Contacts of the helix formed by residues 478 - 489 (chain B) in PDB entry 3OEE
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 HIS 478 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473B TYR* 3.1 46.2 + + - -
474B LEU* 2.9 26.3 + - + +
477B ASN* 1.3 88.5 + - + +
479B ASN* 1.3 62.5 + - - +
480B GLU* 3.3 5.2 - - - +
481B LEU* 3.2 38.0 + - + +
482B LEU* 3.6 8.3 + - - +
501B SER* 6.3 0.9 - - - -
502B ALA* 3.6 24.3 - - + +
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Residues in contact with ASN 479 (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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474B LEU 3.1 4.4 + - - -
475B LYS* 3.0 31.1 - - - +
476B SER 5.1 2.2 - - - +
477B ASN 3.6 1.4 - - - -
478B HIS* 1.3 73.5 - - - +
480B GLU* 1.3 61.0 + - + +
481B LEU 3.1 2.5 - - - -
482B LEU* 3.4 13.9 + - - +
483B THR* 2.7 43.9 + - - -
486B ARG* 4.9 7.0 + - - +
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Residues in contact with GLU 480 (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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477B ASN 6.1 0.7 - - - +
478B HIS* 5.0 1.3 - - - -
479B ASN* 1.3 77.3 - - + +
481B LEU* 1.3 68.5 + - + +
483B THR* 3.5 7.9 - - - -
484B GLU* 3.2 23.2 + - - +
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Residues in contact with LEU 481 (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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474B LEU* 5.7 1.8 - - + -
478B HIS* 3.5 36.1 - - + +
479B ASN 3.1 0.2 - - - -
480B GLU* 1.3 84.6 - - + +
482B LEU* 1.3 67.8 + - + +
483B THR 3.2 0.9 - - - -
484B GLU* 2.9 12.9 + - - +
485B ILE* 3.0 22.4 + - + +
495B LEU* 3.8 23.4 - - + +
498B SER* 3.4 42.2 - - - +
499B LEU* 4.6 13.2 - - + +
502B ALA* 5.0 3.1 - - + -
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Residues in contact with LEU 482 (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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441B GLU* 3.4 42.5 - - + +
442B GLU* 5.4 4.9 - - + -
445B PRO* 4.2 13.9 - - + -
471B LEU* 5.3 2.5 - - + +
474B LEU* 4.1 37.0 - - + +
475B LYS* 4.2 18.4 - - + -
478B HIS 4.0 10.1 - - - +
479B ASN* 3.4 21.5 + - - +
481B LEU* 1.3 77.1 - - + +
483B THR* 1.3 63.1 + - - +
485B ILE* 3.0 15.6 + - + +
486B ARG* 2.9 24.7 + - - +
499B LEU* 5.9 2.0 - - + -
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Residues in contact with THR 483 (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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479B ASN* 2.7 34.2 + - - -
480B GLU* 3.5 9.3 - - - -
482B LEU* 1.3 76.3 - - - +
484B GLU* 1.3 56.7 + - - +
486B ARG* 3.4 34.4 + - - +
487B GLU* 2.9 48.3 + - - +
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Residues in contact with GLU 484 (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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480B GLU 3.2 12.8 + - - +
481B LEU 2.9 9.9 + - - +
483B THR* 1.3 73.2 - - - +
485B ILE* 1.3 61.3 + - - +
487B GLU* 4.5 3.4 - - - +
488B LYS* 3.0 52.9 + - + +
489B GLY 3.9 0.2 + - - -
490B GLU 4.6 4.5 - - - +
492B SER* 3.7 15.3 + - - -
494B GLU* 5.0 8.8 - - - +
495B LEU* 3.3 37.7 - - + +
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Residues in contact with ILE 485 (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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384B ALA* 4.0 18.4 - - + -
440B THR* 4.7 3.6 - - + +
441B GLU* 3.8 22.2 - - + +
444B VAL* 3.5 35.9 - - + -
445B PRO* 5.1 0.7 - - + -
481B LEU* 3.0 21.2 + - + +
482B LEU* 3.3 18.6 - - + +
484B GLU* 1.3 75.7 - - - +
486B ARG* 1.3 55.8 + - - +
489B GLY* 2.8 33.3 + - - +
490B GLU 4.6 4.0 - - - -
491B LEU* 4.0 8.5 - - + -
495B LEU* 3.6 21.5 - - + -
499B LEU* 4.9 15.3 - - + -
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Residues in contact with ARG 486 (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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440B THR* 6.2 2.0 - - - -
441B GLU* 3.1 43.0 + - - +
479B ASN* 4.9 7.7 + - - +
482B LEU* 2.9 15.3 + - - +
483B THR* 3.5 51.3 + - - +
485B ILE* 1.3 79.0 - - - +
487B GLU* 1.3 65.4 + - + +
489B GLY* 4.3 2.9 + - - -
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Residues in contact with GLU 487 (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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483B THR* 2.9 39.9 + - + +
484B GLU* 4.5 3.3 - - - +
486B ARG* 1.3 85.1 - - + +
488B LYS* 1.3 63.9 + - + +
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Residues in contact with LYS 488 (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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484B GLU* 3.0 35.2 + - + +
486B ARG 4.9 0.2 - - - -
487B GLU* 1.3 83.1 - - + +
489B GLY* 1.3 58.3 + - - +
490B GLU* 3.1 28.5 + - + +
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Residues in contact with GLY 489 (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 VAL* 3.9 13.6 - - - +
383B LYS* 3.3 10.8 + - - +
384B ALA* 2.7 35.9 + - - +
484B GLU 3.9 0.2 + - - -
485B ILE 2.8 22.0 + - - -
486B ARG 4.3 3.1 + - - -
487B GLU 3.8 0.6 - - - -
488B LYS* 1.3 76.9 - - - +
490B GLU* 1.3 55.2 + - - +
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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