Contacts of the helix formed by residues 413 - 420 (chain A) in PDB entry 1RDT
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 GLY 413 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A GLN* 3.2 1.6 + - - +
412A PRO* 1.3 77.6 - - - +
414A ARG* 1.3 64.5 + - - +
415A PHE 3.2 2.2 - - - -
416A ALA* 3.4 12.0 + - - +
417A LYS* 3.0 24.0 + - - +
411D ASP* 4.2 20.1 + - - +
414D LEU* 5.5 3.1 - - - +
415D GLN* 5.5 7.4 - - - +
418D GLU* 5.8 1.8 - - - -
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Residues in contact with ARG 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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360A MET* 2.8 49.2 + - + +
361A GLN 3.1 12.9 + - - -
362A MET* 3.4 3.6 - - - +
366A GLU* 2.6 41.1 + - - +
404A CYS* 4.6 9.6 - - + -
408A TYR* 3.1 47.7 + - + -
411A GLN* 3.2 45.5 + - + +
412A PRO 3.4 0.4 - - - -
413A GLY* 1.3 77.7 - - - +
415A PHE* 1.3 63.1 + - - +
417A LYS* 3.2 9.1 + - + +
418A LEU* 2.9 27.5 + - + +
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Residues in contact with PHE 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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397A TYR* 3.7 28.5 - - - -
400A LEU* 4.0 23.8 - - + -
401A GLU* 3.7 44.6 - - + -
404A CYS* 4.3 18.5 - - + +
405A LYS* 6.5 0.7 - - + -
412A PRO 4.4 7.3 + - - +
413A GLY 3.2 0.4 - - - -
414A ARG* 1.3 77.8 - - - +
416A ALA* 1.3 63.1 + - - +
418A LEU* 3.2 6.8 + - - +
419A LEU* 3.1 47.2 + - + +
418D GLU* 6.5 0.2 - - - -
430D GLN* 4.3 4.0 - - - -
432D PHE* 4.7 18.2 - + + -
433D ALA* 4.2 16.8 - - + -
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Residues in contact with ALA 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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413A GLY* 3.4 12.6 + - - +
414A ARG 3.3 0.4 - - - -
415A PHE* 1.3 79.8 - - - +
417A LYS* 1.3 58.8 + - - +
419A LEU* 3.1 4.9 + - - +
420A LEU* 2.9 34.5 + - - +
414D LEU* 3.9 22.0 - - + -
418D GLU* 5.8 0.2 - - - +
432D PHE* 4.0 18.4 - - + -
436D LEU* 3.8 25.6 - - + -
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Residues in contact with LYS 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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356A LYS* 5.6 4.0 + - - +
359A ASP* 6.3 0.6 - - - +
360A MET* 3.9 34.4 - - + +
413A GLY 3.0 15.2 + - - +
414A ARG* 3.4 11.4 - - - +
416A ALA* 1.3 76.2 - - - +
418A LEU* 1.3 61.5 + - - +
420A LEU* 3.5 16.0 + - + +
421A ARG* 3.6 29.2 + - - +
407D GLU* 3.5 37.3 + - - -
411D ASP* 6.1 1.3 - - - +
414D LEU* 5.1 1.3 - - - +
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Residues in contact with LEU 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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360A MET* 3.6 21.8 - - + -
362A MET* 4.1 19.7 - - + -
366A GLU* 3.9 27.8 - - + +
370A LEU* 3.4 24.0 - - + +
400A LEU* 3.8 24.5 - - + -
404A CYS* 3.4 33.7 - - - -
414A ARG* 2.9 16.1 + - + +
415A PHE* 3.3 7.4 - - - +
416A ALA 3.1 0.2 - - - -
417A LYS* 1.3 74.5 - - - +
419A LEU* 1.3 65.4 + - - +
420A LEU 3.0 1.1 - - - -
421A ARG* 3.0 23.9 + - - +
422A LEU 4.2 0.2 + - - -
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Residues in contact with LEU 419 (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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370A LEU* 4.3 9.9 - - + -
373A ILE* 4.0 25.8 - - + -
397A TYR* 4.1 12.3 - - + -
400A LEU* 4.9 1.8 - - + -
415A PHE* 3.1 45.5 + - + +
416A ALA 3.1 7.7 + - - +
418A LEU* 1.3 79.8 - - + +
420A LEU* 1.3 61.0 + - - +
421A ARG 3.1 3.8 + - - -
422A LEU* 3.5 24.3 + - + +
423A PRO* 3.6 6.4 - - - +
432D PHE* 5.9 0.2 - - + -
433D ALA* 3.9 26.9 - - + +
436D LEU* 4.2 27.2 - - + +
437D GLN* 5.6 3.2 - - - +
440D THR* 4.8 1.9 - - - +
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Residues in contact with LEU 420 (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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416A ALA 2.9 17.7 + - - +
417A LYS* 3.8 12.1 - - + +
418A LEU 3.0 0.8 - - - -
419A LEU* 1.3 80.5 - - - +
421A ARG* 1.3 78.2 + - - +
422A LEU 3.3 1.3 - - - -
423A PRO* 3.4 19.1 - - + +
424A ALA 5.1 0.2 + - - -
390D VAL* 4.9 0.4 - - + -
396D ASP* 4.7 5.4 - - - +
410D GLN* 3.6 32.1 - - - +
414D LEU* 3.7 29.8 - - + -
436D LEU* 4.6 14.1 - - + +
439D MET* 3.4 35.9 - - + -
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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