Contacts of the helix formed by residues 478 - 489 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473A TYR* 3.2 41.8 + + - -
474A LEU* 2.8 24.9 + - + +
477A ASN* 1.3 99.6 + - + +
479A ASN* 1.3 52.3 + - - +
480A GLU* 2.6 32.9 + - - -
481A LEU* 2.7 35.0 + - + +
482A LEU* 3.5 6.9 + - - +
501A SER* 6.0 0.7 - - - -
502A ALA* 3.5 28.7 - - + +
505A SER* 5.9 0.4 - - - -
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Residues in contact with ASN 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A LEU 3.0 7.8 + - - -
475A LYS* 3.9 15.0 + - - +
476A SER 4.0 13.9 - - - +
477A ASN 4.4 0.9 - - - -
478A HIS* 1.3 76.7 + - - +
480A GLU* 1.3 69.1 + - - +
482A LEU* 3.7 11.3 + - - +
483A THR* 2.9 35.3 + - - +
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Residues in contact with GLU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A ASN 3.0 25.1 - - - +
478A HIS* 2.6 16.4 + - - +
479A ASN* 1.3 84.4 + - - +
481A LEU* 1.3 88.6 + - + +
483A THR* 3.4 5.4 + - - +
484A GLU* 3.1 24.1 + - - +
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Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A LEU* 4.7 4.3 - - + -
478A HIS* 2.7 31.1 + - + +
480A GLU* 1.3 90.7 - - + +
482A LEU* 1.3 62.7 + - + +
484A GLU* 3.2 7.8 + - - +
485A ILE* 2.9 37.3 + - + +
495A LEU* 4.0 8.4 - - + +
498A SER* 3.7 38.1 - - - +
499A LEU* 4.2 15.5 - - + +
502A ALA* 3.9 28.7 - - + -
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Residues in contact with LEU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A GLU* 3.2 44.2 - - + +
442A GLU* 5.1 6.3 - - + +
445A PRO* 4.0 14.6 - - + -
471A LEU* 4.9 2.2 - - + +
474A LEU* 4.1 30.7 - - + +
475A LYS* 3.9 33.4 - - + -
478A HIS 3.5 6.8 + - - +
479A ASN* 4.0 8.7 - - - +
480A GLU 3.3 0.2 - - - -
481A LEU* 1.3 80.5 - - + +
483A THR* 1.3 63.1 + - - +
485A ILE* 3.3 4.1 + - + -
486A ARG* 3.0 27.6 + - - +
499A LEU* 6.4 0.4 - - + -
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Residues in contact with THR 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A ASN* 2.9 23.0 + - - +
480A GLU* 3.9 5.8 - - - +
481A LEU 3.3 0.2 - - - -
482A LEU* 1.3 76.4 - - - +
484A GLU* 1.3 58.0 + - - +
486A ARG* 3.8 23.5 + - - +
487A GLU* 2.9 57.8 + - - +
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Residues in contact with GLU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A GLU 3.1 16.9 + - - +
481A LEU* 3.2 4.9 + - - +
483A THR* 1.3 75.9 - - - +
485A ILE* 1.3 58.5 + - - +
487A GLU* 4.7 2.9 - - - -
488A LYS* 2.7 76.6 + - + +
492A SER* 5.3 0.7 + - - -
495A LEU* 3.3 40.1 - - + +
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Residues in contact with ILE 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A VAL* 5.5 0.9 - - - +
384A ALA* 4.1 6.5 - - + -
440A THR* 5.0 3.7 - - + +
441A GLU* 3.9 14.8 - - + +
444A VAL* 3.7 44.9 - - + -
445A PRO* 4.2 14.1 - - + -
481A LEU* 2.9 25.2 + - + +
482A LEU* 3.3 7.4 + - + +
484A GLU* 1.3 74.2 - - - +
486A ARG* 1.3 58.0 + - - +
489A GLY* 2.9 30.0 + - - -
490A GLU 4.7 1.8 - - - -
491A LEU* 3.8 27.6 - - + -
495A LEU* 3.8 6.5 - - + -
499A LEU* 5.0 10.5 - - + -
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Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A THR* 6.1 2.5 - - - -
441A GLU* 3.4 43.0 + - - +
482A LEU* 3.0 18.2 + - - +
483A THR* 3.8 28.7 + - - +
485A ILE* 1.3 79.6 - - - +
487A GLU* 1.3 84.8 + - + +
488A LYS 3.6 0.2 + - - -
489A GLY* 4.1 4.0 + - - -
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Residues in contact with GLU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A THR* 2.9 40.0 + - + +
484A GLU* 4.2 3.0 - - - +
486A ARG* 1.3 99.1 + - + +
488A LYS* 1.3 65.3 + - + +
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Residues in contact with LYS 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A GLU* 2.7 54.5 + - + +
487A GLU* 1.3 81.3 - - + +
489A GLY* 1.3 54.0 + - - +
490A GLU* 3.0 30.5 + - + +
492A SER* 5.7 3.1 + - - +
495A LEU* 5.1 3.1 - - + -
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Residues in contact with GLY 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A VAL* 3.3 21.6 - - - +
383A LYS* 3.5 6.2 + - - +
384A ALA* 2.8 35.5 + - - +
485A ILE 2.9 19.6 + - - -
486A ARG 4.1 3.6 + - - -
487A GLU 3.8 0.8 - - - -
488A LYS* 1.3 74.9 - - - +
490A GLU* 1.3 54.8 + - - +
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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