Contacts of the helix formed by residues 399 - 416 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398G ASP* 4.0 27.7 + - + +
399G ASN* 4.0 12.2 - - + +
398L ASP* 1.3 98.7 - - - +
400L TYR* 1.3 62.5 + - - +
401L SER* 2.6 46.1 + - - +
402L ASP* 3.3 24.6 + - - +
403L ARG* 3.1 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 400 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286L GLU* 5.1 8.1 - - - -
359L LYS* 3.7 30.1 - - + +
360L MET* 3.8 31.9 - - + +
363L ASP* 2.9 24.0 + - - -
399L ASN* 1.3 70.3 - - - +
401L SER* 1.3 67.3 + - - +
402L ASP 2.9 4.5 - - - -
403L ARG* 2.7 25.0 + - + +
404L ILE* 2.7 65.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 401 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399L ASN* 2.6 22.1 + - - +
400L TYR* 1.3 83.0 - - - +
402L ASP* 1.3 60.6 + - - +
404L ILE* 3.5 14.5 - - - +
405L GLN* 3.2 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 402 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383L MET* 3.2 27.6 - - + +
388L LYS* 5.0 3.1 + - - -
396L LEU 5.1 0.2 - - - +
397L LEU* 4.1 18.2 - - + +
398L ASP* 3.5 16.6 - - - +
399L ASN* 3.3 27.4 + - - +
400L TYR 2.9 0.6 - - - -
401L SER* 1.3 83.4 + - - +
403L ARG* 1.3 65.9 + - - +
405L GLN* 3.4 4.9 + - - +
406L VAL* 3.2 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 403 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L VAL* 3.7 23.1 + - - -
282L PHE* 3.7 11.9 - - + -
283L THR* 5.2 4.9 - - - +
286L GLU* 2.8 38.0 + - - +
397L LEU* 3.3 38.3 + - + -
398L ASP 2.9 28.1 + - - -
399L ASN 3.1 13.7 + - - +
400L TYR* 2.7 29.9 + - + +
402L ASP* 1.3 73.8 - - - +
404L ILE* 1.3 59.4 + - - +
405L GLN 3.1 0.2 - - - -
406L VAL* 3.2 3.8 + - - +
407L LEU* 3.0 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 404 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360L MET* 3.9 37.5 - - + +
363L ASP* 4.1 15.0 - - + +
364L ILE* 4.1 12.3 - - + -
400L TYR* 2.7 60.7 + - + +
401L SER* 3.5 18.2 - - - +
403L ARG* 1.3 73.4 - - - +
405L GLN* 1.3 60.7 + - + +
407L LEU* 4.3 8.5 - - + -
408L GLN* 2.9 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 405 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376L LEU* 5.2 1.6 - - + -
379L ASP* 3.7 44.1 + - + +
380L LEU* 5.1 0.6 - - + -
383L MET* 3.1 30.9 - - + +
401L SER* 3.2 20.2 + - - +
402L ASP* 3.4 7.3 + - - +
403L ARG 3.1 0.2 - - - -
404L ILE* 1.3 82.3 - - + +
406L VAL* 1.3 57.8 + - - +
408L GLN* 3.4 15.1 + - - +
409L ASN* 2.9 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278L LEU* 4.6 6.7 - - + -
282L PHE* 3.8 22.4 - - + -
380L LEU* 5.4 2.7 - - + -
383L MET* 3.7 20.9 - - - -
395L LEU* 5.7 0.4 - - + -
397L LEU* 3.6 20.4 - - + -
402L ASP 3.2 15.9 - - - +
403L ARG 3.2 6.7 + - - +
405L GLN* 1.3 74.5 - - - +
407L LEU* 1.3 60.1 + - - +
409L ASN* 3.4 5.0 + - - +
410L MET* 2.8 31.2 + - + +
481L TRP* 3.8 24.2 - - + -
484L LEU* 4.3 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273L LEU* 4.1 12.3 - - + -
282L PHE* 3.6 31.4 - - + -
286L GLU* 4.0 36.1 - - + +
289L ALA* 5.8 0.2 - - + -
290L ALA* 4.0 17.9 - - + -
360L MET* 5.0 4.0 - - - -
364L ILE* 4.0 23.6 - - + -
403L ARG* 3.0 20.8 + - + +
404L ILE* 3.8 15.0 - - + +
406L VAL* 1.3 76.9 - - - +
408L GLN* 1.3 63.9 + - - +
410L MET* 3.3 7.8 + - - +
411L VAL* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 408 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363L ASP* 3.1 38.4 - - - +
364L ILE* 3.9 16.1 - - + +
367L ALA* 3.7 20.4 - - + +
368L THR* 6.1 0.2 - - - +
376L LEU* 4.1 16.4 - - + +
404L ILE* 2.9 32.4 + - + +
405L GLN* 3.5 19.2 + - - +
407L LEU* 1.3 78.0 - - - +
409L ASN* 1.3 63.4 + - - +
411L VAL* 3.3 2.3 + - - +
412L HIS* 2.9 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 409 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376L LEU* 3.2 48.0 + - - +
380L LEU* 3.7 44.4 - - + +
405L GLN* 2.9 33.2 + - - +
406L VAL 3.9 3.4 - - - +
408L GLN* 1.3 79.6 - - - +
410L MET* 1.3 51.9 + - - +
412L HIS* 3.3 7.3 - - - +
413L CYS* 2.7 39.7 + - - -
477L LEU* 4.2 9.6 - - + +
481L TRP* 4.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 410 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269L THR* 4.2 11.2 - - + +
272L LEU* 3.7 30.6 - - + +
273L LEU* 3.5 43.5 - - + -
278L LEU* 3.4 33.4 - - + -
282L PHE* 4.3 7.6 - - + -
290L ALA* 5.3 0.4 - - - -
406L VAL* 2.8 20.7 + - + +
407L LEU* 3.4 13.5 - - + +
408L GLN 3.1 0.2 - - - -
409L ASN* 1.3 77.3 - - - +
411L VAL* 1.3 60.4 + - - +
413L CYS* 3.0 7.1 + - - +
414L ALA* 2.8 25.8 + - - +
481L TRP* 3.7 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 411 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265L VAL* 4.3 10.3 - - + -
269L THR* 4.0 10.1 - - + +
290L ALA* 4.0 15.5 - - + +
293L ALA 5.2 0.9 - - - -
294L SER* 3.7 31.9 - - - +
297L HIS* 5.2 2.5 - - + -
364L ILE* 3.5 34.8 - - + -
368L THR* 4.3 16.4 - - + -
407L LEU 3.0 10.9 + - - +
408L GLN 4.0 0.9 - - - +
410L MET* 1.3 76.6 - - + +
412L HIS* 1.3 57.9 + - - +
414L ALA* 3.5 6.4 - - - +
415L ASP* 2.8 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 412 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367L ALA 3.9 17.2 + - - +
368L THR* 4.5 13.3 + - - +
369L ASP 5.1 2.0 - - - -
370L MET* 3.8 16.2 - - - -
373L HIS* 2.9 36.6 + - + +
376L LEU* 4.0 19.5 - - + -
408L GLN 2.9 18.4 + - - +
409L ASN* 3.3 9.4 - - - +
411L VAL* 1.3 75.3 - - - +
413L CYS* 1.3 64.2 + - - +
415L ASP* 3.3 8.5 + - - +
416L LEU* 3.0 45.8 + - + +
477L LEU* 3.4 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 413 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272L LEU* 4.2 4.9 - - + -
409L ASN* 2.7 23.7 + - - -
410L MET* 3.4 8.3 - - - +
412L HIS* 1.3 71.1 - - - +
414L ALA* 1.3 65.5 + - - +
416L LEU 3.1 4.3 + - - -
417L SER 3.0 17.8 + - - -
477L LEU* 3.7 33.9 - - - -
478L TRP* 3.3 33.7 - - + -
481L TRP* 3.8 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 414 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264L ASP* 5.4 0.9 - - - +
265L VAL* 3.8 24.9 - - + +
268L SER* 3.9 13.2 - - - -
269L THR* 3.4 29.4 - - - +
272L LEU* 4.1 5.3 - - + +
410L MET 2.8 11.9 + - - +
411L VAL 3.5 6.7 - - - +
413L CYS* 1.3 77.4 - - - +
415L ASP* 1.3 61.3 + - - +
417L SER* 2.8 28.2 + - - -
418L ASN* 5.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 415 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256L TYR* 4.3 7.4 + - - -
261L HIS* 2.9 17.8 + - - -
265L VAL* 3.9 10.5 - - + +
297L HIS* 2.7 17.8 + - + +
368L THR* 4.1 21.6 - - + +
411L VAL 2.8 21.1 + - - +
412L HIS* 3.6 10.4 + - - +
413L CYS 3.2 0.2 - - - -
414L ALA* 1.3 73.7 - - - +
416L LEU* 1.3 68.2 + - + +
417L SER 3.4 1.9 + - - -
418L ASN* 5.2 2.4 + - - +
2023L ZN 2.3 35.8 - - - -
3012L ZAR 5.9 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370L MET* 4.0 14.8 - - - -
412L HIS* 3.0 47.0 + - + +
413L CYS 3.1 5.1 + - - +
415L ASP* 1.3 88.8 - - + +
417L SER* 1.3 57.6 + - - +
418L ASN* 3.6 3.0 + - - +
419L PRO* 4.0 4.3 - - - +
469L PHE* 3.7 25.8 - - + -
473L ILE* 3.8 21.5 - - + -
474L VAL* 3.7 20.1 - - + +
477L LEU* 3.8 16.4 - - + -
478L TRP* 3.2 14.2 + - - -
3012L ZAR 4.8 14.6 - - + -
----------------------------------------------------------
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