (chain A) 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 ASN 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A PRO* 3.2 8.0 - - - +
406A GLN 3.5 7.3 + - - +
407A PHE 2.8 15.3 + - - +
408A LEU 2.9 1.1 + - - +
409A TYR* 1.3 78.9 - - - +
411A ASN* 1.3 55.0 + - - +
412A SER* 2.9 22.4 - - - +
413A ILE* 2.9 35.2 + - + +
681A NAG 1.5 71.4 + - - +
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Residues in contact with ASN 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A TYR* 3.9 8.2 + - - -
283A LEU* 4.7 18.2 - - + +
285A PHE* 4.7 8.4 - - + -
293A GLY* 2.9 30.2 + - - +
295A VAL 4.0 0.6 - - - -
296A PRO* 3.4 31.6 - - - +
299A MET* 3.5 30.4 - - + +
409A TYR 3.5 4.3 + - - +
410A ASN* 1.3 68.6 - - - +
412A SER* 1.3 66.4 + - - +
413A ILE 2.9 2.0 - - - -
414A LEU* 2.9 20.3 + - + +
415A LEU* 2.9 15.2 + - + +
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Residues in contact with SER 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.9 29.1 - - - +
410A ASN* 2.9 15.9 - - - -
411A ASN* 1.3 77.3 - - - +
413A ILE* 1.3 50.9 + - - +
415A LEU* 3.3 9.5 + - - +
416A GLU* 2.7 38.5 + - - +
681A NAG 3.9 18.5 - - - -
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Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A PRO* 4.5 1.3 - - + -
397A ILE* 4.6 2.9 - - + -
402A TYR* 4.2 34.8 - - + +
406A GLN 4.3 0.9 - - - +
407A PHE* 3.3 42.8 - - + +
410A ASN* 2.9 48.3 + - + +
411A ASN 2.9 0.2 - - - -
412A SER* 1.3 74.9 - - - +
414A LEU* 1.3 65.9 + - - +
416A GLU* 2.8 24.1 + - - +
417A HIS* 3.1 9.7 + - - +
422A PHE* 3.6 21.4 - - + -
681A NAG 4.0 13.9 + - - +
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A TYR* 4.1 11.7 + - + -
285A PHE* 5.5 1.8 - - + -
296A PRO* 3.9 6.0 - - + +
299A MET* 3.6 23.8 - - + +
300A MET* 3.5 32.1 - - + +
303A THR* 4.5 2.9 - - - +
410A ASN 4.1 0.4 + - - -
411A ASN* 2.9 20.7 + - + +
413A ILE* 1.3 75.8 - - - +
415A LEU* 1.3 64.0 + - + +
418A GLY* 2.9 24.1 + - - -
419A LEU* 3.2 31.4 - - + +
422A PHE* 3.0 38.2 - - + -
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Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ILE* 4.3 31.4 - - + -
262A TYR* 3.6 44.8 + - + +
282A ASN* 5.4 1.8 - - - +
283A LEU* 3.7 27.6 - - + -
285A PHE* 4.8 8.7 - - + -
411A ASN* 2.9 12.5 + - + +
412A SER* 3.5 10.3 - - - +
414A LEU* 1.3 77.7 - - + +
416A GLU* 1.3 65.8 + - - +
417A HIS 4.4 0.2 - - - -
418A GLY* 3.9 5.5 + - - -
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A TYR* 4.5 0.7 + - - -
412A SER* 2.7 17.5 + - - +
413A ILE* 2.8 14.4 + - - +
415A LEU* 1.3 74.2 - - - +
417A HIS* 1.3 80.4 + - - +
681A NAG 3.3 27.8 + - - -
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Residues in contact with HIS 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A ILE* 3.2 46.6 + - + +
398A GLU* 3.4 23.8 + - - +
400A GLN* 4.2 9.5 - - + +
402A TYR* 2.8 31.2 + + - -
413A ILE* 3.1 9.3 + - + +
416A GLU* 1.3 100.7 - - + +
418A GLY* 1.3 62.4 + - - +
420A THR* 5.6 0.2 + - - -
421A GLN* 3.9 18.7 + - + +
422A PHE* 4.2 9.4 - + + -
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Residues in contact with GLY 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A GLU* 6.1 2.0 - - - -
262A TYR* 4.0 8.3 - - - -
414A LEU 2.9 17.6 + - - -
415A LEU 3.9 3.3 + - - -
416A GLU 3.6 1.2 - - - -
417A HIS* 1.3 79.9 - - - +
419A LEU* 1.3 66.4 + - - -
420A THR* 3.3 5.3 + - - -
421A GLN 3.4 1.5 + - - -
422A PHE* 3.2 24.3 + - - -
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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