Contacts of the strand formed by residues 425 - 430 (chain E) in PDB entry 1KXT
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 GLY 425 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397E PHE* 3.9 7.4 - - - -
401E VAL* 3.7 13.4 - - - +
420E GLY* 3.2 2.6 - - - -
421E ARG 2.8 33.6 + - - -
422E GLY 4.7 0.7 - - - +
423E ASN 3.7 2.2 - - - -
424E ARG* 1.3 80.6 - - - +
426E PHE* 1.3 61.3 + - - +
442E THR 4.6 0.3 - - - +
444E LEU* 3.9 8.3 - - - +
490E ILE 3.5 10.3 - - - -
491E HIS* 4.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 426 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397E PHE* 3.8 4.1 - - - -
408E ASN* 4.0 11.9 - - + -
410E TRP* 5.9 0.9 - - + -
418E ALA* 3.7 19.5 - - + -
419E PHE 3.5 28.5 - - - -
420E GLY* 3.8 3.6 - - - -
425E GLY* 1.3 73.9 - - - -
427E ILE* 1.3 76.0 + - - +
428E VAL* 4.6 1.1 - - + -
440E LEU* 3.8 29.4 - - + -
441E GLN 3.8 16.6 - - - -
442E THR* 3.5 24.0 - - + -
444E LEU* 3.5 16.8 - - + +
477E PHE* 3.8 30.1 - + - -
489E ALA* 3.6 1.0 - - - -
490E ILE* 2.8 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 427 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E ALA* 4.0 14.1 - - + -
394E MET* 4.6 12.3 - - + -
397E PHE* 4.6 4.5 - - + -
418E ALA* 3.2 5.4 - - - +
419E PHE* 3.0 54.1 + - + +
426E PHE* 1.3 78.5 - - - +
428E VAL* 1.3 87.0 + - - +
429E PHE* 3.1 47.6 - - + -
487E PHE* 3.8 11.7 - - + -
488E ILE 3.2 13.7 - - - +
489E ALA* 3.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 428 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410E TRP* 5.1 0.9 - - + -
417E VAL 3.7 9.6 - - - +
418E ALA* 4.0 10.3 - - + -
426E PHE* 4.6 2.0 - - + -
427E ILE* 1.3 83.3 - - - +
429E PHE* 1.3 61.7 + - - +
436E LEU* 4.0 27.1 - - + -
440E LEU* 4.2 13.7 - - + -
477E PHE* 3.5 26.7 - - + -
479E ILE* 3.8 7.5 - - + +
487E PHE* 3.1 6.2 - - - +
488E ILE* 2.8 61.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 429 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E MET* 3.3 26.0 - - + -
323E ILE* 3.5 42.4 - - + -
326E GLY 4.1 2.7 - - - -
327E PHE* 3.5 42.8 - + + -
416E GLN* 3.3 4.7 - - - -
417E VAL* 2.8 45.6 + - + +
418E ALA* 5.1 0.7 - - - -
419E PHE* 4.6 1.3 - + - -
427E ILE* 3.1 42.0 - - + -
428E VAL* 1.3 74.3 - - - +
430E ASN* 1.3 60.0 + - - +
431E ASN 3.9 0.4 - - - -
436E LEU* 3.6 7.2 - - - +
487E PHE* 3.6 25.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 430 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E ILE* 6.0 0.9 - - - -
415E ASN 4.3 0.4 - - - -
416E GLN* 3.0 22.6 + - - +
429E PHE* 1.3 70.6 - - - +
431E ASN* 1.3 59.0 + - - +
432E ASP 3.1 16.3 + - - +
434E TRP 3.1 19.1 + - - +
436E LEU* 3.4 17.9 - - + +
479E ILE* 2.8 34.2 + - + +
480E SER 3.8 0.2 - - - -
481E ASN* 3.4 15.5 - - - +
486E PRO* 2.8 39.6 + - - +
----------------------------------------------------------
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