Contacts of the helix formed by residues 449 - 469 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B LEU* 5.2 2.6 - - - +
447B LYS* 3.5 31.4 + - - +
450B THR* 1.3 64.9 + - + +
451B VAL* 3.3 7.3 - - - +
452B THR* 2.8 28.4 + - - +
453B GLU* 3.1 16.4 + - - +
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Residues in contact with THR 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B ASP* 1.3 77.4 + - + +
451B VAL* 1.3 66.9 + - - +
453B GLU* 3.4 17.0 - - - +
454B LYS* 2.9 45.6 + - - +
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Residues in contact with VAL 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 3.8 28.9 - - + -
354B VAL* 3.9 16.6 - - + -
355B LEU 3.6 21.5 - - - +
356B THR* 5.0 2.2 - - - -
419B TYR* 4.2 15.3 - - + +
446B LEU* 3.8 28.9 - - + -
449B ASP 3.3 2.4 - - - +
450B THR* 1.3 83.3 + - - +
452B THR* 1.3 59.2 + - + +
454B LYS* 3.4 0.7 + - - +
455B LEU* 3.0 31.5 + - + +
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Residues in contact with THR 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B TYR* 3.6 37.7 - - + -
447B LYS 4.4 17.3 - - - +
449B ASP* 2.8 24.4 + - - +
451B VAL* 1.3 77.3 - - + +
453B GLU* 1.3 57.0 + - - +
455B LEU* 3.6 2.0 - - - +
456B GLN* 2.9 47.7 + - - +
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Residues in contact with GLU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ASP 3.1 11.4 + - - +
450B THR* 3.4 22.6 - - - +
452B THR* 1.3 83.7 + - - +
454B LYS* 1.3 57.5 + - + +
456B GLN* 3.6 7.8 + - - +
457B SER* 3.1 28.4 + - - -
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Residues in contact with LYS 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B ASP 6.4 0.7 - - - -
353B LYS 5.1 6.1 - - - +
354B VAL* 3.6 34.5 - - + -
450B THR* 2.9 29.1 + - - +
451B VAL 3.8 3.8 - - - +
452B THR 3.3 0.2 - - - -
453B GLU* 1.3 76.5 - - + +
455B LEU* 1.3 58.1 + - - +
457B SER* 3.5 7.1 + - - -
458B SER* 3.0 31.6 + - - -
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Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 4.1 12.8 - - + -
347B GLY* 3.9 28.0 - - - +
354B VAL* 4.0 24.2 - - + -
419B TYR* 4.0 36.3 - - + -
421B ILE* 4.5 2.7 - - + -
427B LEU* 3.7 30.4 - - + +
429B LEU* 4.7 5.2 - - + -
451B VAL 3.0 24.9 + - - +
452B THR* 3.6 7.0 - - - +
454B LYS* 1.3 76.3 - - - +
456B GLN* 1.3 60.4 + - - +
458B SER* 3.4 6.1 + - - +
459B ALA* 2.9 29.2 + - - +
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Residues in contact with GLN 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B TYR* 2.8 28.8 + - + +
420B ASP* 3.4 20.2 - - - +
421B ILE* 4.4 8.7 - - + +
452B THR* 2.9 29.5 + - - +
453B GLU* 4.0 6.8 - - - +
455B LEU* 1.3 72.1 - - - +
457B SER* 1.3 60.9 + - - +
459B ALA* 3.4 7.6 + - - +
460B SER* 2.9 30.1 + - - -
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Residues in contact with SER 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B GLU 3.1 18.8 + - - -
454B LYS* 3.6 8.7 - - - -
456B GLN* 1.3 76.1 - - - +
458B SER* 1.3 61.1 + - - +
460B SER* 3.3 6.3 + - - -
461B SER* 3.1 23.7 + - - -
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Residues in contact with SER 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B GLY* 5.7 0.2 - - - -
348B GLU* 2.9 42.4 + - - +
427B LEU* 3.9 9.2 - - - -
454B LYS 3.0 18.1 + - - -
455B LEU* 3.6 7.1 - - - +
457B SER* 1.3 74.1 - - - +
459B ALA* 1.3 64.7 - - - +
461B SER* 3.0 8.3 + - - -
462B ILE* 2.9 30.7 + - - +
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Residues in contact with ALA 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B ILE* 3.8 26.7 - - + -
423B SER* 4.5 2.7 - - - +
425B VAL* 3.6 30.7 - - + +
427B LEU* 4.3 2.4 - - + +
455B LEU 2.9 17.1 + - - +
456B GLN* 3.5 5.6 - - - +
458B SER* 1.3 76.0 - - - +
460B SER* 1.3 56.7 + - - +
462B ILE* 4.7 1.3 - - - -
463B HIS* 3.0 32.6 + - - +
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Residues in contact with SER 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B GLN 2.9 17.2 + - - -
457B SER* 3.6 7.6 - - - -
458B SER 3.2 0.2 - - - -
459B ALA* 1.3 77.0 - - - +
461B SER* 1.3 56.9 + - - +
463B HIS* 3.5 6.0 + - - +
464B SER* 3.0 31.7 + - - -
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Residues in contact with SER 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLU* 4.2 9.4 + - - -
457B SER 3.1 12.8 + - - -
458B SER* 3.0 16.8 + - - -
460B SER* 1.3 74.4 + - - +
462B ILE* 1.3 66.0 + - - +
464B SER* 3.4 7.6 + - - -
465B LEU* 3.2 22.2 + - - +
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Residues in contact with ILE 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLU* 3.7 35.9 - - + +
298B ILE* 4.1 16.8 - - + +
348B GLU* 4.1 24.7 - - + +
425B VAL* 4.0 12.8 - - + -
426B PHE 4.4 1.1 - - - +
427B LEU* 3.8 19.3 - - + -
458B SER 2.9 20.9 + - - +
459B ALA* 4.0 3.4 - - - +
461B SER* 1.3 78.0 + - - +
463B HIS* 1.3 58.4 + - - +
465B LEU* 3.2 7.7 + - - +
466B GLN* 3.0 51.4 + - - +
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Residues in contact with HIS 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B SER* 3.9 26.8 - - - +
424B GLU* 5.0 5.1 + - + -
425B VAL* 3.9 11.7 - - + -
459B ALA 3.0 20.4 + - - +
460B SER* 3.7 6.6 + - - +
462B ILE* 1.3 76.6 - - - +
464B SER* 1.3 62.0 + - - +
466B GLN* 3.3 14.3 + - + +
467B GLN* 3.0 61.0 + - + +
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Residues in contact with SER 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B SER* 3.0 21.2 + - - -
461B SER* 3.6 8.5 - - - -
462B ILE 3.3 0.2 - - - -
463B HIS* 1.3 77.0 + - - +
465B LEU* 1.3 60.5 + - - +
467B GLN* 3.5 22.7 + - - +
468B GLN* 3.4 23.1 + - - +
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Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B TYR* 3.6 36.6 - - + -
263B LEU* 3.8 25.1 - - + -
266B VAL* 4.1 15.3 - - + -
298B ILE* 3.2 29.8 - - + -
461B SER 3.2 12.7 + - - +
462B ILE* 3.2 7.8 + - - +
464B SER* 1.3 74.0 - - - +
466B GLN* 1.3 65.3 + - - +
468B GLN* 3.2 34.3 + - - +
469B LEU* 3.2 16.6 + - + +
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Residues in contact with GLN 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLU 4.3 1.4 + - - -
298B ILE* 4.0 23.1 - - + +
301B TYR* 3.3 53.0 - - + +
424B GLU 3.2 21.0 + - - +
425B VAL* 4.1 8.0 - - - +
426B PHE 5.0 0.2 - - - +
462B ILE* 3.0 37.0 + - - +
463B HIS* 3.3 15.8 + - + +
465B LEU* 1.3 77.4 - - - +
467B GLN* 1.3 60.3 + - - +
469B LEU* 3.3 22.3 + - + +
471B LEU* 3.7 14.1 - - + +
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Residues in contact with GLN 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B HIS* 3.0 52.8 + - + +
464B SER* 3.6 18.6 + - - +
465B LEU 3.3 0.2 - - - -
466B GLN* 1.3 76.4 - - - +
468B GLN* 1.3 59.2 + - - +
469B LEU 3.7 4.7 + - - +
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Residues in contact with GLN 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B LEU* 3.8 35.4 - - + +
267B GLN* 4.7 1.4 - - - +
464B SER* 3.4 17.8 + - - +
465B LEU* 3.2 36.4 + - - +
467B GLN* 1.3 76.2 - - - +
469B LEU* 1.3 61.9 + - - +
470B LYS* 4.0 3.5 + - - +
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Residues in contact with LEU 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B LEU* 4.0 9.9 - - + -
266B VAL* 3.8 28.7 - - + -
267B GLN* 3.4 29.4 - - - +
270B VAL* 4.2 11.2 - - + -
298B ILE* 3.8 29.4 - - + -
302B VAL* 5.0 2.0 - - + -
465B LEU* 3.2 19.6 + - + +
466B GLN* 3.3 21.1 + - + +
467B GLN 4.0 5.0 - - - +
468B GLN* 1.3 81.4 - - - +
470B LYS* 1.3 64.7 + - - +
471B LEU* 3.7 21.2 + - + +
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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