Contacts of the strand formed by residues 446 - 450 (chain x) in PDB entry 5GJQ
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 TRP 446 (chain x).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350x LEU* 4.6 15.0 - - + -
419x LEU* 3.7 34.5 - - + -
420x GLN 3.2 20.4 + - - -
422x VAL* 4.6 2.3 - - + +
438x TRP* 3.6 22.3 + - + +
439x VAL 3.8 12.5 - - - -
440x LYS* 3.2 55.0 - - + -
444x ASP 3.9 0.8 + - - -
445x GLU* 1.3 75.4 - - - +
447x ILE* 1.3 57.2 + - - +
456x ILE* 3.9 3.2 - - - +
457x VAL* 2.7 53.5 + - + +
459x PRO* 4.2 24.5 - - + -
462x ILE* 2.9 47.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 447 (chain x).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102x LEU* 5.8 2.9 - - + -
103x PRO* 4.1 21.1 - - + -
438x TRP* 3.2 9.9 - - - +
439x VAL* 2.9 36.2 + - + +
441x ARG* 3.8 44.0 - - + +
442x LYS* 6.4 1.6 - - + -
445x GLU 5.3 1.1 - - - +
446x TRP* 1.3 75.0 - - - +
448x LYS* 1.3 64.8 + - - +
449x PHE* 3.2 38.7 + - + -
454x VAL* 3.8 8.7 - - + -
455x SER 3.4 14.1 - - - +
456x ILE* 4.4 15.5 - - + -
457x VAL* 4.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 448 (chain x).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436x VAL* 3.9 11.7 - - + -
437x SER 3.8 3.6 - - - -
438x TRP* 3.5 40.4 - - + -
446x TRP 4.1 0.6 + - - -
447x ILE* 1.3 76.6 - - - +
449x PHE* 1.3 52.8 + - - +
450x ASP* 2.6 45.9 + - - +
453x LYS* 3.2 14.2 - - - +
455x SER* 3.1 35.3 + - - +
457x VAL* 4.2 15.5 - - + -
471x TRP* 5.6 7.4 - - - -
472x HIS* 5.5 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 449 (chain x).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103x PRO* 4.2 8.3 - - + -
104x CYS 4.1 12.1 - - - -
105x GLY* 5.9 0.7 - - - -
117x ALA* 5.9 0.5 - - - -
120x GLN* 2.8 60.3 - - + +
123x ARG* 4.1 15.3 - - - -
436x VAL* 3.8 2.9 - - - +
437x SER* 3.2 36.0 + - - +
439x VAL* 5.1 10.8 - - + -
441x ARG* 4.0 26.9 - - - -
447x ILE* 3.2 34.0 + - + -
448x LYS* 1.3 67.3 - - - +
450x ASP* 1.3 59.6 + - - +
451x ASP 3.7 3.3 + - - -
454x VAL* 3.6 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 450 (chain x).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434x HIS* 3.2 32.7 + - - -
435x TYR 5.8 0.2 - - - -
436x VAL* 4.1 9.6 - - + +
448x LYS* 2.6 35.7 + - - -
449x PHE* 1.3 70.2 - - - +
451x ASP* 1.3 70.9 + - - +
452x ASP 4.5 0.3 + - - -
453x LYS* 2.4 64.7 + - + +
454x VAL* 5.0 0.5 - - - +
472x HIS* 5.7 0.5 + - - -
----------------------------------------------------------
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