Contacts of the helix formed by residues 455 - 468 (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 ASN 455 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417B MET* 3.3 45.5 - - + +
420B PHE* 5.1 1.2 - - - -
421B ALA* 5.7 2.9 - - - +
451B VAL* 3.8 6.2 - - + +
452B ASP* 3.2 18.3 + - + +
453B PRO 2.8 1.7 + - - -
454B GLU* 1.3 74.9 - - - +
456B ASN* 1.3 61.9 + - - +
457B PRO* 3.0 10.9 - - - +
458B THR* 3.1 28.5 + - - +
459B LEU* 3.4 24.3 + - - +
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Residues in contact with ASN 456 (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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453B PRO 2.6 20.4 + - - +
454B GLU* 3.0 15.8 - - - +
455B ASN* 1.3 71.1 - - - +
457B PRO* 1.4 80.6 - - - +
459B LEU* 3.7 14.8 - - + -
460B VAL* 2.9 33.1 + - + +
491B VAL* 5.1 3.8 - - + -
494B ARG* 6.4 0.9 - - + -
495B ASN* 3.5 31.8 + - - +
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Residues in contact with PRO 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B GLU 3.5 8.5 - - - +
455B ASN* 3.0 10.8 - - - +
456B ASN* 1.4 102.4 - - - +
458B THR* 1.3 59.9 + - - +
460B VAL* 3.3 19.2 - - + +
461B GLU* 3.6 12.1 - - - +
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Residues in contact with THR 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B PHE* 4.8 7.9 - - + -
421B ALA* 4.8 18.3 - - + +
424B TYR* 4.4 21.3 - - + -
455B ASN* 3.1 29.6 + - - +
457B PRO* 1.3 77.3 - - - +
459B LEU* 1.3 58.2 + - - +
461B GLU* 2.7 32.9 + - - +
462B VAL* 2.9 16.5 + - + +
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Residues in contact with LEU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B PHE* 3.7 23.8 - - + -
448B ALA 5.7 1.8 - - - +
451B VAL* 3.9 20.0 - - + +
452B ASP 4.0 18.4 - - - +
453B PRO* 4.3 5.2 - - + +
455B ASN* 3.4 20.4 + - - +
456B ASN* 3.3 21.3 + - + +
458B THR* 1.3 77.9 - - - +
460B VAL* 1.3 52.0 + - - +
462B VAL* 2.7 27.3 + - - +
463B LEU 2.7 16.3 + - - -
488B MET* 3.5 25.8 - - + +
491B VAL* 3.7 26.0 - - + -
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Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ASN* 2.9 31.5 + - - +
457B PRO* 3.3 15.0 - - + +
459B LEU* 1.3 71.8 - - - +
461B GLU* 1.3 61.0 + - - +
463B LEU* 4.2 8.5 - - + -
464B GLU* 2.9 33.3 + - - +
491B VAL* 4.2 11.0 - - + -
495B ASN* 3.5 33.7 - - + +
498B PHE* 3.8 21.4 - - + -
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Residues in contact with GLU 461 (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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424B TYR* 3.6 21.7 + - + +
428B LYS* 3.0 34.0 + - - -
457B PRO 3.6 12.3 - - - +
458B THR* 2.7 21.9 + - - +
460B VAL* 1.3 78.3 - - + +
462B VAL* 1.3 62.2 + - - +
464B GLU* 3.9 9.1 - - - +
465B GLY* 3.2 17.2 + - - -
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Residues in contact with VAL 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B PHE* 3.7 35.9 - - + -
424B TYR* 3.7 37.0 - - + -
444B MET* 4.3 8.7 - - + -
458B THR* 2.9 15.9 + - + +
459B LEU* 2.7 8.0 + - - +
461B GLU* 1.3 75.5 - - - +
463B LEU* 1.3 54.7 + - - +
465B GLY* 2.7 22.4 + - - -
466B VAL* 2.7 26.6 + - + +
484B LEU* 4.0 27.4 - - + -
488B MET* 4.6 3.4 - - + -
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Residues in contact with LEU 463 (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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459B LEU 2.7 16.1 + - - +
460B VAL* 4.1 4.5 - - - +
462B VAL* 1.3 71.6 - - - +
464B GLU* 1.3 56.3 + - - +
466B VAL* 2.8 27.3 + - - +
467B VAL* 2.9 33.6 + - + +
485B VAL* 4.2 26.0 - - + -
488B MET* 4.0 18.3 - - + +
491B VAL* 4.3 18.6 - - + -
492B VAL* 3.8 26.7 - - + +
498B PHE* 4.0 27.6 - - + -
502B VAL* 4.2 9.4 - - + -
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Residues in contact with GLU 464 (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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460B VAL 2.9 23.3 + - - +
461B GLU* 3.9 10.4 - - - +
463B LEU* 1.3 74.3 - - - +
465B GLY* 1.3 61.8 + - - +
467B VAL* 4.1 7.7 - - - +
468B ARG* 2.5 73.1 + - - +
498B PHE* 3.8 22.1 - - + -
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Residues in contact with GLY 465 (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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424B TYR* 5.6 2.9 - - - -
461B GLU 3.2 15.0 + - - -
462B VAL* 2.7 17.8 + - - -
464B GLU* 1.3 78.9 - - - +
466B VAL* 1.3 58.3 + - - +
467B VAL 3.4 2.1 + - - -
468B ARG* 4.4 4.5 - - - +
469B LEU* 3.9 19.8 + - - +
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Residues in contact with VAL 466 (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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424B TYR* 6.3 1.8 - - + -
427B LEU* 6.5 0.2 - - + -
441B LEU* 4.0 28.5 - - + -
462B VAL* 2.7 24.2 + - + +
463B LEU* 2.8 18.3 + - + +
465B GLY* 1.3 75.3 - - - +
467B VAL* 1.3 58.7 + - - +
469B LEU* 3.2 22.8 - - + +
481B SER* 4.2 12.4 + - - +
484B LEU* 4.2 15.7 - - + -
485B VAL* 3.7 22.0 - - + +
488B MET* 5.5 0.4 - - - -
505B TYR* 3.4 16.1 + - - -
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Residues in contact with VAL 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B LEU* 2.9 29.1 + - + +
464B GLU* 4.4 7.2 - - - +
466B VAL* 1.3 82.4 - - - +
468B ARG* 1.3 62.5 + - + +
469B LEU 3.6 1.9 - - - +
485B VAL* 4.4 7.4 - - + -
498B PHE* 6.0 1.3 - - + -
501B PRO* 4.0 34.3 - - + +
502B VAL* 3.9 25.6 - - + -
505B TYR* 3.1 31.8 - - + +
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Residues in contact with ARG 468 (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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464B GLU* 2.5 60.8 + - - +
465B GLY* 4.2 5.4 + - - +
467B VAL* 1.3 82.0 - - + +
469B LEU* 1.3 63.6 + - - +
470B PRO* 3.6 4.2 - - - +
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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