Contacts of the helix formed by residues 391 - 407 (chain E) in PDB entry 1XSK
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 ASN 391 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363E LYS 5.1 0.8 + - - -
364E GLY 3.0 28.1 + - - -
365E TYR* 3.9 8.1 - - - +
388E ASP* 3.1 16.3 + - + +
390E THR* 1.3 77.5 + - - +
392E PRO* 1.3 69.0 - - - +
393E ASP* 3.1 20.1 + - - +
394E ALA* 3.0 21.5 + - + +
395E CYS* 3.0 15.9 + - - -
428E PHE* 3.3 40.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 392 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390E THR 3.2 11.9 - - - +
391E ASN* 1.3 86.3 - - - +
393E ASP* 1.3 60.8 + - - +
395E CYS* 3.5 10.5 + - + +
396E LYS* 3.1 25.5 + - - +
428E PHE* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 393 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365E TYR* 3.4 30.5 + - + +
391E ASN* 3.1 8.9 + - - +
392E PRO* 1.3 78.3 - - - +
394E ALA* 1.3 65.0 + - - +
395E CYS 3.2 0.2 - - - -
396E LYS* 3.5 14.9 + - - +
397E TRP* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 394 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365E TYR* 3.7 38.1 - - + +
387E TYR* 5.3 5.0 - - + -
388E ASP 3.2 26.9 - - - +
389E PHE* 4.9 2.9 - - + -
391E ASN* 3.0 14.4 + - + +
393E ASP* 1.3 77.8 - - - +
395E CYS* 1.3 64.7 + - - +
397E TRP* 3.2 4.0 + - - +
398E TYR* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 395 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389E PHE* 3.0 46.7 - - - -
391E ASN 3.0 14.5 + - - -
392E PRO* 3.6 11.7 - - + +
393E ASP 3.2 0.2 - - - -
394E ALA* 1.3 77.6 - - - +
396E LYS* 1.3 57.0 + - - +
398E TYR* 3.3 2.6 + - - +
399E ALA* 2.9 32.6 + - - +
443E ILE* 5.5 1.6 - - - -
447E LEU* 3.9 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 396 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392E PRO 3.1 14.9 + - - +
393E ASP* 3.8 16.2 - - - +
395E CYS* 1.3 80.0 - - - +
397E TRP* 1.3 61.6 + - - +
399E ALA* 3.8 5.3 - - - +
400E ASP* 3.0 51.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 397 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E ASP* 4.8 1.1 - - - -
318E PHE* 4.3 8.5 - + - -
356E VAL* 3.3 35.9 - - + -
359E GLU* 3.7 25.5 + - - -
360E LEU* 3.7 15.0 - - + +
363E LYS* 4.8 5.4 - - - -
365E TYR* 4.0 23.1 - + + +
387E TYR* 3.5 34.5 - + - -
393E ASP 3.0 14.3 + - - +
394E ALA 3.2 8.3 + - - +
396E LYS* 1.3 78.1 - - - +
398E TYR* 1.3 68.9 + - + +
400E ASP* 3.4 8.1 + - - +
401E LYS* 3.3 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 398 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E CYS* 5.0 0.2 - - - -
318E PHE* 3.4 30.5 - + - -
346E ILE* 3.8 10.9 - - - +
347E ASN 3.0 32.3 + - - -
387E TYR* 3.8 32.1 - + + -
389E PHE* 3.8 27.8 - + + -
394E ALA 3.0 15.7 + - - +
395E CYS 3.7 4.0 - - - +
397E TRP* 1.3 85.5 - - + +
399E ALA* 1.3 62.1 + - - +
401E LYS* 3.1 14.5 + - - +
402E LEU* 3.2 34.2 + - + +
444E TYR* 3.7 10.8 - + - -
447E LEU* 3.7 20.6 - - + -
448E VAL* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 399 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395E CYS 2.9 19.3 + - - +
396E LYS* 3.8 6.5 - - - +
398E TYR* 1.3 78.0 - - - +
400E ASP* 1.3 60.4 + - - +
402E LEU* 3.0 8.9 + - - +
403E LYS* 2.9 37.8 + - - +
447E LEU* 4.3 7.2 - - + -
451E VAL* 3.9 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 400 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396E LYS* 3.0 50.6 + - - +
397E TRP* 3.7 7.0 - - - +
398E TYR 3.3 0.2 - - - -
399E ALA* 1.3 78.7 - - - +
401E LYS* 1.3 61.7 + - + +
403E LYS* 3.5 21.1 + - - +
404E GLY* 3.1 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 401 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E ASP 3.9 13.7 - - - -
318E PHE* 3.4 44.1 - - + +
319E GLU* 4.2 10.5 - - - -
356E VAL* 5.2 2.5 - - - -
397E TRP* 3.3 46.4 + - + +
398E TYR 3.1 9.3 + - - +
400E ASP* 1.3 78.3 - - + +
402E LEU* 1.3 62.3 + - - +
404E GLY* 3.3 9.5 + - - -
405E LEU* 3.3 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E PHE* 3.7 26.9 - - + -
346E ILE* 3.9 19.1 - - + -
398E TYR* 3.2 30.4 + - + +
399E ALA 3.0 6.6 + - - +
401E LYS* 1.3 74.0 - - - +
403E LYS* 1.3 63.9 + - - +
404E GLY 3.1 1.8 - - - -
405E LEU* 3.0 15.8 + - + +
406E VAL* 3.1 16.3 + - - +
413E PHE* 3.7 21.6 - - + -
447E LEU* 3.8 10.1 - - + -
448E VAL* 4.0 16.2 - - + -
451E VAL* 3.7 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 403 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399E ALA* 2.9 24.0 + - - +
400E ASP* 3.9 19.7 + - - +
402E LEU* 1.3 74.4 - - - +
404E GLY* 1.3 57.4 + - - +
406E VAL* 3.8 6.5 - - - +
407E ALA* 3.0 31.5 + - - +
451E VAL* 3.6 28.7 - - + +
454E ASP* 4.7 18.2 + - - +
455E THR* 3.9 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 404 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400E ASP 3.1 13.2 + - - -
401E LYS* 3.3 6.2 + - - -
402E LEU 3.1 0.8 - - - -
403E LYS* 1.3 80.1 - - - +
405E LEU* 1.3 59.4 + - - +
407E ALA* 3.9 4.5 + - - +
408E MET* 3.3 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 405 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E TRP* 3.8 30.3 - - + -
318E PHE* 3.9 26.5 - - + +
320E TRP* 3.8 32.8 - - + +
344E VAL* 4.3 3.1 - - + -
346E ILE* 4.8 0.7 - - + -
401E LYS 3.3 10.4 + - - +
402E LEU* 3.0 9.0 + - - +
404E GLY* 1.3 77.3 - - - +
406E VAL* 1.3 63.5 + - - +
408E MET* 3.1 23.0 - - + +
410E VAL* 3.2 27.2 + - + +
413E PHE* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402E LEU 3.1 17.7 + - - +
403E LYS* 3.8 9.4 - - - +
404E GLY 3.4 0.2 - - - -
405E LEU* 1.3 72.3 - - - +
407E ALA* 1.3 56.3 + - - +
408E MET 2.8 4.5 - - - -
409E GLY* 2.7 27.0 + - - -
410E VAL 3.5 19.0 - - - +
413E PHE* 3.9 9.9 - - + -
451E VAL* 5.0 1.3 - - + -
452E LEU* 3.8 27.6 - - + -
455E THR* 3.7 30.7 - - + +
456E VAL* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329E GLU* 4.4 3.3 - - - +
333E ARG* 3.3 17.5 + - - -
403E LYS 3.0 17.4 + - - +
404E GLY* 4.2 5.6 - - - +
405E LEU 3.5 0.2 - - - -
406E VAL* 1.3 77.2 - - + +
408E MET* 1.3 56.0 + - - +
409E GLY 3.4 0.4 - - - -
----------------------------------------------------------
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