Contacts of the helix formed by residues 504 - 514 (chain F) in PDB entry 2AJQ
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 504 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499F GLU* 4.3 5.7 + - - -
502F ASN* 3.9 2.8 - - - +
503F GLY* 1.3 84.1 - - - +
505F ILE* 1.3 55.0 + - - +
506F HIS* 3.1 3.4 - - - -
507F THR* 2.8 44.0 + - + +
508F LYS* 3.1 9.2 + - - +
518F ARG* 4.7 13.5 + - - +
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Residues in contact with ILE 505 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481F LEU* 3.7 25.1 - - + -
496F TYR* 3.4 45.1 - - + +
499F GLU* 4.2 15.4 + - + -
500F ILE* 3.6 33.8 + - + -
503F GLY 3.8 1.6 + - - -
504F ASP* 1.3 75.4 - - - +
506F HIS* 1.3 73.5 + - + +
508F LYS* 3.0 18.6 + - + +
509F ASN* 2.8 29.5 + - - +
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Residues in contact with HIS 506 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481F LEU* 3.7 25.8 - - + +
504F ASP 3.0 1.0 + - - -
505F ILE* 1.3 88.0 - - + +
507F THR* 1.3 60.8 + - - +
509F ASN* 4.4 8.5 + - - +
510F GLN* 3.0 27.4 + - - +
518F ARG* 4.2 26.6 - - + +
521F ALA* 3.6 7.4 + - - +
522F LYS* 3.3 57.8 + - + +
525F ILE* 4.3 3.3 - - + +
526F TYR* 3.8 18.6 + + - -
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Residues in contact with THR 507 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504F ASP* 2.8 27.5 + - + +
506F HIS* 1.3 78.1 - - - +
508F LYS* 1.3 64.3 + - - +
510F GLN* 3.1 13.9 + - - +
511F ILE* 3.0 41.8 + - + +
518F ARG* 4.3 15.8 - - - +
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Residues in contact with LYS 508 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496F TYR* 4.2 14.6 - - + -
499F GLU* 3.4 48.9 - - + +
504F ASP 3.1 7.4 + - - +
505F ILE* 3.0 23.4 + - + +
507F THR* 1.3 79.7 - - - +
509F ASN* 1.3 59.1 + - - +
511F ILE* 3.5 8.8 + - - +
512F ALA* 3.0 28.3 + - + +
559F THR* 6.4 0.9 - - + -
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Residues in contact with ASN 509 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481F LEU* 4.5 2.6 - - - +
496F TYR* 2.7 38.4 + - - -
505F ILE* 2.8 24.7 + - - +
506F HIS* 4.1 9.8 + - - +
508F LYS* 1.3 76.1 - - - +
510F GLN* 1.3 66.5 + - - +
512F ALA* 3.2 2.1 + - - +
513F ALA* 2.8 28.3 + - - +
521F ALA* 4.5 8.7 - - + +
524F PHE* 5.4 2.7 - - + -
525F ILE* 3.7 29.6 - - + +
555F PHE* 3.9 26.6 - - + -
559F THR* 5.7 0.2 - - - +
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Residues in contact with GLN 510 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506F HIS 3.0 17.2 + - - +
507F THR* 3.1 14.3 + - - +
509F ASN* 1.3 76.2 - - - +
511F ILE* 1.3 56.0 + - + +
513F ALA 3.5 0.2 - - - -
514F GLU 2.7 31.5 + - - -
515F LEU* 3.2 40.1 + - + +
516F PRO 3.4 10.5 + - - -
517F THR* 3.3 31.4 - - - +
518F ARG* 3.4 21.6 - - - +
521F ALA* 3.7 12.1 - - + +
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Residues in contact with ILE 511 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507F THR* 3.0 36.1 + - + +
508F LYS* 3.8 8.1 - - - +
510F GLN* 1.3 79.6 - - + +
512F ALA* 1.3 62.8 + - - +
514F GLU* 3.3 21.1 + - - +
558F ASN* 4.5 7.1 + - - +
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Residues in contact with ALA 512 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508F LYS* 3.0 20.7 + - + +
509F ASN* 3.2 4.7 + - - +
511F ILE* 1.3 80.2 - - - +
513F ALA* 1.3 58.9 + - - +
514F GLU* 3.2 1.9 + - - +
554F LYS* 3.7 16.6 - - - +
555F PHE* 4.0 10.1 - - + -
558F ASN* 3.7 42.0 - - + +
559F THR* 3.9 15.0 - - - +
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Residues in contact with ALA 513 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509F ASN 2.8 19.1 + - - +
512F ALA* 1.3 72.1 - - - +
514F GLU* 1.3 71.2 + - - +
515F LEU* 3.6 23.8 - - + -
524F PHE* 3.9 13.9 - - + -
551F LEU* 3.3 22.1 - - + +
554F LYS* 4.6 5.7 - - - +
555F PHE* 3.8 27.6 - - + +
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Residues in contact with GLU 514 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510F GLN 2.7 10.4 + - - -
511F ILE* 3.3 14.6 + - - +
512F ALA 3.2 2.2 - - - +
513F ALA* 1.3 82.7 - - - +
515F LEU* 1.3 57.9 + - - +
516F PRO* 4.6 0.7 - - - +
547F ARG* 3.9 16.8 + - - +
554F LYS* 3.4 41.9 + - + +
558F ASN* 4.9 4.3 + - - +
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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