Contacts of the helix formed by residues 409 - 419 (chain A) in PDB entry 5K9S
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 409 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLN* 3.3 35.0 - - + +
408A GLY* 1.3 77.8 - - - -
410A VAL* 1.3 65.1 + - - +
411A GLU* 3.6 7.8 + - - +
412A GLN* 2.7 41.2 + - - +
413A ILE* 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A THR* 1.3 75.1 - - - +
411A GLU* 1.3 65.2 + - - +
413A ILE* 3.2 3.5 + - + +
414A VAL* 3.0 23.4 + - + +
450A ALA* 4.0 22.9 - - + +
453A LYS* 4.0 33.7 - - + +
454A LEU* 3.8 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A THR* 3.3 7.6 + - - +
410A VAL* 1.3 81.6 - - - +
412A GLN* 1.3 62.6 + - + +
414A VAL* 3.5 19.7 + - - +
415A TYR* 3.2 21.7 + - - +
454A LEU* 5.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLN* 3.1 27.2 + - - +
370A ILE* 3.6 15.2 - - + +
371A GLN* 3.0 36.0 + - - +
374A VAL* 4.5 5.8 - - + -
404A TYR* 2.9 35.5 + - + +
408A GLY* 3.2 9.3 - - - -
409A THR* 2.7 53.0 + - - +
411A GLU* 1.3 74.7 - - + +
413A ILE* 1.3 61.1 + - - +
415A TYR* 3.4 5.3 + - - +
416A LEU 3.0 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A TYR* 4.4 5.4 - - + -
405A THR* 3.5 38.4 - - + +
408A GLY 4.2 10.8 - - - +
409A THR 3.1 15.1 + - - +
410A VAL 3.2 6.9 + - - +
412A GLN* 1.3 76.1 - - - +
414A VAL* 1.3 64.7 + - + +
416A LEU* 3.0 8.9 + - + +
417A VAL* 2.9 22.6 + - + +
446A ASN 4.3 7.6 - - - +
447A ILE* 3.9 35.7 - - + -
450A ALA* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A VAL* 3.0 18.2 + - + +
411A GLU* 3.7 23.6 - - - +
412A GLN 3.4 0.2 - - - -
413A ILE* 1.3 76.5 - - + +
415A TYR* 1.3 57.8 + - - +
417A VAL* 3.0 11.0 + - + +
418A HIS* 2.8 54.5 + - + +
450A ALA* 6.2 0.7 - - + -
454A LEU* 3.7 28.7 - - + -
456A GLU* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A VAL* 3.8 32.6 + - + -
377A GLY* 5.0 2.8 - - - -
379A VAL* 3.6 24.2 - - + -
380A PRO* 3.9 16.5 - - - +
404A TYR* 3.9 13.5 - - - -
411A GLU 3.2 11.5 + - - +
412A GLN* 3.6 8.1 - - - +
414A VAL* 1.3 79.6 - - - +
416A LEU* 1.3 65.3 + - - +
418A HIS* 3.2 14.2 + + + -
419A CYS* 3.0 44.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A VAL* 3.9 22.2 - - + -
383A VAL* 4.9 1.3 - - + -
401A ILE* 4.1 21.5 - - + -
404A TYR* 3.9 22.0 - - + -
405A THR* 3.5 32.8 - - + -
412A GLN 3.0 14.4 + - - +
413A ILE* 3.0 10.5 + - - +
415A TYR* 1.3 79.1 - - - +
417A VAL* 1.3 63.5 + - - +
419A CYS* 3.2 15.7 + - - +
421A ILE* 3.5 44.3 + - + +
447A ILE* 4.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ILE* 2.9 18.3 + - + +
414A VAL* 3.0 10.5 + - + +
416A LEU* 1.3 76.3 - - - +
418A HIS* 1.3 68.0 + - + +
420A GLY* 3.0 20.1 + - - -
421A ILE* 4.0 14.9 + - + -
422A ILE* 4.6 8.1 + - + +
447A ILE* 3.9 28.0 - - + -
460A LEU* 4.7 4.9 - - + -
463A MET* 3.5 37.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A VAL* 2.8 42.0 + - + +
415A TYR* 3.2 16.4 + + + +
417A VAL* 1.3 84.3 - - + +
419A CYS* 1.3 59.2 + - - +
420A GLY 3.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A VAL* 3.7 24.7 - - + -
380A PRO* 4.3 14.4 - - + +
383A VAL* 4.0 19.9 - - + +
415A TYR* 3.0 48.9 + - - -
416A LEU 3.6 9.0 - - - +
417A VAL 3.1 0.8 - - - -
418A HIS* 1.3 78.8 - - - +
420A GLY* 1.3 60.1 + - - +
421A ILE 3.6 0.9 - - - -
----------------------------------------------------------
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