Contacts of the strand formed by residues 446 - 451 (chain A) in PDB entry 2JI8
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 VAL 446 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A SER* 3.5 15.9 - - - +
397A VAL* 4.0 12.6 - - + -
435A CYS* 3.9 35.2 - - - +
438A ALA* 3.9 8.7 - - + -
439A ALA* 3.6 37.5 - - + +
442A THR* 5.1 0.2 - - - +
444A LYS 4.1 1.3 - - - +
445A PRO* 1.3 79.8 - - - +
447A ILE* 1.3 73.5 + - - +
471A PRO 3.0 6.7 + - - +
472A VAL* 3.4 11.1 - - + -
473A THR* 2.8 27.9 + - - -
533A VAL* 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A VAL* 4.9 2.9 - - + -
387A PHE* 3.7 36.1 - - + -
388A MET* 3.9 18.4 - - + -
394A ILE* 3.9 10.1 - - + -
395A SER 2.8 9.2 + - - +
396A LEU* 3.3 20.0 - - + +
397A VAL* 2.8 24.1 + - - +
446A VAL* 1.3 80.5 - - - +
448A ALA* 1.3 63.5 + - - +
449A VAL* 4.7 1.8 - - + -
473A THR* 3.4 7.4 - - - +
475A ILE* 3.8 28.5 - - + -
529A LEU* 3.8 14.8 - - + -
533A VAL* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A VAL* 3.3 9.2 - - + -
432A MET* 4.5 2.0 - - + -
435A CYS* 3.9 24.9 - - - -
447A ILE* 1.3 75.0 - - - +
449A VAL* 1.3 59.9 + - - +
450A GLU* 3.8 26.0 - - + +
473A THR 2.9 11.1 + - - +
474A VAL* 4.3 7.2 - - - -
475A ILE* 2.7 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LEU* 3.6 22.9 - - + -
384A VAL* 4.4 11.2 - - + -
396A LEU* 4.4 16.8 - - + -
397A VAL 2.9 9.4 + - - +
398A ASN* 2.7 36.6 + - - +
399A GLU 3.5 9.0 + - - +
403A ALA* 3.9 3.4 - - + +
407A THR* 3.3 31.4 - - + +
447A ILE* 4.7 0.2 - - + -
448A ALA* 1.3 72.8 - - - +
450A GLU* 1.3 59.9 + - - +
451A GLY 4.1 0.2 + - - -
475A ILE* 3.7 15.3 - - + -
477A MET* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A VAL* 3.7 13.3 - - - +
399A GLU* 2.5 39.9 + - - +
403A ALA* 4.2 3.4 - - - -
431A GLY* 3.5 13.3 - - - -
432A MET* 3.7 23.9 - - + +
448A ALA* 3.9 8.3 - - + +
449A VAL* 1.3 76.2 - - - +
451A GLY* 1.3 68.7 + - - +
455A PHE* 3.6 23.1 - - + -
458A SER* 5.0 0.5 + - - -
474A VAL* 4.0 13.2 - - + -
475A ILE 2.8 13.8 + - - +
476A ILE* 3.6 4.9 - - + -
477A MET* 2.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A GLU 3.0 15.3 + - - -
403A ALA* 3.6 18.8 - - - +
450A GLU* 1.3 76.6 - - - +
452A ASP* 1.3 60.3 + - - -
453A SER 3.5 2.5 - - - -
454A ALA* 4.0 0.6 - - - +
455A PHE* 2.8 25.8 + - - +
477A MET* 4.5 4.5 - - - -
1566A TPP 3.4 23.1 - - - -
----------------------------------------------------------
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