Contacts of the helix formed by residues 449 - 468 (chain A) in PDB entry 3DL2
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 ASP 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A LEU* 4.3 25.0 - - - +
450A THR* 1.3 62.4 + - - +
451A VAL* 3.3 24.3 + - - +
452A THR* 2.8 49.2 + - + +
453A GLU* 3.3 8.8 + - - +
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Residues in contact with THR 450 (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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449A ASP* 1.3 71.7 + - - +
451A VAL* 1.3 65.9 + - - +
453A GLU* 3.2 8.0 + - + +
454A LYS* 2.9 52.4 + - - +
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Residues in contact with VAL 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 3.9 26.9 - - + -
354A VAL* 4.0 15.3 - - + -
355A LEU 3.7 20.2 - - - +
356A THR* 4.9 6.7 - - - +
419A TYR* 4.2 15.5 - - + +
445A THR 6.0 2.5 - - - +
449A ASP* 3.3 13.4 + - - +
450A THR* 1.3 81.9 - - - +
452A THR* 1.3 63.3 + - - +
454A LYS* 4.0 1.4 - - - +
455A LEU* 3.1 30.4 + - + +
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Residues in contact with THR 452 (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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419A TYR* 3.6 39.2 - - + +
446A LEU* 5.8 7.2 - - + -
449A ASP* 2.8 37.8 + - + +
451A VAL* 1.3 74.9 - - - +
453A GLU* 1.3 57.8 + - - +
455A LEU* 3.3 2.3 + - - +
456A GLN* 2.8 45.2 + - - +
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Residues in contact with GLU 453 (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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449A ASP 3.3 9.4 + - - +
450A THR* 3.2 14.1 + - + +
452A THR* 1.3 82.1 + - - +
454A LYS* 1.3 58.8 + - + +
456A GLN* 3.4 9.2 + - - +
457A SER* 3.0 30.2 + - - -
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Residues in contact with LYS 454 (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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352A ASP* 3.9 24.7 + - - +
353A LYS 5.2 3.8 - - - +
354A VAL* 3.7 32.8 - - + -
450A THR* 2.9 36.7 + - - +
451A VAL 4.0 1.8 - - - +
453A GLU* 1.3 75.0 - - + +
455A LEU* 1.3 58.9 + - - +
457A SER* 3.5 7.7 + - - -
458A SER* 3.0 32.2 + - - -
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 4.2 12.1 - - + -
347A GLY* 3.7 26.9 - - - +
354A VAL* 3.8 26.9 - - + -
419A TYR* 4.2 35.2 - - + -
421A ILE* 4.6 1.8 - - + -
427A LEU* 3.7 31.8 - - + +
429A LEU* 4.8 4.0 - - + -
451A VAL 3.1 25.8 + - - +
452A THR* 3.6 7.0 - - - +
453A GLU 3.3 0.2 - - - -
454A LYS* 1.3 75.8 - - - +
456A GLN* 1.3 59.9 + - - +
458A SER* 3.3 7.0 + - - +
459A ALA* 2.9 28.3 + - - +
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Residues in contact with GLN 456 (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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419A TYR* 2.8 29.5 + - + +
420A ASP* 3.6 20.9 + - - +
421A ILE* 4.4 7.4 - - + -
452A THR* 2.8 28.5 + - - +
453A GLU* 3.8 7.3 - - - +
455A LEU* 1.3 73.0 - - - +
457A SER* 1.3 60.7 + - - +
459A ALA* 3.4 8.1 + - - +
460A SER* 2.9 29.8 + - - -
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Residues in contact with SER 457 (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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453A GLU* 3.0 19.3 + - - -
454A LYS* 3.5 8.7 - - - -
456A GLN* 1.3 76.9 - - - +
458A SER* 1.3 60.6 + - - +
460A SER* 3.3 6.9 + - - -
461A SER* 3.1 24.0 + - - -
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Residues in contact with SER 458 (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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347A GLY* 5.8 0.2 - - - -
348A GLU* 2.8 45.1 + - - +
427A LEU* 3.9 9.4 - - - -
454A LYS 3.0 16.1 + - - -
455A LEU* 3.5 10.7 - - - +
456A GLN 3.3 0.2 - - - -
457A SER* 1.3 74.3 - - - +
459A ALA* 1.3 59.8 + - - +
461A SER* 3.0 5.0 + - - -
462A ILE* 2.9 35.9 + - - +
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Residues in contact with ALA 459 (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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421A ILE* 3.9 26.0 - - + -
423A SER* 4.4 3.6 - - - +
425A VAL* 3.6 31.4 - - + +
427A LEU* 4.3 2.6 - - + +
455A LEU 2.9 16.8 + - - +
456A GLN* 3.6 6.1 - - - +
458A SER* 1.3 75.7 - - - +
460A SER* 1.3 57.0 + - - +
462A ILE* 4.6 1.3 - - - -
463A HIS* 2.9 33.4 + - - +
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Residues in contact with SER 460 (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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456A GLN 2.9 17.9 + - - -
457A SER* 3.5 8.3 - - - -
458A SER 3.2 0.2 - - - -
459A ALA* 1.3 76.7 - - - +
461A SER* 1.3 57.9 + - - +
463A HIS* 3.7 6.0 + - - +
464A SER* 3.0 29.5 + - - -
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Residues in contact with SER 461 (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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348A GLU* 4.1 9.0 + - - -
457A SER 3.1 13.0 + - - -
458A SER* 3.0 16.6 + - - -
460A SER* 1.3 72.9 + - - +
462A ILE* 1.3 66.3 + - - +
464A SER* 3.4 7.5 + - - -
465A LEU* 3.1 23.0 + - - +
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Residues in contact with ILE 462 (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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297A GLU* 3.7 31.9 - - + +
298A ILE* 4.2 16.7 - - + +
348A GLU* 4.1 23.6 - - - +
425A VAL* 3.9 13.9 - - + -
426A PHE 4.4 1.3 - - - +
427A LEU* 3.7 25.4 - - + -
458A SER 2.9 19.7 + - - +
459A ALA* 4.0 2.9 - - - +
461A SER* 1.3 78.4 + - - +
463A HIS* 1.3 56.3 + - - +
465A LEU* 3.3 6.7 + - - +
466A GLN* 3.0 52.2 + - - +
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Residues in contact with HIS 463 (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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423A SER* 3.9 26.0 - - - +
424A GLU* 4.9 5.1 + - + -
425A VAL* 3.9 12.3 - - + -
459A ALA 2.9 20.6 + - - +
460A SER* 3.7 5.4 + - - +
461A SER 3.4 0.2 - - - -
462A ILE* 1.3 75.5 - - - +
464A SER* 1.3 61.7 + - - +
466A GLN* 3.4 14.8 + - + +
467A GLN* 3.1 60.8 + - + +
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Residues in contact with SER 464 (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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460A SER* 3.0 17.6 + - - -
461A SER* 3.7 7.6 - - - -
462A ILE 3.3 0.2 - - - -
463A HIS* 1.3 76.8 + - - +
465A LEU* 1.3 60.1 + - - +
467A GLN* 3.4 28.3 + - - +
468A GLN* 3.6 17.9 - - - +
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Residues in contact with LEU 465 (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* 3.7 34.8 - - + -
263A LEU* 4.3 16.4 - - + -
266A VAL* 4.3 17.0 - - + -
298A ILE* 3.2 30.1 - - + -
461A SER 3.1 13.1 + - - +
462A ILE* 3.3 7.8 + - - +
464A SER* 1.3 73.8 - - - +
466A GLN* 1.3 66.1 + - - +
468A GLN* 3.2 38.4 + - - +
469A LEU* 3.4 13.5 + - + +
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Residues in contact with GLN 466 (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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297A GLU 4.3 1.4 + - - -
298A ILE* 4.0 22.3 - - + +
301A TYR* 3.3 53.4 - - + +
424A GLU 3.2 22.0 + - - +
425A VAL* 4.2 6.6 - - - +
462A ILE* 3.0 40.9 + - - +
463A HIS* 3.6 12.6 - - + +
465A LEU* 1.3 75.4 - - - +
467A GLN* 1.3 61.7 + - + +
469A LEU* 3.3 27.2 + - + +
471A LEU* 4.1 7.3 - - + +
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Residues in contact with GLN 467 (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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463A HIS* 3.1 45.3 + - + +
464A SER* 3.5 23.2 - - - +
465A LEU 3.2 0.2 - - - -
466A GLN* 1.3 77.7 - - - +
468A GLN* 1.3 59.0 + - + +
469A LEU 3.4 4.2 + - - +
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Residues in contact with GLN 468 (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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263A LEU* 3.7 34.3 - - + +
267A GLN* 4.5 1.4 - - - +
464A SER* 3.6 13.6 - - - +
465A LEU* 3.3 38.9 - - - +
467A GLN* 1.3 77.2 - - - +
469A LEU* 1.3 62.2 + - - +
470A LYS* 4.0 3.1 + - - +
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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