Contacts of the helix formed by residues 394 - 403 (chain A) in PDB entry 1KTW
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 LYS 394 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PHE* 4.1 5.9 - - + -
273A LEU* 4.3 13.7 - - + -
303A ARG* 4.4 4.9 - - - +
393A LEU* 1.3 79.5 - - - +
395A GLN* 1.3 66.8 + - - +
396A ASP 3.3 1.3 - - - +
397A GLN* 3.1 45.6 + - + +
398A LEU* 3.6 9.9 + - - +
424A GLN* 2.9 28.3 + - - +
425A ILE* 5.6 0.2 - - + -
426A TYR* 4.4 2.5 - - - -
3D G4S 3.1 56.5 + - - +
4D DGS 3.1 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LYS* 1.3 73.3 - - - +
396A ASP* 1.3 64.4 + - - +
397A GLN 3.0 5.6 + - - -
398A LEU* 3.3 18.8 + - + +
399A ASP* 4.7 0.9 + - - +
423A GLY* 3.6 17.3 + - - +
426A TYR* 3.1 37.8 + - + +
478A TYR* 3.6 43.0 + - + -
479A TYR* 3.0 33.7 + - - -
1D G4S 5.2 1.7 - - - -
2D DGS 3.8 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LYS* 3.3 2.4 - - - +
395A GLN* 1.3 83.7 - - - +
397A GLN* 1.3 62.3 + - + +
398A LEU 3.7 0.2 - - - -
399A ASP* 5.2 4.6 + - - +
400A TYR* 4.0 12.8 - - - -
2D DGS 5.2 4.7 - - - +
3D G4S 4.0 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 5.2 2.9 - - - +
299A GLY* 5.6 2.8 - - - -
303A ARG* 4.5 21.0 - - - +
392A ASP 4.9 0.9 - - - +
393A LEU* 4.0 13.4 - - + +
394A LYS* 3.1 45.5 + - + +
395A GLN 3.0 1.2 - - - -
396A ASP* 1.3 82.3 - - + +
398A LEU* 1.3 66.0 + - - +
399A ASP 3.3 2.7 - - - -
400A TYR* 3.2 29.8 + - + -
431A LEU* 3.3 25.7 - - + +
435A ILE* 4.0 29.8 - - + +
3D G4S 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 4.1 19.3 - - + -
394A LYS 3.8 13.5 - - - +
395A GLN* 3.3 9.5 + - - +
397A GLN* 1.3 74.1 - - - +
399A ASP* 1.3 61.7 + - - +
400A TYR 3.0 7.0 + - - -
401A PHE* 3.3 44.1 + - + +
411A VAL* 4.4 12.1 - - + -
426A TYR* 4.0 39.9 - - + -
431A LEU* 6.0 0.2 - - + -
475A VAL* 4.4 2.4 - - - +
476A CYS* 4.2 16.6 - - + -
478A TYR* 4.1 25.6 - - + -
481A MET* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLN 5.4 1.1 - - - -
396A ASP* 5.7 4.3 - - - +
397A GLN 3.2 2.0 + - - +
398A LEU* 1.3 77.9 - - - +
400A TYR* 1.3 59.0 + - + +
401A PHE 3.1 5.6 + - - -
402A SER* 3.4 7.3 + - - -
472A SER* 3.4 19.4 + - - +
473A SER* 3.0 41.8 + - - +
474A ARG* 3.6 21.4 + - - +
475A VAL 4.7 1.2 + - - +
476A CYS 5.5 0.2 + - - -
478A TYR* 2.8 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASP 4.0 17.0 + - - -
397A GLN* 3.3 30.5 - - + +
398A LEU 3.0 1.6 - - - -
399A ASP* 1.3 77.4 - - + +
401A PHE* 1.3 58.7 + - - +
402A SER* 3.2 7.3 + - - -
403A THR* 4.0 3.3 + - - -
404A SER* 5.4 1.0 + - - -
431A LEU* 4.1 11.0 - - + +
435A ILE* 6.4 0.7 - - + -
437A THR* 5.6 5.2 - - - +
463A HIS* 3.1 26.4 + - + +
466A ILE* 3.7 48.6 - - + +
467A ASP 4.4 6.9 + - - -
468A THR* 5.8 0.7 - - - -
470A THR* 3.9 27.9 + - + -
471A GLU 4.0 6.7 - - - -
472A SER* 3.7 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 3.9 19.5 - - + -
398A LEU* 3.5 30.7 - - + +
399A ASP 3.1 1.2 - - - -
400A TYR* 1.3 75.6 - - - +
402A SER* 1.3 60.9 + - - +
403A THR 3.0 3.8 + - - -
404A SER* 4.2 7.4 - - - +
405A ASN* 2.8 66.3 + - + +
411A VAL* 3.9 12.1 - - + -
429A PRO* 3.3 53.2 - - + -
430A SER 4.4 3.1 - - - -
431A LEU* 3.5 24.9 - - + -
475A VAL* 4.1 6.5 - - + -
476A CYS* 4.3 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ASP 3.4 15.2 + - - -
400A TYR 3.2 1.8 - - - -
401A PHE* 1.3 78.3 - - - +
403A THR* 1.3 70.6 + - - +
406A PRO* 4.2 14.4 - - - +
471A GLU* 4.6 2.8 + - - +
472A SER* 3.8 8.1 - - - -
473A SER* 3.0 35.8 + - - -
475A VAL* 4.0 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A TYR 4.0 3.3 + - - -
402A SER* 1.3 88.3 - - - +
404A SER* 1.3 64.5 + - - +
406A PRO* 4.4 4.4 - - - +
461A ASN* 2.9 37.7 + - - +
462A SER* 4.4 0.3 - - - -
463A HIS* 3.6 35.3 + - + +
471A GLU* 5.2 4.7 - - + +
----------------------------------------------------------
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