Contacts of the helix formed by residues 399 - 416 (chain J) in PDB entry 1MKD
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 399 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398H ASP* 4.6 6.9 + - - +
399H ASN* 3.4 35.2 - - + +
398J ASP* 1.3 97.0 - - - +
400J TYR* 1.3 61.4 + - - +
401J SER* 2.6 46.3 + - - +
402J ASP* 3.2 23.0 + - - +
403J ARG* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 400 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398H ASP* 6.5 0.9 - - + -
286J GLU* 5.1 7.9 - - - -
359J LYS* 3.7 29.8 - - + +
360J MET* 3.7 30.6 - - + +
363J ASP* 2.9 24.8 + - - -
399J ASN* 1.3 70.7 - - - +
401J SER* 1.3 59.0 + - - +
402J ASP 2.9 4.5 - - - -
403J ARG* 2.7 24.1 + - + +
404J ILE* 2.7 66.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 401 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399J ASN* 2.6 21.9 + - - +
400J TYR* 1.3 85.3 - - - +
402J ASP* 1.3 61.0 + - - +
404J ILE* 3.5 14.6 - - - +
405J GLN* 3.2 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 402 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383J MET* 3.2 26.6 - - + +
388J LYS* 5.0 3.5 + - - -
397J LEU* 4.1 17.7 - - + +
398J ASP* 3.5 16.3 - - - +
399J ASN* 3.2 26.5 - - - +
400J TYR 2.9 0.8 - - - -
401J SER* 1.3 83.7 + - - +
403J ARG* 1.3 66.3 + - - +
405J GLN* 3.4 4.7 + - - +
406J VAL* 3.2 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 403 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281J VAL* 3.7 22.6 + - - -
282J PHE* 3.7 11.6 - - + -
283J THR* 5.2 4.5 - - - +
286J GLU* 2.8 37.1 + - - +
397J LEU* 3.3 38.2 + - + -
398J ASP 2.9 28.5 + - - -
399J ASN 3.1 9.2 + - - +
400J TYR* 2.7 30.1 + - + +
402J ASP* 1.3 73.6 - - - +
404J ILE* 1.3 58.9 + - - +
406J VAL* 3.1 3.8 + - - +
407J LEU* 2.9 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 404 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360J MET* 3.9 37.9 - - + +
363J ASP* 4.1 14.6 - - + +
364J ILE* 4.2 12.1 - - + -
400J TYR* 2.7 58.2 + - + +
401J SER* 3.5 17.9 - - - +
403J ARG* 1.3 73.8 - - - +
405J GLN* 1.3 61.7 + - - +
407J LEU* 3.5 9.4 + - + -
408J GLN* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 405 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376J LEU* 5.2 1.3 - - + -
379J ASP* 3.6 45.2 + - + +
380J LEU* 5.8 0.9 - - + -
383J MET* 3.1 30.1 - - + +
401J SER* 3.2 19.7 + - - +
402J ASP* 3.4 6.9 + - - +
404J ILE* 1.3 83.3 - - + +
406J VAL* 1.3 62.0 + - - +
408J GLN* 3.4 16.1 + - - +
409J ASN* 2.9 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278J LEU* 4.6 7.4 - - + -
282J PHE* 3.8 22.4 - - + -
380J LEU* 5.4 2.9 - - + -
383J MET* 3.8 20.6 - - - -
395J LEU* 5.7 0.7 - - + -
397J LEU* 3.6 20.0 - - + -
402J ASP 3.2 14.6 - - - +
403J ARG 3.1 7.4 + - - +
405J GLN* 1.3 75.4 - - - +
407J LEU* 1.3 59.4 + - - +
409J ASN* 3.4 4.4 + - - +
410J MET* 2.8 28.0 + - + +
481J TRP* 3.8 25.2 - - + -
484J LEU* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273J LEU* 4.1 12.6 - - + -
282J PHE* 3.6 32.5 - - + -
286J GLU* 4.0 35.2 - - + +
290J ALA* 4.0 17.9 - - + -
360J MET* 5.0 4.3 - - - -
364J ILE* 4.0 24.6 - - + +
403J ARG 2.9 19.8 + - - +
404J ILE* 3.8 15.0 - - + +
406J VAL* 1.3 73.4 - - - +
408J GLN* 1.3 64.4 + - - +
410J MET* 3.5 8.2 - - - +
411J VAL* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 408 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363J ASP* 3.1 37.8 - - - +
364J ILE* 3.9 16.4 - - + +
367J ALA* 3.7 21.5 - - + +
368J THR* 6.1 0.3 - - - +
376J LEU* 4.0 16.2 - - + +
404J ILE* 2.9 29.4 + - + +
405J GLN* 3.6 19.3 - - - +
407J LEU* 1.3 78.6 - - - +
409J ASN* 1.3 63.5 + - - +
411J VAL* 3.3 2.3 + - - +
412J HIS* 2.9 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 409 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376J LEU* 3.2 48.5 + - - +
380J LEU* 3.7 40.7 - - + +
405J GLN* 2.9 31.2 + - - +
406J VAL 3.9 3.4 - - - +
408J GLN* 1.3 79.6 - - - +
410J MET* 1.3 56.6 + - - +
412J HIS* 3.4 6.9 - - - +
413J CYS* 2.8 34.4 + - - -
477J LEU* 4.3 11.1 - - + +
481J TRP* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 410 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269J THR* 4.2 11.9 - - + +
272J LEU* 3.7 30.9 - - + +
273J LEU* 3.5 42.8 - - + -
278J LEU* 3.4 33.0 - - + -
282J PHE* 4.4 7.0 - - + -
290J ALA* 5.4 0.7 - - - -
406J VAL* 2.8 20.6 + - + +
407J LEU* 3.5 13.2 - - + +
408J GLN 3.1 0.2 - - - -
409J ASN* 1.3 76.5 - - - +
411J VAL* 1.3 58.5 + - - +
413J CYS* 3.0 8.0 + - - +
414J ALA* 2.8 26.7 + - - +
481J TRP* 3.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 411 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265J VAL* 4.4 9.6 - - + -
269J THR* 4.0 11.4 - - + +
290J ALA* 4.0 15.7 - - + +
293J ALA 5.2 0.9 - - - -
294J SER* 3.7 32.5 - - - +
297J HIS* 5.2 2.0 - - + -
364J ILE* 3.5 34.1 - - + +
368J THR* 4.3 16.6 - - + -
407J LEU 3.0 10.7 + - - +
408J GLN 4.0 1.1 - - - +
410J MET* 1.3 75.8 - - + +
412J HIS* 1.3 57.9 + - - +
414J ALA* 3.5 6.7 - - - +
415J ASP* 2.8 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 412 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367J ALA 3.9 15.5 + - - +
368J THR* 4.5 14.6 + - + +
369J ASP 5.3 0.4 - - - -
370J MET* 3.9 16.4 - - - -
373J HIS* 2.8 37.1 + - + +
376J LEU* 4.0 20.4 - - + -
377J LEU 6.2 0.2 - - - -
408J GLN 2.9 17.8 + - - +
409J ASN* 3.4 8.7 - - - +
411J VAL* 1.3 75.1 - - - +
413J CYS* 1.3 59.8 + - - +
415J ASP* 3.3 7.9 + - - +
416J LEU* 3.0 51.2 + - + +
477J LEU* 3.5 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 413 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272J LEU* 4.2 4.7 - - + -
380J LEU* 5.7 0.2 - - - -
409J ASN 2.8 19.2 + - - +
410J MET* 3.3 9.2 - - - +
412J HIS* 1.3 73.2 - - - +
414J ALA* 1.3 65.5 + - - +
416J LEU 3.0 5.0 + - - -
417J SER 3.0 18.5 + - - -
477J LEU* 3.7 34.1 - - - -
478J TRP* 3.3 32.2 - - + -
481J TRP* 3.8 34.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 414 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264J ASP* 5.4 0.5 - - - +
265J VAL* 3.8 23.8 - - + +
268J SER* 3.9 14.8 - - - -
269J THR* 3.4 29.2 - - - +
272J LEU* 4.2 5.7 - - + +
410J MET 2.8 10.8 + - - +
411J VAL 3.5 7.0 - - - +
412J HIS 3.3 0.2 - - - -
413J CYS* 1.3 75.9 - - - +
415J ASP* 1.3 59.8 + - - +
417J SER* 2.8 29.0 + - - -
418J ASN* 5.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 415 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256J TYR* 4.3 6.8 + - - -
261J HIS* 2.9 18.4 + - - -
265J VAL* 3.9 9.6 - - + +
297J HIS* 2.7 18.4 + - + +
368J THR* 4.1 21.6 - - + +
411J VAL 2.8 18.3 + - - +
412J HIS* 3.6 11.2 + - - +
413J CYS 3.2 0.4 - - - -
414J ALA* 1.3 77.0 - - - +
416J LEU* 1.3 69.4 + - + +
417J SER 3.4 1.4 + - - -
418J ASN* 5.2 2.4 + - - +
2019J ZN 2.2 35.6 - - - -
3010J ZAR 6.0 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370J MET* 4.0 14.1 - - - -
412J HIS* 3.0 47.6 + - + +
413J CYS 3.0 5.3 + - - +
415J ASP* 1.3 88.5 - - + +
417J SER* 1.3 57.9 + - - -
418J ASN* 3.5 2.9 - - - -
419J PRO* 4.0 4.2 - - - +
469J PHE* 3.7 27.6 - - + -
473J ILE* 3.9 21.1 - - + -
474J VAL* 3.7 19.2 - - + +
477J LEU* 3.8 17.7 - - + -
478J TRP* 3.2 13.3 + - - -
3010J ZAR 4.8 13.9 - - + -
----------------------------------------------------------
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