Contacts of the helix formed by residues 412 - 423 (chain B) in PDB entry 5ODS
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 SER 412 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377B TYR* 5.0 0.4 - - - -
404B VAL 3.6 12.1 + - - -
406B ALA* 3.9 27.5 + - - +
410B GLN 3.9 0.8 + - - -
411B THR* 1.3 79.3 - - - +
413B PRO* 1.3 73.9 - - - +
414B LEU* 3.0 18.6 + - - +
415B LEU* 3.2 19.6 + - - +
416B GLN* 4.0 3.5 + - - +
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Residues in contact with PRO 413 (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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372B PHE* 5.9 0.7 - - + -
377B TYR* 3.8 44.2 - - + +
401B PHE* 3.6 33.3 - - + +
404B VAL* 3.7 39.0 - - + +
405B PRO 4.8 2.9 - - - +
411B THR 3.6 3.3 - - - +
412B SER* 1.3 91.4 - - - +
414B LEU* 1.3 60.5 + - - +
416B GLN* 3.6 4.9 + - + +
417B TYR* 3.5 15.6 + - - +
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ILE* 3.8 39.7 - - + +
401B PHE* 3.9 17.5 + - + +
402B GLN* 3.8 32.3 - - + +
412B SER* 3.0 12.1 + - - +
413B PRO* 1.3 81.0 - - - +
415B LEU* 1.3 61.7 - - - +
417B TYR* 3.6 10.7 + - + +
418B PHE* 3.2 36.2 + - + -
434B GLU* 5.4 2.5 - - + +
435B LEU* 6.4 0.2 - - - -
438B PRO* 5.0 16.8 - - + -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B THR* 4.0 24.2 - - + -
412B SER* 3.2 13.3 + - - +
414B LEU* 1.3 76.0 - - - +
416B GLN* 1.3 65.3 + - - +
418B PHE* 3.4 8.6 + - - +
419B GLY* 3.1 19.6 + - - -
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Residues in contact with GLN 416 (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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377B TYR* 3.4 35.7 - - + +
378B SER* 3.5 32.4 + - - -
381B ALA* 5.1 0.2 - - + -
411B THR* 5.6 6.7 + - - -
412B SER 4.0 2.3 + - - +
413B PRO* 3.6 10.0 + - + +
414B LEU 3.4 0.6 - - - -
415B LEU* 1.3 80.1 - - - +
417B TYR* 1.3 63.2 + - - +
419B GLY* 3.3 2.3 + - - +
420B ILE* 3.3 41.7 + - + +
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Residues in contact with TYR 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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381B ALA* 3.8 26.3 - - + +
384B ALA* 3.7 22.7 - - + +
385B ALA 4.9 0.2 - - - -
392B LEU 3.6 18.2 + - - -
393B ARG* 4.0 14.7 - - - +
394B THR 4.7 1.4 + - - -
397B THR* 3.8 12.0 - - + +
398B ILE* 3.9 27.8 - - + +
401B PHE* 3.7 31.0 - + + -
413B PRO 3.5 9.6 + - - +
414B LEU* 3.7 11.2 - - + +
415B LEU 3.3 0.4 - - - -
416B GLN* 1.3 79.2 - - - +
418B PHE* 1.3 72.1 + + - +
420B ILE* 3.8 2.3 + - - +
421B LEU* 3.3 54.6 + - + +
431B GLU* 5.8 2.3 - - + +
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Residues in contact with PHE 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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398B ILE* 4.2 22.2 - - + -
414B LEU* 3.2 46.6 + - + -
415B LEU* 3.4 8.6 + - - +
416B GLN 3.3 0.4 - - - -
417B TYR* 1.3 84.4 - + - +
419B GLY* 1.3 65.0 + - - +
421B LEU* 3.1 16.2 + - + +
422B LEU* 3.1 31.0 + - + +
427B LEU* 5.2 2.9 - - + -
431B GLU* 3.1 34.8 - - + -
434B GLU* 4.3 5.8 - - + -
435B LEU* 3.7 46.9 - - + -
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Residues in contact with GLY 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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415B LEU 3.1 14.8 + - - -
416B GLN* 3.3 4.4 + - - -
418B PHE* 1.3 77.4 - - - +
420B ILE* 1.3 59.5 + - - +
422B LEU* 3.7 17.4 + - - +
423B ASP* 3.2 21.5 - - - +
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Residues in contact with ILE 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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378B SER* 3.7 23.3 - - - +
381B ALA* 3.8 14.6 - - + -
382B LYS* 4.3 29.2 - - + +
385B ALA* 4.7 15.3 - - + +
386B ASN* 6.1 0.2 - - - +
416B GLN* 3.3 31.7 + - + +
417B TYR 4.3 2.9 - - - +
419B GLY* 1.3 74.2 - - - +
421B LEU* 1.3 65.9 + - - +
422B LEU 3.2 0.7 + - - -
423B ASP* 3.4 19.3 + - - +
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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
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385B ALA* 4.1 29.2 - - + +
393B ARG* 3.4 54.5 + - + +
417B TYR* 3.3 55.8 + - + +
418B PHE* 3.3 20.4 - - + +
420B ILE* 1.3 81.3 - - - +
422B LEU* 1.3 63.9 + - - +
423B ASP 3.5 4.2 + - - -
427B LEU* 4.6 9.6 - - + +
431B GLU* 5.3 7.9 - - + -
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Residues in contact with LEU 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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418B PHE* 3.1 26.2 + - + +
419B GLY* 3.7 18.4 - - - +
420B ILE 3.2 0.2 - - - -
421B LEU* 1.3 78.4 - - - +
423B ASP* 1.3 65.2 + - - +
427B LEU* 3.8 28.7 - - + +
435B LEU* 5.5 8.5 - - + -
451B TRP* 4.2 45.1 - - + +
454B GLU* 5.6 2.5 - - - +
456B LYS* 5.2 14.4 - - + +
457B LEU* 5.0 7.9 - - + -
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Residues in contact with ASP 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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419B GLY 3.2 16.8 - - - +
420B ILE* 3.4 13.9 + - - +
421B LEU 3.4 4.2 - - - -
422B LEU* 1.3 85.1 - - - +
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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