Contacts of the helix formed by residues 407 - 420 (chain A) in PDB entry 4DKK
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 ARG 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A THR* 1.3 86.9 - - - +
408A PRO* 1.3 73.2 - - + +
409A SER* 4.0 6.1 - - - +
410A GLU* 3.1 29.4 + - - +
411A GLN* 3.0 23.2 + - - +
458A GLU* 3.2 34.4 - - - +
462A ASP* 3.5 22.8 + - - +
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Residues in contact with PRO 408 (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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406A THR 4.2 3.6 - - - +
407A ARG* 1.3 84.6 - - + +
409A SER* 1.3 63.6 + - - +
411A GLN* 3.2 16.6 + - - +
412A LEU* 2.8 26.7 + - - +
462A ASP* 3.4 42.0 - - + +
465A ALA* 3.8 1.6 - - - -
466A LEU* 3.7 33.7 - - + +
469A LEU* 3.6 5.5 - - + +
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Residues in contact with SER 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ARG* 4.0 6.6 - - - +
408A PRO* 1.3 78.7 - - - +
410A GLU* 1.3 62.0 + - - +
412A LEU* 3.5 1.6 + - - +
413A ASP* 3.0 28.9 + - - +
425A TYR* 3.6 19.0 + - - -
458A GLU* 3.2 16.8 + - - -
461A HIS* 4.6 5.6 - - - -
462A ASP* 2.7 23.7 + - - -
465A ALA* 3.7 12.7 - - - +
502A CL 4.0 17.4 - - - +
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Residues in contact with GLU 410 (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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404A PRO* 3.1 48.5 - - - +
405A LEU* 3.6 8.6 - - + +
406A THR* 3.2 8.5 + - - -
407A ARG* 3.1 47.1 + - + +
409A SER* 1.3 76.2 - - - +
411A GLN* 1.3 67.0 + - - +
413A ASP* 3.3 9.3 + - - +
414A TYR* 3.0 23.9 + - - +
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Residues in contact with GLN 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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405A LEU* 3.1 35.6 + - + +
406A THR* 3.8 16.4 + - - +
407A ARG 3.0 17.2 + - - +
408A PRO* 3.6 11.1 - - - +
410A GLU* 1.3 76.5 - - - +
412A LEU* 1.3 56.6 + - - +
414A TYR* 3.3 8.2 + - - +
415A LEU* 3.0 27.0 + - - +
466A LEU* 5.8 1.6 - - - +
469A LEU* 3.7 22.3 - - + +
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Residues in contact with LEU 412 (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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408A PRO 2.8 19.8 + - - +
409A SER 3.9 3.1 - - - +
411A GLN* 1.3 70.4 - - - +
413A ASP* 1.3 60.5 + - - +
415A LEU* 4.2 4.3 - - + -
416A SER* 2.9 29.8 + - - -
421A PHE* 4.0 24.2 - - + -
423A VAL* 3.9 17.0 - - + -
425A TYR* 4.8 0.4 - - - +
440A ILE* 3.6 31.0 - - + -
442A CYS* 4.0 2.0 - - - -
465A ALA* 3.9 13.9 - - + +
468A ILE* 3.9 30.1 - - + -
469A LEU* 4.0 23.5 - - + +
472A LEU* 4.4 0.2 - - + -
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Residues in contact with ASP 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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409A SER 3.0 18.8 + - - +
410A GLU* 3.4 9.6 - - - +
412A LEU* 1.3 74.1 - - - +
414A TYR* 1.3 58.3 + - - +
416A SER* 2.9 25.1 + - - -
417A ARG* 3.0 16.5 + - - +
423A VAL* 5.6 6.0 - - - +
502A CL 4.1 11.6 - - - +
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Residues in contact with TYR 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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405A LEU* 3.9 35.0 - - + -
410A GLU 3.0 12.3 + - - +
411A GLN* 3.5 9.0 - - - +
413A ASP* 1.3 74.0 - - - +
415A LEU* 1.3 69.9 + - + +
417A ARG* 3.1 34.0 + - - +
418A VAL* 3.1 42.0 + - + +
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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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411A GLN 3.0 14.0 + - - +
412A LEU* 3.3 7.8 + - + +
414A TYR* 1.3 78.9 - - + +
416A SER* 1.3 57.5 + - - +
418A VAL* 3.2 6.4 + - + +
419A GLN* 2.9 49.2 + - + +
421A PHE* 3.9 9.9 - - + -
469A LEU* 3.8 25.1 - - + -
472A LEU* 3.8 28.3 - - + -
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Residues in contact with SER 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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412A LEU 2.9 14.3 + - - -
413A ASP* 2.9 16.5 + - - -
415A LEU* 1.3 78.3 - - - +
417A ARG* 1.3 59.4 + - - +
420A GLY* 2.6 35.5 + - - -
421A PHE* 3.3 48.1 + - - +
423A VAL* 3.7 12.2 + - - +
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Residues in contact with ARG 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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413A ASP* 3.0 12.6 + - - +
414A TYR* 3.1 36.7 + - - +
416A SER* 1.3 84.9 + - - +
418A VAL* 1.3 64.9 + - - +
420A GLY* 3.9 5.2 + - - -
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Residues in contact with VAL 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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414A TYR* 3.1 40.4 + - + +
415A LEU* 3.8 7.0 - - + +
417A ARG* 1.3 82.6 - - + +
419A GLN* 1.3 77.5 + - + +
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Residues in contact with GLN 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LEU* 2.9 35.5 + - + +
418A VAL* 1.3 94.0 - - + +
420A GLY* 1.3 59.6 + - - +
421A PHE* 3.7 19.6 + - + -
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Residues in contact with GLY 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 SER 2.6 18.7 + - - -
417A ARG 4.3 5.4 - - - -
418A VAL 3.4 1.2 - - - -
419A GLN* 1.3 75.7 - - - +
421A PHE* 1.3 63.3 + - - +
422A GLN* 3.2 17.2 + - - +
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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