Contacts of the helix formed by residues 416 - 432 (chain B) in PDB entry 3OAA
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 ALA 416 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B LEU* 3.1 7.9 + - + +
414B ASP 3.1 0.4 - - - -
415B ASP* 1.3 78.8 - - - +
417B THR* 1.3 61.9 + - - +
419B LYS* 3.1 4.4 + - - +
420B GLN* 2.8 38.4 + - - +
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Residues in contact with THR 417 (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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403B LEU* 4.4 15.4 - - + +
406B PHE* 5.0 14.6 - - + -
409B PHE* 6.5 0.9 - - + -
412B ASP* 3.7 19.7 - - + +
413B LEU* 3.0 13.5 + - - +
416B ALA* 1.3 79.1 - - - +
418B ARG* 1.3 64.6 + - - +
420B GLN* 3.5 16.9 + - - +
421B LEU* 3.1 27.0 + - + +
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Residues in contact with ARG 418 (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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411B SER* 4.5 10.1 - - - -
414B ASP* 2.5 49.9 + - + +
417B THR* 1.3 75.7 - - - +
419B LYS* 1.3 56.5 + - - +
421B LEU* 4.0 2.2 - - - +
422B ASP* 3.0 39.9 + - - +
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Residues in contact with LYS 419 (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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414B ASP 2.9 5.8 + - - +
415B ASP 3.1 21.5 - - - +
416B ALA 3.1 1.7 + - - +
418B ARG* 1.3 72.9 - - - +
420B GLN* 1.3 90.3 + - - +
422B ASP* 3.1 5.1 + - - +
423B HIS* 2.8 44.4 + - + +
457B ALA* 6.2 1.8 - - + -
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Residues in contact with GLN 420 (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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396B ALA* 6.1 0.5 - - - +
399B GLN 4.5 4.2 + - - -
400B TYR* 4.6 5.1 - - - +
402B GLU* 5.0 0.4 + - - -
403B LEU* 2.9 42.6 - - - +
416B ALA* 2.8 21.1 - - - +
417B THR* 3.5 23.6 + - - +
419B LYS* 1.3 88.7 - - - +
421B LEU* 1.3 57.8 + - - +
423B HIS* 3.9 2.3 - - - +
424B GLY* 2.9 26.0 + - - -
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B TYR* 3.6 19.1 - - + +
403B LEU* 4.1 22.7 - - + +
404B ALA* 6.1 0.2 - - - -
406B PHE* 3.4 33.4 - - + -
407B SER 4.6 1.1 - - - +
408B GLN* 3.6 25.6 - - + +
417B THR* 3.1 23.9 + - + +
418B ARG* 4.0 2.7 - - - +
420B GLN* 1.3 75.5 - - - +
422B ASP* 1.3 66.1 + - - +
424B GLY* 3.1 1.2 + - - -
425B GLN* 2.7 57.5 + - + +
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Residues in contact with ASP 422 (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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408B GLN* 4.5 5.9 - - - +
418B ARG* 3.0 24.0 + - - +
419B LYS* 3.8 3.1 - - - +
421B LEU* 1.3 90.8 - - - +
423B HIS* 1.3 63.8 + - - +
425B GLN* 3.8 6.9 + - - +
426B LYS* 3.5 29.6 + - - +
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Residues in contact with HIS 423 (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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396B ALA* 5.3 9.7 - - + +
419B LYS* 2.8 39.2 + - + +
420B GLN* 3.9 3.1 + - - +
422B ASP* 1.3 75.1 - - - +
424B GLY* 1.3 66.4 + - - +
426B LYS* 3.0 15.3 + - + +
427B VAL* 3.1 31.4 + - + +
451B ALA 3.6 15.6 + - - -
452B GLU* 3.3 33.0 - - - -
453B ARG 5.6 0.9 - - - -
454B GLY* 6.2 0.7 - - - -
456B LEU* 5.1 3.6 - - + -
457B ALA* 4.6 24.7 - - + +
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Residues in contact with GLY 424 (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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396B ALA* 5.1 9.4 - - - -
397B LEU* 4.4 1.1 - - - +
400B TYR* 3.8 22.0 - - - -
420B GLN 2.9 17.3 + - - -
421B LEU 3.6 2.5 - - - -
423B HIS* 1.3 77.7 - - - +
425B GLN* 1.3 61.1 + - - +
427B VAL* 3.0 19.6 + - - +
428B THR* 3.1 18.4 + - - +
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Residues in contact with GLN 425 (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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400B TYR* 3.3 30.6 + - + +
407B SER 6.2 0.2 - - - -
408B GLN* 3.6 14.8 - - - +
421B LEU* 2.7 37.5 + - - +
422B ASP* 4.0 4.8 - - - +
424B GLY* 1.3 72.0 - - - +
426B LYS* 1.3 82.6 + - - +
428B THR* 2.8 17.6 + - - +
429B GLU* 3.6 9.6 + - + +
462B SER* 5.2 2.6 + - - -
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Residues in contact with LYS 426 (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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422B ASP* 3.5 18.5 + - - +
423B HIS* 3.0 10.7 + - - +
425B GLN* 1.3 106.3 + - - +
427B VAL* 1.3 62.7 + - - +
428B THR 3.5 0.2 - - - -
429B GLU* 3.9 15.9 - - + +
430B LEU* 3.7 18.4 + - - +
456B LEU* 4.5 13.5 - - + +
457B ALA* 5.9 4.5 - - - -
460B GLU* 4.2 22.4 - - - +
461B LEU 4.9 1.1 - - - -
462B SER* 2.8 51.0 + - - +
465B GLY* 5.1 2.2 - - - +
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ILE* 4.8 15.5 - - + +
396B ALA* 5.5 5.6 - - + -
397B LEU* 3.4 23.3 - - + -
423B HIS* 3.1 39.4 + - + +
424B GLY* 3.0 11.3 + - - +
426B LYS* 1.3 77.8 - - - +
428B THR* 1.3 59.6 + - - +
429B GLU 3.1 1.6 - - - -
430B LEU* 2.8 22.2 + - + +
431B LEU* 2.9 22.5 + - + +
451B ALA* 4.1 19.3 - - + -
452B GLU* 5.1 2.2 - - - +
456B LEU* 5.5 1.1 - - + -
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Residues in contact with THR 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ILE* 5.0 16.9 - - - +
397B LEU* 3.5 33.2 - - + -
400B TYR* 3.7 25.2 + - + -
401B ARG* 4.0 9.4 - - - +
424B GLY 3.1 13.4 + - - +
425B GLN* 2.8 25.3 + - - +
427B VAL* 1.3 77.6 - - - +
429B GLU* 1.3 59.9 + - - +
431B LEU* 3.5 9.0 + - - +
432B LYS* 3.3 19.8 + - - +
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Residues in contact with GLU 429 (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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425B GLN 3.6 14.5 + - - +
426B LYS* 4.2 20.4 - - + +
427B VAL 3.1 0.6 - - - -
428B THR* 1.3 80.8 + - - +
430B LEU* 1.3 61.7 + - - +
432B LYS* 3.3 46.2 + - - +
462B SER* 4.5 15.6 - - - +
463B LYS* 5.9 0.9 - - - -
465B GLY 5.7 2.2 - - - -
466B SER* 3.4 33.3 + - - +
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Residues in contact with LEU 430 (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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151B LYS* 3.1 21.7 + - - +
426B LYS 3.7 7.7 + - - +
427B VAL* 2.8 13.8 + - + +
429B GLU* 1.3 77.2 - - - +
431B LEU* 1.3 66.7 + - + +
432B LYS 3.0 9.4 - - - +
446B LEU* 3.2 50.0 - - + +
447B VAL* 4.5 2.0 - - - -
451B ALA* 3.5 23.8 - - + -
456B LEU* 3.4 31.9 - - + -
465B GLY 4.4 11.0 - - - +
466B SER* 5.3 2.0 - - - -
469B ALA* 4.2 11.2 - - + -
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Residues in contact with LEU 431 (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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151B LYS* 4.0 16.2 - - + +
152B ALA* 3.9 34.6 - - + +
155B SER* 4.5 7.6 - - - +
156B MET* 4.1 19.7 - - + -
364B ILE* 6.3 0.9 - - + -
366B PRO* 3.7 12.2 - - - +
368B VAL* 6.2 0.7 - - + -
393B ILE* 4.5 10.3 - - + -
397B LEU* 3.7 39.5 - - + -
427B VAL* 2.9 19.3 + - + +
428B THR* 3.5 6.5 + - - +
430B LEU* 1.3 74.3 - - + +
432B LYS* 1.3 65.3 + - - +
433B GLN* 3.4 9.4 + - - +
447B VAL* 5.7 7.6 - - + -
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Residues in contact with LYS 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LYS* 4.9 1.4 + - - +
362B ALA 4.9 2.4 + - - -
363B GLY* 3.3 37.2 + - - +
364B ILE* 4.3 14.8 - - + +
365B ARG 4.4 1.3 - - - +
366B PRO* 4.1 7.0 - - - -
428B THR 3.3 12.1 + - - +
429B GLU* 3.3 48.5 + - - +
430B LEU 3.0 13.4 - - - +
431B LEU* 1.3 77.0 - - - +
433B GLN* 1.3 66.4 + - - +
434B LYS* 4.3 14.6 - - + +
466B SER* 6.3 0.7 - - - -
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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