Contacts of the helix formed by residues 484 - 489 (chain A) in PDB entry 5AM8
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 484 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A HIS 5.4 0.8 + - - -
168A GLY* 3.3 44.8 - - - +
169A ILE* 4.5 0.6 - - - +
171A LEU* 3.9 8.1 - - + -
172A LYS* 3.6 27.4 - - + -
175A TYR* 3.7 43.7 - + + -
445A TRP* 3.6 22.4 - + - -
459A TYR* 3.5 33.2 - + + -
460A ASN* 3.8 1.6 - - - -
482A THR 3.8 1.5 + - - +
483A HIS* 1.3 75.7 - - - +
485A ASP* 1.3 61.6 + - - +
486A ALA* 3.3 7.4 - - + -
487A GLY* 2.9 37.5 + - - -
492A VAL* 4.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TRP* 4.9 0.2 - - - -
164A HIS* 3.6 30.8 + - + +
257A TRP* 5.7 0.9 - - - -
460A ASN* 2.9 22.8 + - - +
463A TRP* 3.7 25.9 + - + +
464A TRP* 2.9 25.6 + - + +
479A ARG* 2.9 43.2 + - - -
483A HIS* 4.0 1.9 - - - +
484A PHE* 1.3 72.4 + - - +
486A ALA* 1.3 65.1 + - - +
488A ALA* 3.3 16.7 + - - +
489A LYS* 4.2 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A TRP* 3.6 38.1 - - + -
460A ASN* 4.4 0.4 + - - -
463A TRP* 3.6 42.5 - - + +
484A PHE* 3.3 4.0 - - + -
485A ASP* 1.3 78.2 - - - +
487A GLY* 1.3 60.9 + - - +
488A ALA 3.4 0.5 + - - -
489A LYS* 3.4 10.4 + - - +
492A VAL* 3.2 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 3.8 1.9 - - - -
168A GLY* 4.3 1.6 - - - -
171A LEU* 3.1 27.0 - - - +
484A PHE* 2.9 38.3 + - - -
486A ALA* 1.3 78.9 - - - +
488A ALA* 1.3 56.5 + - - +
489A LYS 3.2 2.2 + - - -
492A VAL* 4.2 7.0 - - - -
493A PRO* 3.4 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 3.5 8.0 - - - -
163A TRP* 3.0 24.8 + - - +
164A HIS* 3.7 37.2 - - + +
167A ALA* 4.1 14.4 - - + -
168A GLY* 4.2 1.5 - - - +
257A TRP* 2.9 19.0 + - - -
484A PHE 3.7 2.8 + - - -
485A ASP 3.3 13.8 + - - +
486A ALA 3.2 1.6 - - - -
487A GLY* 1.3 75.6 - - - +
489A LYS* 1.3 56.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 3.6 2.2 - - - -
257A TRP* 3.6 39.9 - - + +
259A GLN* 2.7 32.7 + - - +
331A HIS* 4.7 9.1 - - - -
438A PHE* 3.9 17.7 - - + -
442A VAL* 5.5 3.1 - - + -
463A TRP* 5.0 7.6 - - + -
485A ASP 4.2 0.9 + - - +
486A ALA 3.4 11.8 + - - +
487A GLY 3.2 1.0 - - - -
488A ALA* 1.3 78.3 - - - +
490A PHE* 1.3 68.0 + - - +
491A HIS* 3.0 36.0 + - + +
492A VAL* 3.1 10.4 + - + +
493A PRO* 3.0 16.5 - - - +
498A TYR* 3.7 16.0 + - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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