Contacts of the helix formed by residues 512 - 523 (chain B) in PDB entry 2AUG
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 ASP 512 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433B ILE* 4.7 14.0 - - + +
501B HIS* 3.8 13.2 - - - -
510B PHE* 3.3 6.2 - - - +
511B THR* 1.3 86.1 + - - +
513B LEU* 1.3 64.2 + - - +
514B ILE* 3.9 13.8 - - - +
515B GLN* 2.7 25.8 + - - +
516B LEU* 3.2 14.7 + - - +
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Residues in contact with LEU 513 (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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434B HIS* 3.5 46.4 - - + +
439B TRP* 4.4 7.2 - - + -
440B PHE* 4.2 7.2 - - + -
465B VAL* 4.4 7.2 - - + -
475B PHE* 3.6 44.9 - - + -
490B ILE* 4.1 31.9 - - + -
501B HIS* 4.0 9.5 - - + +
512B ASP* 1.3 73.7 - - - +
514B ILE* 1.3 64.7 + - - +
516B LEU* 3.0 12.3 + - + +
517B VAL* 3.0 25.8 + - + +
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Residues in contact with ILE 514 (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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433B ILE* 3.8 37.2 - - + +
434B HIS* 4.4 7.6 - - + -
437B GLN* 4.0 37.9 - - + +
439B TRP* 4.1 12.1 - - + -
512B ASP* 3.3 11.2 + - - +
513B LEU* 1.3 76.5 - - - +
515B GLN* 1.3 63.6 + - - +
517B VAL* 3.4 1.0 + - - +
518B GLU* 3.0 53.9 + - + +
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Residues in contact with GLN 515 (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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509B ARG 4.5 1.0 - - - +
510B PHE* 3.0 19.6 - - + -
511B THR* 2.6 44.2 + - - +
512B ASP* 2.7 25.7 + - - +
514B ILE* 1.3 73.8 - - - +
516B LEU* 1.3 62.4 + - - +
518B GLU* 3.9 9.0 - - - +
519B PHE* 3.1 24.3 + - - +
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Residues in contact with LEU 516 (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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465B VAL* 5.9 0.2 - - + -
477B LEU* 5.5 4.9 - - + -
490B ILE* 3.8 46.9 - - + -
501B HIS* 4.5 7.4 - - + -
502B THR* 4.6 4.9 - - - +
503B LEU* 4.5 13.5 - - + -
510B PHE* 3.6 38.7 - - + -
512B ASP 3.2 7.6 + - - +
513B LEU* 3.0 12.4 + - + +
515B GLN* 1.3 79.3 - - - +
517B VAL* 1.3 76.7 + - + +
519B PHE* 3.3 2.6 + - - +
520B TYR* 3.1 43.3 + - + -
531B LEU* 5.5 1.3 - - + -
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Residues in contact with VAL 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B TRP* 3.6 50.7 - - + +
463B PHE* 3.9 24.9 - - + -
465B VAL* 3.9 15.9 - - + -
477B LEU* 5.9 0.2 - - + -
513B LEU* 3.0 19.8 + - + +
514B ILE 3.9 1.1 - - - +
516B LEU* 1.3 83.5 - - + +
518B GLU* 1.3 68.3 + - + +
519B PHE 3.2 0.2 + - - -
520B TYR 3.2 2.1 + - - -
521B GLN* 3.0 36.5 + - - +
531B LEU* 3.9 8.7 - - + +
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Residues in contact with GLU 518 (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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439B TRP* 6.3 1.6 - - + +
514B ILE* 3.0 41.3 + - + +
515B GLN* 3.9 7.2 - - - +
517B VAL* 1.3 77.8 - - + +
519B PHE* 1.3 63.5 + - - +
521B GLN* 3.4 26.0 + - - +
522B LEU* 3.5 13.3 + - - +
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Residues in contact with PHE 519 (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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508B THR* 3.9 22.0 - - + -
510B PHE* 3.4 28.3 - + + -
515B GLN* 3.1 14.8 + - + +
516B LEU 3.3 9.2 - - - +
518B GLU* 1.3 77.4 - - - +
520B TYR* 1.3 76.4 + + - +
522B LEU* 3.0 4.1 + - - -
523B ASN* 2.6 75.3 + - + +
525B GLY* 5.2 5.6 - - - -
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Residues in contact with TYR 520 (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 LEU* 5.7 0.2 - - + -
503B LEU* 3.5 32.4 + - + +
504B ASP* 4.0 5.5 + - - -
508B THR* 3.9 22.0 + - - -
510B PHE* 3.7 23.6 - + - -
516B LEU* 3.1 36.9 + - + +
517B VAL 3.2 0.6 + - - -
519B PHE* 1.3 91.5 - + - +
521B GLN* 1.3 62.0 + - - +
522B LEU 3.1 2.2 - - - -
523B ASN 3.1 24.6 - - - +
524B LYS 3.6 13.0 - - - -
525B GLY* 4.3 7.4 - - - -
526B VAL* 4.6 2.6 + - - +
527B LEU* 3.5 24.2 - - + -
530B LYS* 3.5 4.7 - - - -
531B LEU* 2.9 44.7 + - + -
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Residues in contact with GLN 521 (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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439B TRP* 4.9 6.3 + - - -
463B PHE* 4.0 20.4 - - - -
517B VAL* 3.0 30.3 + - + +
518B GLU* 3.6 23.1 + - - +
519B PHE 3.2 0.6 - - - -
520B TYR* 1.3 78.9 - - - +
522B LEU* 1.3 60.4 + - + +
530B LYS* 4.1 12.4 + - - +
531B LEU* 3.3 32.8 + - + +
532B LYS 5.3 4.2 + - - -
534B TYR* 5.3 6.1 - - - -
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Residues in contact with LEU 522 (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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518B GLU 3.5 9.3 + - - +
519B PHE* 3.0 7.3 + - - +
521B GLN* 1.3 82.7 - - - +
523B ASN* 1.3 75.6 + - - +
530B LYS* 3.2 22.3 + - - +
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Residues in contact with ASN 523 (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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519B PHE* 2.6 63.8 + - + +
520B TYR* 3.1 27.4 - - - +
522B LEU* 1.3 100.8 - - - +
524B LYS* 1.3 65.2 + - - +
525B GLY* 4.6 3.1 - - - +
530B LYS* 3.7 3.8 - - - -
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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