Contacts of the helix formed by residues 415 - 429 (chain B) in PDB entry 4OL0
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 GLY 415 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B LYS* 5.1 2.0 - - - +
411B ILE 4.2 0.9 - - - -
414B ILE* 1.3 82.0 - - - +
416B SER* 1.3 57.5 + - - -
417B MET* 3.2 3.6 - - - -
418B GLU* 3.5 23.5 - - - +
419B CYS* 2.6 38.0 + - - +
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Residues in contact with SER 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ILE* 3.8 17.9 + - - +
412B PHE* 6.1 0.2 - - - -
414B ILE 3.6 4.6 + - - -
415B GLY* 1.3 69.7 - - - +
417B MET* 1.3 58.3 + - - +
419B CYS* 3.8 4.1 - - - +
420B PHE* 2.9 32.1 + - - +
447B ILE* 3.1 28.0 - - - +
450B SER* 3.3 37.9 - - - -
451B VAL* 3.6 2.1 + - - +
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Residues in contact with MET 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B GLY* 5.0 0.7 - - - -
416B SER* 1.3 79.5 - - - +
418B GLU* 1.3 82.0 + - + +
420B PHE* 3.3 3.1 + - - +
421B ALA* 2.8 31.4 + - + +
451B VAL* 3.8 22.4 - - + +
452B ASP* 4.7 15.2 - - + +
455B ASN* 3.3 45.1 - - + +
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LYS* 6.4 0.7 - - - +
414B ILE* 5.5 2.7 - - + -
415B GLY* 3.1 24.8 + - - +
417B MET* 1.3 102.4 - - + +
419B CYS* 1.3 57.9 + - - +
421B ALA* 3.2 7.7 + - - +
422B GLN* 2.9 41.5 + - - +
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Residues in contact with CYS 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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373B LEU* 4.5 22.0 - - - -
411B ILE* 4.6 6.3 - - + -
414B ILE* 5.3 9.4 - - + +
415B GLY 2.6 20.2 + - - +
416B SER* 3.9 5.2 - - - +
418B GLU* 1.3 72.0 - - - +
420B PHE* 1.3 52.9 + - - +
422B GLN* 3.3 20.2 - - - +
423B LEU* 2.8 51.3 + - - +
443B ILE* 5.6 1.1 - - - -
447B ILE* 4.0 22.2 - - + -
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Residues in contact with PHE 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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416B SER 2.9 19.5 + - - +
417B MET* 3.5 4.5 - - - +
419B CYS* 1.3 77.1 - - - +
421B ALA* 1.3 60.4 + - - +
423B LEU* 3.3 9.3 + - - +
424B TYR* 2.8 26.7 + - - +
444B MET* 3.8 52.0 - - + +
447B ILE* 4.7 6.2 - - + +
448B ALA* 4.4 13.9 - - + -
451B VAL* 4.1 18.2 - - + -
455B ASN* 5.1 2.0 - - - -
458B THR* 4.8 5.4 - - + -
459B LEU* 3.7 29.4 - - + -
462B VAL* 3.7 36.1 - - + -
484B LEU* 4.5 2.2 - - + -
488B MET* 4.7 10.1 - - + -
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B MET* 2.8 24.0 + - + +
418B GLU* 3.2 9.6 + - - +
420B PHE* 1.3 78.3 - - - +
422B GLN* 1.3 57.8 + - - +
424B TYR* 3.1 8.9 + - - +
425B SER* 2.8 27.8 + - - -
455B ASN* 5.7 2.9 - - - +
458B THR* 4.8 15.0 - - + +
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Residues in contact with GLN 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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370B GLN* 4.6 19.0 + - - +
414B ILE* 5.3 4.4 - - - +
418B GLU* 2.9 28.9 + - - +
419B CYS* 3.3 25.8 - - - +
421B ALA* 1.3 73.3 - - - +
423B LEU* 1.3 61.9 - - + +
425B SER* 3.6 11.0 - - - -
426B THR* 3.3 19.6 + - - -
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Residues in contact with LEU 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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377B ALA* 4.9 15.7 - - + -
419B CYS* 2.8 39.0 + - - +
420B PHE* 3.4 5.8 - - - +
422B GLN* 1.3 77.1 - - + +
424B TYR* 1.3 65.5 + - - +
426B THR* 3.1 23.4 + - - +
427B LEU* 3.5 0.7 - - - +
440B VAL* 3.3 31.7 - - + +
443B ILE* 3.6 32.5 - - + -
444B MET* 3.9 23.6 - - + -
447B ILE* 4.1 6.5 - - + -
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Residues in contact with TYR 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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420B PHE* 2.8 14.9 + - + +
421B ALA* 3.1 9.2 + - - +
423B LEU* 1.3 76.0 - - - +
425B SER* 1.3 64.0 + - - +
426B THR 3.1 1.2 + - - -
427B LEU* 3.1 33.8 + - + +
428B LYS* 3.5 41.3 + - + +
444B MET* 4.0 10.9 - - + -
458B THR* 4.4 11.4 - - + -
461B GLU* 3.6 39.3 + - + +
462B VAL* 3.7 37.0 - - + -
465B GLY* 5.6 2.6 - - - -
466B VAL* 6.3 1.6 - - + -
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Residues in contact with SER 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ALA 2.8 15.9 + - - -
422B GLN* 3.6 13.9 - - - -
423B LEU 3.2 0.2 - - - -
424B TYR* 1.3 80.1 - - - +
426B THR* 1.3 61.9 + - - +
428B LYS* 3.4 18.1 + - - +
429B GLU* 3.4 29.6 + - - +
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Residues in contact with THR 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B GLN 3.3 10.6 + - - -
423B LEU* 3.2 18.3 + - - +
424B TYR 3.0 0.4 - - - -
425B SER* 1.3 79.5 - - - +
427B LEU* 1.3 62.0 + - - +
429B GLU 3.4 21.5 - - - +
430B GLY* 3.9 2.4 + - - -
432B PRO* 4.1 8.7 - - + +
436B VAL* 4.6 13.7 - - + -
440B VAL* 4.6 18.4 - - + +
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Residues in contact with LEU 427 (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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423B LEU 3.5 2.9 - - - +
424B TYR* 3.1 39.6 + - + +
426B THR* 1.3 75.0 - - - +
428B LYS* 1.3 65.6 + - - +
429B GLU 3.4 0.2 + - - -
430B GLY 4.2 1.0 + - - -
431B ASN* 4.3 5.5 - - - +
432B PRO* 3.6 24.4 - - + +
437B THR* 3.6 42.6 - - + +
440B VAL* 3.5 32.3 - - + -
441B LEU* 4.6 11.0 - - + -
444B MET* 4.2 5.6 - - + -
466B VAL* 6.5 0.2 - - + -
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Residues in contact with LYS 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B TYR* 3.5 36.4 + - + +
425B SER* 3.4 16.1 + - - +
426B THR 3.3 0.2 - - - -
427B LEU* 1.3 80.9 - - - +
429B GLU* 1.3 70.8 + - + +
430B GLY 4.0 1.0 + - - -
431B ASN* 5.1 3.5 - - - +
461B GLU* 3.0 29.7 + - - -
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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 SER* 3.4 26.9 + - - +
426B THR* 3.4 12.2 - - - +
427B LEU 3.3 0.2 - - - -
428B LYS* 1.3 88.5 - - + +
430B GLY* 1.3 56.9 + - - +
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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