Contacts of the helix formed by residues 398 - 412 (chain A) in PDB entry 5MKE
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 THR 398 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A SER* 2.9 38.5 + - - +
397A ARG* 1.3 77.0 - - - +
399A ARG* 1.3 60.3 + - - +
400A GLU* 2.2 36.1 + - + +
401A GLU* 4.0 20.0 - - + +
402A THR* 3.1 6.5 + - - +
543A ASN* 5.8 1.0 - - - +
1001A NAG 3.5 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 3.5 36.5 + - + +
289A ASP* 4.4 2.5 - - - +
291A LEU* 2.7 33.1 + - - +
292A TYR* 4.3 4.9 + - - +
293A TRP* 3.2 60.9 - - + +
315A LEU* 5.7 4.8 - - - +
395A LEU* 5.1 6.5 - - - +
396A SER 4.1 6.1 + - - -
397A ARG* 3.3 21.9 + - - +
398A THR* 1.3 71.0 - - - +
400A GLU* 1.3 73.0 + - - +
402A THR* 3.2 25.8 + - - +
403A ALA* 4.1 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A THR* 2.2 34.3 + - - +
399A ARG* 1.3 83.0 + - - +
401A GLU* 1.3 71.7 + - + +
403A ALA* 3.4 9.9 + - - +
404A ALA* 3.5 7.6 + - - +
1001A NAG 4.5 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A SER* 4.2 1.3 - - - +
398A THR* 4.0 13.6 - - + +
400A GLU* 1.3 80.9 - - + +
402A THR* 1.3 56.8 + - - +
403A ALA 3.0 2.5 - - - -
404A ALA* 2.6 19.7 + - + -
405A GLN* 2.3 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 3.3 31.2 - - + +
395A LEU* 3.1 23.7 - - - +
396A SER* 3.1 27.0 + - - -
398A THR 3.1 15.3 - - - +
399A ARG* 3.2 26.7 + - - +
401A GLU* 1.3 76.3 - - - +
403A ALA* 1.3 61.3 + - - +
405A GLN* 3.5 15.3 - - - +
406A VAL* 3.7 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 6.5 0.2 - - + -
288A LEU* 4.3 18.8 - - + -
399A ARG 4.4 5.2 - - - +
400A GLU 3.4 9.1 + - - +
401A GLU 3.0 0.4 - - - -
402A THR* 1.3 82.4 - - - +
404A ALA* 1.3 51.7 + - - +
405A GLN 3.2 0.4 - - - -
406A VAL* 3.1 11.5 + - - +
407A ALA* 2.6 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A GLU 3.5 3.4 + - - +
401A GLU* 2.6 35.8 + - + +
403A ALA* 1.3 71.9 - - - +
405A GLN* 1.3 53.2 + - - +
407A ALA* 3.1 12.0 - - + +
408A SER* 2.2 39.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ILE* 5.4 0.2 - - - +
393A LEU* 3.9 25.2 - - + +
394A ASP 3.9 19.2 + - - -
395A LEU* 3.2 28.2 - - - +
396A SER* 4.2 15.7 - - - -
401A GLU* 2.3 34.6 + - + +
402A THR* 3.5 15.0 - - - +
404A ALA* 1.3 65.6 - - - +
406A VAL* 1.3 52.0 - - + +
408A SER* 2.8 10.8 + - - -
409A LEU* 2.2 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A TRP* 4.4 0.4 - - + -
283A THR* 4.3 29.8 - - + +
284A GLU* 5.6 4.5 - - + +
288A LEU* 5.9 3.1 - - + -
402A THR 3.7 14.4 - - - +
403A ALA* 3.1 13.4 + - + +
405A GLN* 1.3 76.0 - - + +
407A ALA* 1.3 50.2 + - - +
409A LEU* 3.0 21.8 + - + +
410A LYS 2.5 29.1 + - - -
414A TRP* 3.2 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ALA 2.6 12.6 + - - +
404A ALA* 3.3 21.1 - - + +
406A VAL* 1.3 71.8 - - - +
408A SER* 1.3 60.0 + - - +
409A LEU 3.1 0.2 - - - -
410A LYS* 3.0 11.6 + - + +
411A LYS* 2.8 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ASN* 3.9 7.6 + - - -
404A ALA 2.2 30.9 + - - -
405A GLN* 3.0 9.6 - - - -
407A ALA* 1.3 68.4 - - - +
409A LEU* 1.3 51.0 + - - +
411A LYS* 3.1 12.8 - - - +
412A ASN* 2.7 37.7 + - - -
1002A NAG 3.5 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ILE* 5.9 6.1 - - + -
365A ALA* 6.0 2.9 - - + -
393A LEU* 5.8 8.1 - - + -
405A GLN* 2.2 31.6 + - + +
406A VAL* 3.0 28.9 + - + +
408A SER* 1.3 68.1 - - - +
410A LYS* 1.3 52.6 + - - +
412A ASN* 3.4 14.1 - - + +
413A VAL 2.5 9.5 + - - -
414A TRP* 2.2 78.2 + - + +
415A LEU* 4.4 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A VAL 2.5 13.2 + - - +
407A ALA* 3.1 13.5 - - + +
409A LEU* 1.3 70.5 - - - +
411A LYS* 1.3 60.2 + - - +
412A ASN 3.0 1.6 - - - -
413A VAL* 2.6 34.3 + - + +
414A TRP* 3.4 32.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A PRO* 4.0 11.7 - - - +
407A ALA 2.8 11.1 + - - +
408A SER* 3.1 23.6 - - - +
410A LYS* 1.3 73.8 - - - +
412A ASN* 1.3 61.6 + - - +
413A VAL* 4.8 2.6 - - - +
1002A NAG 2.9 58.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A PRO* 3.4 36.8 + - + +
362A ASN* 4.9 4.9 + - - +
365A ALA* 3.8 25.4 - - + +
366A TRP* 4.8 5.1 - - + -
408A SER* 2.7 25.8 + - - +
409A LEU* 3.3 16.2 + - + +
410A LYS 3.0 0.2 - - - -
411A LYS* 1.3 78.5 - - - +
413A VAL* 1.3 69.1 + - - +
414A TRP* 2.9 18.4 - - - +
1002A NAG 3.3 22.1 + - - +
----------------------------------------------------------
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