Contacts of the helix formed by residues 433 - 446 (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 PRO 433 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431B ASN 4.4 1.6 - - - +
432B PRO* 1.3 92.8 - - + +
434B TRP* 1.3 66.9 + - + +
435B GLU* 3.2 30.2 + - - +
436B VAL* 3.5 15.9 + - + -
437B THR* 3.2 19.3 + - - -
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Residues in contact with TRP 434 (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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382B LEU* 3.6 29.2 - - + -
383B GLU 3.1 26.7 - - - -
384B PRO* 3.8 14.5 + - + +
386B HIS* 3.5 21.1 - + + -
433B PRO* 1.3 74.6 - - + +
435B GLU* 1.3 82.7 + - + +
437B THR* 4.3 3.8 - - - -
438B GLU* 2.8 37.1 + - + +
473B VAL* 6.0 0.4 - - + -
474B HIS* 3.5 43.7 - + + -
476B ALA* 3.5 22.4 - - + -
477B VAL* 3.6 24.3 - - + +
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Residues in contact with GLU 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLN* 4.1 13.8 - - + +
382B LEU 3.8 29.4 - - - +
383B GLU 4.9 0.2 - - - -
384B PRO* 3.4 30.7 - - + +
433B PRO* 3.2 29.1 - - + +
434B TRP* 1.3 117.8 + - + +
436B VAL* 1.3 67.8 + - + +
438B GLU* 3.6 3.5 - - - +
439B ALA* 2.9 29.8 + - - +
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Residues in contact with VAL 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLN* 3.8 33.2 - - - +
426B THR* 4.6 9.9 - - + -
432B PRO* 3.6 23.8 - - + -
433B PRO* 3.5 23.5 + - + +
434B TRP 3.3 0.4 - - - -
435B GLU* 1.3 74.8 - - + +
437B THR* 1.3 61.1 + - - +
439B ALA* 3.1 2.4 + - - +
440B VAL* 2.8 47.5 + - + +
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Residues in contact with THR 437 (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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427B LEU* 3.6 26.3 - - + +
432B PRO* 3.5 20.5 + - - +
433B PRO 3.2 13.6 + - - -
434B TRP* 3.7 10.7 - - - -
436B VAL* 1.3 78.6 - - - +
438B GLU* 1.3 58.6 + - - +
440B VAL* 3.4 3.2 + - - +
441B LEU* 2.8 41.2 + - + +
477B VAL* 3.7 24.9 - - + -
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Residues in contact with GLU 438 (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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380B CYS 4.0 4.0 - - - +
382B LEU* 4.1 13.6 + - - +
390B PRO* 4.0 1.9 - - - +
400B ARG* 2.8 39.4 + - - -
434B TRP* 2.8 32.5 + - + +
435B GLU 3.6 4.6 - - - +
437B THR* 1.3 74.6 - - - +
439B ALA* 1.3 59.3 + - - +
441B LEU* 3.3 9.4 + - - +
442B PHE* 2.8 25.5 + - - +
476B ALA* 3.8 26.7 - - + +
477B VAL* 4.2 4.9 - - + +
480B THR* 2.4 31.3 + - - +
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Residues in contact with ALA 439 (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 4.0 10.3 - - - +
380B CYS* 3.9 7.2 - - + -
381B GLN* 3.5 35.9 - - + +
435B GLU 2.9 17.8 + - - +
436B VAL 3.1 4.0 + - - +
438B GLU* 1.3 81.7 + - - +
440B VAL* 1.3 57.9 + - + +
442B PHE* 3.1 7.6 + - - +
443B ILE* 2.9 34.3 + - - +
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Residues in contact with VAL 440 (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* 6.4 2.5 - - + -
423B LEU* 3.3 44.8 - - + +
426B THR* 4.6 15.0 - - + -
427B LEU* 3.5 20.9 - - + -
432B PRO* 6.4 0.2 - - + -
436B VAL* 2.8 37.4 + - + +
437B THR* 3.7 5.6 - - - +
439B ALA* 1.3 72.3 - - + +
441B LEU* 1.3 59.2 + - - +
443B ILE* 3.2 7.7 + - - +
444B MET* 2.8 35.0 + - + +
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Residues in contact with LEU 441 (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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427B LEU* 4.6 7.9 - - + -
437B THR* 2.8 29.5 + - + +
438B GLU* 3.6 2.5 - - - +
440B VAL* 1.3 75.6 - - - +
442B PHE* 1.3 57.6 - - - +
444B MET* 3.5 25.9 - - + +
445B ALA* 2.8 30.7 + - - +
466B VAL* 4.0 16.6 - - + -
477B VAL* 3.7 39.7 - - + +
480B THR* 3.4 16.4 - - + +
481B SER* 4.1 10.5 - - - -
484B LEU* 3.6 20.8 - - + +
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Residues in contact with PHE 442 (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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380B CYS* 4.0 25.8 - - + -
400B ARG* 3.3 76.5 - - + +
401B MET* 4.4 4.0 - - + -
404B SER* 4.0 19.7 - - - -
438B GLU* 2.8 18.6 + - - +
439B ALA* 3.1 7.8 + - - +
441B LEU* 1.3 75.0 - - - +
443B ILE* 1.3 66.1 + - + +
445B ALA* 3.4 6.1 + - + +
446B ALA* 3.4 17.8 + - + +
480B THR* 3.2 13.8 - - + +
483B GLU* 4.7 13.9 - - - -
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Residues in contact with ILE 443 (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 5.0 1.1 - - - +
376B LEU 4.2 1.8 - - - +
377B ALA* 3.5 37.5 - - + +
380B CYS* 4.1 15.3 - - + -
403B VAL* 4.6 8.3 - - + -
407B VAL* 4.7 17.9 - - + -
419B CYS* 5.6 1.1 - - - -
423B LEU* 3.6 24.5 - - + -
439B ALA 2.9 20.9 + - - +
440B VAL* 3.8 5.4 - - - +
442B PHE* 1.3 83.6 - - + +
444B MET* 1.3 64.4 + - - +
446B ALA* 3.0 15.0 + - - +
447B ILE* 3.3 25.2 - - + +
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Residues in contact with MET 444 (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* 3.8 36.6 - - + +
423B LEU* 3.9 21.8 - - + -
424B TYR* 4.0 27.8 - - + -
427B LEU* 4.2 9.6 - - + -
440B VAL* 2.8 24.9 + - + +
441B LEU* 3.5 36.8 - - + +
443B ILE* 1.3 75.6 - - - +
445B ALA* 1.3 59.0 + - - +
447B ILE* 3.0 4.2 + - - +
448B ALA* 2.9 32.1 + - - +
462B VAL* 4.3 8.7 - - + -
466B VAL* 5.8 0.2 - - + -
484B LEU* 3.8 13.0 - - + +
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Residues in contact with ALA 445 (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 LYS* 5.7 0.5 + - - -
441B LEU 2.8 17.4 + - - +
442B PHE* 3.5 9.9 - - + +
443B ILE 3.2 0.2 - - - -
444B MET* 1.3 76.2 - - - +
446B ALA* 1.3 59.8 + - - +
447B ILE 3.2 1.0 + - - -
448B ALA 3.9 2.6 + - - -
480B THR* 4.7 1.3 - - + +
483B GLU* 4.5 11.7 - - + +
484B LEU* 3.6 34.7 - - + +
487B GLU* 3.3 34.2 - - + +
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Residues in contact with ALA 446 (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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404B SER* 3.2 38.6 - - - +
407B VAL* 4.4 7.2 - - + -
408B LYS* 3.4 35.7 - - - +
411B ILE* 5.8 0.2 - - - +
442B PHE* 3.4 9.5 + - + +
443B ILE* 3.0 12.8 + - - +
445B ALA* 1.3 78.0 - - - +
447B ILE* 1.3 61.3 + - - +
449B LYS 5.6 0.2 - - - -
450B SER* 5.2 1.6 + - - -
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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