Contacts of the helix formed by residues 455 - 460 (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 PHE 455 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F PHE* 3.6 40.2 - + + -
233F PRO 3.6 4.9 - - - -
234F PHE* 3.9 15.5 - + + -
406F TRP* 3.7 40.4 - + - -
416F ILE* 3.8 15.9 - - + -
437F LEU* 3.6 22.9 - - + -
440F ILE* 3.8 25.6 - - + -
451F CYS 3.3 19.7 - - - -
452F ARG* 3.0 9.6 + - - +
453F ALA 4.0 1.3 - - - -
454F ALA* 1.3 78.4 - - - +
456F GLY* 1.3 57.9 + - - +
699F ASN* 3.4 0.5 - - - +
700F TRP* 2.8 36.5 + + + +
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Residues in contact with GLY 456 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232F PHE* 3.6 5.9 - - - -
233F PRO* 3.1 24.1 + - - +
455F PHE* 1.3 75.3 - - - +
457F ALA* 1.3 67.4 + - - -
458F GLU 3.0 2.7 - - - -
459F HIS* 2.9 20.7 + - - +
471F GLN* 3.1 11.4 - - - -
698F PRO 3.7 0.2 - - - -
699F ASN* 3.6 13.5 - - - -
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Residues in contact with ALA 457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F PRO* 4.3 6.1 - - - -
456F GLY* 1.3 72.2 - - - -
458F GLU* 1.3 63.0 + - - +
460F HIS* 2.9 24.5 + - - +
469F TRP* 3.5 14.1 - - + +
470F VAL 3.1 35.0 - - - +
471F GLN* 3.0 13.9 + - + +
642F TRP* 5.3 1.1 - - + -
649F MET* 4.2 10.1 - - - -
659F GLY* 4.0 15.9 - - - -
698F PRO 3.4 0.8 + - - -
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Residues in contact with GLU 458 (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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453F ALA 4.5 0.2 - - - +
456F GLY 3.0 0.2 - - - -
457F ALA* 1.3 78.4 - - - +
459F HIS* 1.3 88.1 + - + +
460F HIS 3.1 3.9 + - - +
461F LEU* 4.3 4.3 - - - +
468F PRO* 3.3 24.2 - - + +
469F TRP 3.4 13.3 + - - +
698F PRO* 2.9 40.2 + - + +
699F ASN* 2.9 27.9 + - + -
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Residues in contact with HIS 459 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F PRO* 3.9 11.6 - - + +
234F PHE 4.2 12.5 - - - +
235F ASP* 3.1 38.3 + - + +
414F GLY 5.0 4.3 - - - +
453F ALA 2.9 22.9 + - - -
454F ALA 3.2 21.8 - - - -
456F GLY 2.9 26.8 + - - +
458F GLU* 1.3 102.5 + - + +
460F HIS* 1.3 57.8 + - - +
461F LEU* 4.1 5.9 + - - +
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Residues in contact with HIS 460 (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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233F PRO* 3.7 19.5 - - + +
415F LYS* 3.5 24.5 + - - +
457F ALA 2.9 9.9 + - - +
459F HIS* 1.3 79.7 - - - +
461F LEU* 1.3 78.3 + - - +
462F ASP* 4.1 2.4 - - - -
463F GLY* 4.6 3.5 + - - -
468F PRO* 3.4 3.3 - - - +
469F TRP* 3.1 58.9 + + - -
642F TRP* 3.4 47.3 + + + +
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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