Contacts of the helix formed by residues 449 - 466 (chain A) in PDB entry 3WOO
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 VAL 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A ASN* 5.3 3.4 - - - +
316A ASP* 3.7 14.8 - - - +
317A ILE* 3.8 38.6 - - + -
320A LYS* 3.6 20.9 - - + +
321A TYR* 3.0 17.3 + - + -
448A TYR* 1.3 83.0 - - - +
450A ALA* 1.3 69.8 + - - +
451A ALA* 3.9 12.8 - - + +
452A MET* 3.0 3.8 + - + +
453A ASP* 2.9 20.8 + - - +
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Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A TYR* 3.5 33.9 - - + +
449A VAL* 1.3 74.4 - - - +
451A ALA* 1.3 62.7 + - - +
453A ASP* 4.0 0.3 - - - +
454A ARG* 3.0 26.0 + - - +
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Residues in contact with ALA 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 5.3 5.4 - - + -
449A VAL* 3.2 10.2 - - + +
450A ALA* 1.3 79.2 - - - +
452A MET* 1.4 62.4 + - - +
454A ARG* 3.9 9.6 - - - +
455A GLN* 3.5 27.5 + - - +
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Residues in contact with MET 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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306A MET* 3.8 20.9 - - + +
307A VAL* 3.8 28.9 - - + -
310A ALA* 3.5 24.0 - - - -
317A ILE* 3.7 23.8 - - + +
321A TYR* 3.6 36.1 - - + -
449A VAL* 3.0 11.1 + - - +
451A ALA* 1.4 77.2 - - - +
453A ASP* 1.3 64.6 + - - +
455A GLN* 3.1 41.2 + - + +
456A LEU* 3.3 11.9 + - + +
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Residues in contact with ASP 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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321A TYR* 3.7 4.4 + - - +
402A THR* 3.5 11.5 - - - +
403A ALA* 3.0 26.4 + - - +
404A MET* 3.8 14.9 + - - +
448A TYR* 3.5 33.0 + - + +
449A VAL 2.9 11.2 + - - +
450A ALA 4.0 2.5 - - - +
452A MET* 1.3 70.7 - - - +
454A ARG* 1.3 54.2 + - - +
456A LEU* 2.9 16.8 + - - +
457A GLN* 2.7 57.1 + - - +
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Residues in contact with ARG 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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450A ALA 3.0 17.7 + - - +
451A ALA* 3.9 10.5 - - - +
452A MET 3.2 0.2 - - - -
453A ASP* 1.3 76.4 + - - +
455A GLN* 1.3 58.1 + - + +
457A GLN* 3.3 15.5 + - - +
458A GLU* 2.9 28.0 + - - +
489A LYS* 4.2 14.1 + - - +
492A LEU* 3.5 52.5 + - + +
493A ASP* 2.7 33.1 + - - +
496A ALA* 4.1 13.6 - - + +
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Residues in contact with GLN 455 (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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306A MET* 3.4 39.0 + - + +
310A ALA* 4.4 10.4 - - - +
451A ALA* 3.5 17.7 + - - +
452A MET* 3.1 26.8 + - + +
454A ARG* 1.3 77.4 - - + +
456A LEU* 1.3 58.0 + - - +
458A GLU* 3.4 18.8 + - - +
459A TYR* 2.9 23.2 + - - +
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Residues in contact with LEU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLN* 3.8 36.6 - - + +
306A MET* 3.3 21.8 - - + -
307A VAL* 4.4 5.6 - - + -
321A TYR* 4.3 19.1 - - + -
328A TRP* 4.2 17.7 - - + -
402A THR* 4.2 14.1 - - + -
452A MET* 3.3 17.0 + - + +
453A ASP* 2.9 19.1 + - - +
455A GLN* 1.3 74.7 - - - +
457A GLN* 1.3 65.3 + - - +
459A TYR* 3.3 3.4 + - - +
460A TRP* 3.1 30.9 + - - -
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Residues in contact with GLN 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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399A PHE* 3.9 15.2 - - + -
402A THR* 4.0 20.2 + - - +
404A MET* 4.3 15.2 - - - +
405A LEU* 4.5 6.4 - - + +
453A ASP* 2.7 36.9 + - - +
454A ARG* 3.4 16.7 - - - +
456A LEU* 1.3 71.9 - - - +
458A GLU* 1.3 56.1 + - - +
460A TRP* 3.1 3.3 + - - +
461A LEU* 2.9 32.9 + - + +
492A LEU* 3.5 23.3 - - + +
495A LEU* 3.8 38.1 + - + +
496A ALA* 5.5 0.3 + - - -
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Residues in contact with GLU 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ARG* 2.9 17.8 + - - +
455A GLN* 3.4 21.3 - - - +
457A GLN* 1.3 68.4 - - - +
459A TYR* 1.3 69.5 + - - +
461A LEU* 3.3 6.2 + - - +
462A ASN* 3.0 38.8 + - - +
488A VAL* 4.4 6.8 - - + +
492A LEU* 3.6 29.3 - - + +
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Residues in contact with TYR 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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298A ARG* 3.4 6.5 + - - -
299A HIS* 2.7 36.8 + + - -
302A ASN* 3.0 45.9 + - + -
303A GLN* 4.2 13.9 - - + -
306A MET* 4.1 18.8 - - + -
455A GLN 2.9 14.5 + - - +
456A LEU* 3.5 9.2 - - - +
458A GLU* 1.3 76.5 - - - +
460A TRP* 1.3 85.4 + + - +
462A ASN* 3.2 10.2 + - + +
463A GLU* 2.9 54.1 + - + +
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Residues in contact with TRP 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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299A HIS* 3.4 40.6 - + + -
303A GLN* 3.0 39.1 - - - +
395A THR* 4.1 33.7 - - + +
398A LEU* 3.4 46.0 + - + +
399A PHE* 3.5 33.2 - - + -
402A THR* 3.9 18.8 - - + +
456A LEU 3.1 22.3 + - - +
457A GLN 3.8 0.2 - - - +
459A TYR* 1.3 91.1 - + - +
461A LEU* 1.3 57.0 + - - +
463A GLU* 3.2 7.6 + - + +
464A TYR* 2.8 35.8 + - - +
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Residues in contact with LEU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A PHE* 3.4 35.6 - - + -
457A GLN* 2.9 19.7 + - + +
458A GLU 3.6 4.3 - - - +
460A TRP* 1.3 76.3 - - - +
462A ASN* 1.3 60.4 + - - +
464A TYR* 3.3 10.7 + - + +
465A ILE* 3.1 28.6 + - - +
476A VAL* 5.4 3.4 - - + -
479A TRP* 4.0 15.5 - - + -
480A LEU* 4.3 20.9 - - + -
488A VAL* 4.0 17.0 - - + -
491A ALA* 4.4 17.0 - - + -
492A LEU* 3.9 26.7 - - + -
495A LEU* 5.3 1.3 - - + -
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Residues in contact with ASN 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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458A GLU* 3.0 37.0 + - - +
459A TYR* 3.6 10.0 - - + +
461A LEU* 1.3 75.1 - - - +
463A GLU* 1.3 62.8 + - - +
465A ILE* 3.4 10.2 + - - +
466A LYS* 3.4 32.9 + - - +
485A ALA* 5.5 3.6 - - - +
488A VAL* 3.8 21.8 - - - +
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Residues in contact with GLU 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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298A ARG* 3.0 31.8 + - - -
299A HIS* 3.3 11.7 - - + -
395A THR* 4.3 6.9 + - + +
459A TYR* 2.9 47.7 + - + +
460A TRP* 3.6 19.3 - - + +
462A ASN* 1.3 75.9 - - - +
464A TYR* 1.3 66.5 + - - +
466A LYS* 2.8 46.2 + - - +
467A LEU* 3.6 10.9 + - - +
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Residues in contact with TYR 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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392A ARG* 6.1 0.2 - - + -
395A THR* 3.9 16.3 - - + +
396A LEU* 5.4 9.4 - - + -
399A PHE* 5.9 7.2 - + + -
460A TRP 2.8 20.3 + - - +
461A LEU* 3.3 12.1 + - + +
463A GLU* 1.3 71.3 - - - +
465A ILE* 1.3 61.0 + - - +
467A LEU* 3.0 46.7 + - + +
472A ARG* 3.4 19.6 - - - -
473A VAL* 2.9 45.3 + - + -
476A VAL* 3.6 33.4 - - + -
477A ASP* 2.6 31.2 + - - -
480A LEU* 4.3 15.7 - - + -
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Residues in contact with ILE 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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461A LEU 3.1 15.9 + - - +
462A ASN* 3.7 9.6 - - - +
463A GLU 3.1 0.4 - - - -
464A TYR* 1.3 78.6 - - + +
466A LYS* 1.3 63.0 + - + +
467A LEU 3.2 1.1 - - - +
472A ARG* 3.2 19.1 + - - +
480A LEU* 3.9 24.9 - - + -
483A ASN* 3.7 46.9 + - - +
484A ASP* 4.4 2.2 - - - +
488A VAL* 3.2 36.3 - - + -
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Residues in contact with LYS 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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298A ARG* 3.5 16.6 - - - +
462A ASN* 3.4 20.2 + - - +
463A GLU* 2.8 40.5 + - - +
464A TYR 3.1 1.0 - - - -
465A ILE* 1.3 79.7 - - + +
467A LEU* 1.3 63.7 + - - +
468A PRO* 3.6 3.8 - - - +
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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
------------------------------------------------------------
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