Contacts of the helix formed by residues 510 - 514 (chain A) in PDB entry 3A8X
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 510 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A LYS 3.7 6.3 - - - -
482A SER* 3.1 24.1 + - - -
483A VAL* 3.5 36.6 + - + +
486A SER* 3.9 6.1 + - - -
496A LEU* 4.2 23.6 - - + -
506A ASP 3.2 10.6 + - - +
507A ILE 3.1 14.5 + - - +
509A GLY* 1.3 79.0 - - - +
511A PRO* 1.3 79.5 - - + +
512A PHE* 2.9 30.1 + - - +
513A PHE* 2.8 28.9 + - + +
514A ARG* 3.4 7.1 + - - -
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Residues in contact with PRO 511 (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 LYS* 3.9 28.6 - - + +
482A SER* 5.7 1.8 - - - +
509A GLY 3.5 5.1 - - - +
510A HIS* 1.3 104.3 - - + +
512A PHE* 1.3 60.4 + - - +
514A ARG* 3.2 49.3 - - + +
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Residues in contact with PHE 512 (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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343A GLU* 4.2 6.7 - - - -
346A ALA 4.7 0.4 - - - -
347A ARG* 2.6 83.4 + - + +
434A MET* 3.5 24.7 - - + -
438A MET* 4.1 26.9 - - + -
479A LYS* 3.7 19.0 - - + +
480A ALA* 3.8 27.4 - - + -
483A VAL* 3.8 12.1 - - + -
510A HIS* 2.9 18.9 + - - +
511A PRO* 1.3 77.6 - - - +
513A PHE* 1.3 81.9 + + + +
514A ARG 3.3 0.9 + - - -
515A ASN 5.1 0.3 + - - -
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Residues in contact with PHE 513 (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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347A ARG* 3.8 19.3 - - + -
350A SER* 3.9 17.5 - - - -
351A ALA* 4.0 10.8 - - - -
354A SER* 4.7 6.3 - - - -
434A MET* 4.0 5.8 - - + -
483A VAL* 4.1 14.4 - - + -
487A PHE* 4.5 5.2 - + - -
496A LEU* 5.5 0.2 - - + -
507A ILE* 3.4 36.3 - - + +
508A GLN 4.2 5.5 - - - +
510A HIS* 2.8 17.1 + - + +
512A PHE* 1.3 105.6 - + - +
514A ARG* 1.3 63.9 + - - +
515A ASN 3.3 2.9 - - - -
516A VAL* 3.0 35.4 + - + +
518A TRP* 3.7 28.1 + + + -
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Residues in contact with ARG 514 (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 LYS* 4.4 19.4 - - - +
508A GLN 5.5 1.1 - - - -
510A HIS 3.4 4.7 + - - -
511A PRO* 3.2 45.1 + - + +
512A PHE 3.3 1.2 - - - -
513A PHE* 1.3 77.9 - - - +
515A ASN* 1.3 72.7 + - - +
516A VAL 3.3 5.2 + - - +
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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